[1] "ofn"        "-oTBLCA-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/BLCA-TP/15076720/BLCA-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/BLCA-TP/15190396/transformed.cor.cli.txt"

nPatients in clinical file=393, in cluster file=395, common to both=376
[1] 118 376
[1] "TP53 MUTATION ANALYSIS"
[1] 3
  TP53 MUTATED TP53 WILD-TYPE 
           187            189 
  TP53 MUTATED TP53 WILD-TYPE 
           187            189 
[1] "PIK3CA MUTATION ANALYSIS"
[1] 3
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              85              291 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              85              291 
[1] "RB1 MUTATION ANALYSIS"
[1] 3
  RB1 MUTATED RB1 WILD-TYPE 
           65           311 
  RB1 MUTATED RB1 WILD-TYPE 
           65           311 
[1] "FGFR3 MUTATION ANALYSIS"
[1] 3
  FGFR3 MUTATED FGFR3 WILD-TYPE 
             56             320 
  FGFR3 MUTATED FGFR3 WILD-TYPE 
             56             320 
[1] "CDKN2A MUTATION ANALYSIS"
[1] 3
  CDKN2A MUTATED CDKN2A WILD-TYPE 
              25              351 
  CDKN2A MUTATED CDKN2A WILD-TYPE 
              25              351 
[1] "RHOB MUTATION ANALYSIS"
[1] 3
  RHOB MUTATED RHOB WILD-TYPE 
            24            352 
  RHOB MUTATED RHOB WILD-TYPE 
            24            352 
[1] "ELF3 MUTATION ANALYSIS"
[1] 3
  ELF3 MUTATED ELF3 WILD-TYPE 
            41            335 
  ELF3 MUTATED ELF3 WILD-TYPE 
            41            335 
[1] "TSC1 MUTATION ANALYSIS"
[1] 3
  TSC1 MUTATED TSC1 WILD-TYPE 
            30            346 
  TSC1 MUTATED TSC1 WILD-TYPE 
            30            346 
[1] "KDM6A MUTATION ANALYSIS"
[1] 3
  KDM6A MUTATED KDM6A WILD-TYPE 
             98             278 
  KDM6A MUTATED KDM6A WILD-TYPE 
             98             278 
[1] "CDKN1A MUTATION ANALYSIS"
[1] 3
  CDKN1A MUTATED CDKN1A WILD-TYPE 
              33              343 
  CDKN1A MUTATED CDKN1A WILD-TYPE 
              33              343 
[1] "EP300 MUTATION ANALYSIS"
[1] 3
  EP300 MUTATED EP300 WILD-TYPE 
             58             318 
  EP300 MUTATED EP300 WILD-TYPE 
             58             318 
[1] "ARID1A MUTATION ANALYSIS"
[1] 3
  ARID1A MUTATED ARID1A WILD-TYPE 
              93              283 
  ARID1A MUTATED ARID1A WILD-TYPE 
              93              283 
[1] "STAG2 MUTATION ANALYSIS"
[1] 3
  STAG2 MUTATED STAG2 WILD-TYPE 
             52             324 
  STAG2 MUTATED STAG2 WILD-TYPE 
             52             324 
[1] "ERCC2 MUTATION ANALYSIS"
[1] 3
  ERCC2 MUTATED ERCC2 WILD-TYPE 
             34             342 
  ERCC2 MUTATED ERCC2 WILD-TYPE 
             34             342 
[1] "ZFP36L1 MUTATION ANALYSIS"
[1] 3
  ZFP36L1 MUTATED ZFP36L1 WILD-TYPE 
               26               350 
  ZFP36L1 MUTATED ZFP36L1 WILD-TYPE 
               26               350 
[1] "FBXW7 MUTATION ANALYSIS"
[1] 3
  FBXW7 MUTATED FBXW7 WILD-TYPE 
             31             345 
  FBXW7 MUTATED FBXW7 WILD-TYPE 
             31             345 
[1] "HRAS MUTATION ANALYSIS"
[1] 3
  HRAS MUTATED HRAS WILD-TYPE 
            17            359 
  HRAS MUTATED HRAS WILD-TYPE 
            17            359 
[1] "CREBBP MUTATION ANALYSIS"
[1] 3
  CREBBP MUTATED CREBBP WILD-TYPE 
              45              331 
  CREBBP MUTATED CREBBP WILD-TYPE 
              45              331 
[1] "KRAS MUTATION ANALYSIS"
[1] 3
  KRAS MUTATED KRAS WILD-TYPE 
            13            363 
  KRAS MUTATED KRAS WILD-TYPE 
            13            363 
[1] "NFE2L2 MUTATION ANALYSIS"
[1] 3
  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
              24              352 
  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
              24              352 
[1] "RHOA MUTATION ANALYSIS"
[1] 3
  RHOA MUTATED RHOA WILD-TYPE 
            17            359 
  RHOA MUTATED RHOA WILD-TYPE 
            17            359 
[1] "PTEN MUTATION ANALYSIS"
[1] 3
  PTEN MUTATED PTEN WILD-TYPE 
            13            363 
  PTEN MUTATED PTEN WILD-TYPE 
            13            363 
[1] "C3ORF70 MUTATION ANALYSIS"
[1] 3
  C3ORF70 MUTATED C3ORF70 WILD-TYPE 
               17               359 
  C3ORF70 MUTATED C3ORF70 WILD-TYPE 
               17               359 
[1] "RBM10 MUTATION ANALYSIS"
[1] 3
  RBM10 MUTATED RBM10 WILD-TYPE 
             21             355 
  RBM10 MUTATED RBM10 WILD-TYPE 
             21             355 
[1] "PSIP1 MUTATION ANALYSIS"
[1] 3
  PSIP1 MUTATED PSIP1 WILD-TYPE 
             19             357 
  PSIP1 MUTATED PSIP1 WILD-TYPE 
             19             357 
[1] "ASXL2 MUTATION ANALYSIS"
[1] 3
  ASXL2 MUTATED ASXL2 WILD-TYPE 
             35             341 
  ASXL2 MUTATED ASXL2 WILD-TYPE 
             35             341 
[1] "FAT1 MUTATION ANALYSIS"
[1] 3
  FAT1 MUTATED FAT1 WILD-TYPE 
            50            326 
  FAT1 MUTATED FAT1 WILD-TYPE 
            50            326 
[1] "SPTAN1 MUTATION ANALYSIS"
[1] 3
  SPTAN1 MUTATED SPTAN1 WILD-TYPE 
              44              332 
  SPTAN1 MUTATED SPTAN1 WILD-TYPE 
              44              332 
[1] "ZBTB7B MUTATION ANALYSIS"
[1] 3
  ZBTB7B MUTATED ZBTB7B WILD-TYPE 
              10              366 
  ZBTB7B MUTATED ZBTB7B WILD-TYPE 
              10              366 
[1] "CUL1 MUTATION ANALYSIS"
[1] 3
  CUL1 MUTATED CUL1 WILD-TYPE 
            18            358 
  CUL1 MUTATED CUL1 WILD-TYPE 
            18            358 
[1] "KLF5 MUTATION ANALYSIS"
[1] 3
  KLF5 MUTATED KLF5 WILD-TYPE 
            22            354 
  KLF5 MUTATED KLF5 WILD-TYPE 
            22            354 
[1] "RXRA MUTATION ANALYSIS"
[1] 3
  RXRA MUTATED RXRA WILD-TYPE 
            23            353 
  RXRA MUTATED RXRA WILD-TYPE 
            23            353 
[1] "GNA13 MUTATION ANALYSIS"
[1] 3
  GNA13 MUTATED GNA13 WILD-TYPE 
             10             366 
  GNA13 MUTATED GNA13 WILD-TYPE 
             10             366 
[1] "METTL3 MUTATION ANALYSIS"
[1] 3
  METTL3 MUTATED METTL3 WILD-TYPE 
              16              360 
  METTL3 MUTATED METTL3 WILD-TYPE 
              16              360 
[1] "ERBB3 MUTATION ANALYSIS"
[1] 3
  ERBB3 MUTATED ERBB3 WILD-TYPE 
             40             336 
  ERBB3 MUTATED ERBB3 WILD-TYPE 
             40             336 
[1] "RUNX1 MUTATION ANALYSIS"
[1] 3
  RUNX1 MUTATED RUNX1 WILD-TYPE 
             12             364 
  RUNX1 MUTATED RUNX1 WILD-TYPE 
             12             364 
[1] "MBD1 MUTATION ANALYSIS"
[1] 3
  MBD1 MUTATED MBD1 WILD-TYPE 
            11            365 
  MBD1 MUTATED MBD1 WILD-TYPE 
            11            365 
[1] "FOXQ1 MUTATION ANALYSIS"
[1] 3
  FOXQ1 MUTATED FOXQ1 WILD-TYPE 
             14             362 
  FOXQ1 MUTATED FOXQ1 WILD-TYPE 
             14             362 
[1] "RPTN MUTATION ANALYSIS"
[1] 3
  RPTN MUTATED RPTN WILD-TYPE 
            15            361 
  RPTN MUTATED RPTN WILD-TYPE 
            15            361 
[1] "SF1 MUTATION ANALYSIS"
[1] 3
  SF1 MUTATED SF1 WILD-TYPE 
            9           367 
  SF1 MUTATED SF1 WILD-TYPE 
            9           367 
[1] "DNAH6 MUTATION ANALYSIS"
[1] 3
  DNAH6 MUTATED DNAH6 WILD-TYPE 
             15             361 
  DNAH6 MUTATED DNAH6 WILD-TYPE 
             15             361 
[1] "ZNF185 MUTATION ANALYSIS"
[1] 3
  ZNF185 MUTATED ZNF185 WILD-TYPE 
               5              371 
  ZNF185 MUTATED ZNF185 WILD-TYPE 
               5              371 
[1] "ATM MUTATION ANALYSIS"
[1] 3
  ATM MUTATED ATM WILD-TYPE 
           49           327 
  ATM MUTATED ATM WILD-TYPE 
           49           327 
[1] "UNC93B1 MUTATION ANALYSIS"
[1] 3
  UNC93B1 MUTATED UNC93B1 WILD-TYPE 
                7               369 
  UNC93B1 MUTATED UNC93B1 WILD-TYPE 
                7               369 
[1] "UBA52 MUTATION ANALYSIS"
[1] 3
  UBA52 MUTATED UBA52 WILD-TYPE 
              6             370 
  UBA52 MUTATED UBA52 WILD-TYPE 
              6             370 
[1] "CNOT1 MUTATION ANALYSIS"
[1] 3
  CNOT1 MUTATED CNOT1 WILD-TYPE 
             21             355 
  CNOT1 MUTATED CNOT1 WILD-TYPE 
             21             355 
[1] "ERBB2 MUTATION ANALYSIS"
[1] 3
  ERBB2 MUTATED ERBB2 WILD-TYPE 
             45             331 
  ERBB2 MUTATED ERBB2 WILD-TYPE 
             45             331 
[1] "FAM47C MUTATION ANALYSIS"
[1] 3
  FAM47C MUTATED FAM47C WILD-TYPE 
              20              356 
  FAM47C MUTATED FAM47C WILD-TYPE 
              20              356 
[1] "SF3B1 MUTATION ANALYSIS"
[1] 3
  SF3B1 MUTATED SF3B1 WILD-TYPE 
             24             352 
  SF3B1 MUTATED SF3B1 WILD-TYPE 
             24             352 
[1] "EPS8 MUTATION ANALYSIS"
[1] 3
  EPS8 MUTATED EPS8 WILD-TYPE 
            12            364 
  EPS8 MUTATED EPS8 WILD-TYPE 
            12            364 
[1] "EPHA2 MUTATION ANALYSIS"
[1] 3
  EPHA2 MUTATED EPHA2 WILD-TYPE 
             16             360 
  EPHA2 MUTATED EPHA2 WILD-TYPE 
             16             360 
[1] "OGDH MUTATION ANALYSIS"
[1] 3
  OGDH MUTATED OGDH WILD-TYPE 
            19            357 
  OGDH MUTATED OGDH WILD-TYPE 
            19            357 
[1] "SCARF2 MUTATION ANALYSIS"
[1] 3
  SCARF2 MUTATED SCARF2 WILD-TYPE 
               7              369 
  SCARF2 MUTATED SCARF2 WILD-TYPE 
               7              369 
[1] "SSH3 MUTATION ANALYSIS"
[1] 3
  SSH3 MUTATED SSH3 WILD-TYPE 
            15            361 
  SSH3 MUTATED SSH3 WILD-TYPE 
            15            361 
[1] "HLA-A MUTATION ANALYSIS"
[1] 3
  HLA-A MUTATED HLA-A WILD-TYPE 
              5             371 
  HLA-A MUTATED HLA-A WILD-TYPE 
              5             371 
[1] "PARD3 MUTATION ANALYSIS"
[1] 3
  PARD3 MUTATED PARD3 WILD-TYPE 
             21             355 
  PARD3 MUTATED PARD3 WILD-TYPE 
             21             355 
[1] "BAP1 MUTATION ANALYSIS"
[1] 3
  BAP1 MUTATED BAP1 WILD-TYPE 
            14            362 
  BAP1 MUTATED BAP1 WILD-TYPE 
            14            362 
[1] "RIPK4 MUTATION ANALYSIS"
[1] 3
  RIPK4 MUTATED RIPK4 WILD-TYPE 
             17             359 
  RIPK4 MUTATED RIPK4 WILD-TYPE 
             17             359 
[1] "TMCO4 MUTATION ANALYSIS"
[1] 3
  TMCO4 MUTATED TMCO4 WILD-TYPE 
             11             365 
  TMCO4 MUTATED TMCO4 WILD-TYPE 
             11             365 
[1] "CDH1 MUTATION ANALYSIS"
[1] 3
  CDH1 MUTATED CDH1 WILD-TYPE 
            13            363 
  CDH1 MUTATED CDH1 WILD-TYPE 
            13            363 
[1] "NRAS MUTATION ANALYSIS"
[1] 3
  NRAS MUTATED NRAS WILD-TYPE 
             7            369 
  NRAS MUTATED NRAS WILD-TYPE 
             7            369 
[1] "ARID1B MUTATION ANALYSIS"
[1] 3
  ARID1B MUTATED ARID1B WILD-TYPE 
              21              355 
  ARID1B MUTATED ARID1B WILD-TYPE 
              21              355 
[1] "ZNF511 MUTATION ANALYSIS"
[1] 3
  ZNF511 MUTATED ZNF511 WILD-TYPE 
               8              368 
  ZNF511 MUTATED ZNF511 WILD-TYPE 
               8              368 
[1] "TFG MUTATION ANALYSIS"
[1] 3
  TFG MUTATED TFG WILD-TYPE 
           11           365 
  TFG MUTATED TFG WILD-TYPE 
           11           365 
[1] "FUS MUTATION ANALYSIS"
[1] 3
  FUS MUTATED FUS WILD-TYPE 
            8           368 
  FUS MUTATED FUS WILD-TYPE 
            8           368 
[1] "ASXL1 MUTATION ANALYSIS"
[1] 3
  ASXL1 MUTATED ASXL1 WILD-TYPE 
             22             354 
  ASXL1 MUTATED ASXL1 WILD-TYPE 
             22             354 
[1] "CNOT3 MUTATION ANALYSIS"
[1] 3
  CNOT3 MUTATED CNOT3 WILD-TYPE 
             11             365 
  CNOT3 MUTATED CNOT3 WILD-TYPE 
             11             365 
[1] "ARID2 MUTATION ANALYSIS"
[1] 3
  ARID2 MUTATED ARID2 WILD-TYPE 
             25             351 
  ARID2 MUTATED ARID2 WILD-TYPE 
             25             351 
[1] "ZNF773 MUTATION ANALYSIS"
[1] 3
  ZNF773 MUTATED ZNF773 WILD-TYPE 
               7              369 
  ZNF773 MUTATED ZNF773 WILD-TYPE 
               7              369 
[1] "DAZAP1 MUTATION ANALYSIS"
[1] 3
  DAZAP1 MUTATED DAZAP1 WILD-TYPE 
               6              370 
  DAZAP1 MUTATED DAZAP1 WILD-TYPE 
               6              370 
[1] "ADC MUTATION ANALYSIS"
[1] 3
  ADC MUTATED ADC WILD-TYPE 
            6           370 
  ADC MUTATED ADC WILD-TYPE 
            6           370 
[1] "FUT5 MUTATION ANALYSIS"
[1] 3
  FUT5 MUTATED FUT5 WILD-TYPE 
             3            373 
  FUT5 MUTATED FUT5 WILD-TYPE 
             3            373 
[1] "AHR MUTATION ANALYSIS"
[1] 3
  AHR MUTATED AHR WILD-TYPE 
           19           357 
  AHR MUTATED AHR WILD-TYPE 
           19           357 
[1] "THRAP3 MUTATION ANALYSIS"
[1] 3
  THRAP3 MUTATED THRAP3 WILD-TYPE 
              14              362 
  THRAP3 MUTATED THRAP3 WILD-TYPE 
              14              362 
[1] "TFPI2 MUTATION ANALYSIS"
[1] 3
  TFPI2 MUTATED TFPI2 WILD-TYPE 
              6             370 
  TFPI2 MUTATED TFPI2 WILD-TYPE 
              6             370 
[1] "NPAS4 MUTATION ANALYSIS"
[1] 3
  NPAS4 MUTATED NPAS4 WILD-TYPE 
             12             364 
  NPAS4 MUTATED NPAS4 WILD-TYPE 
             12             364 
[1] "NFE2L3 MUTATION ANALYSIS"
[1] 3
  NFE2L3 MUTATED NFE2L3 WILD-TYPE 
              14              362 
  NFE2L3 MUTATED NFE2L3 WILD-TYPE 
              14              362 
[1] "TAF11 MUTATION ANALYSIS"
[1] 3
  TAF11 MUTATED TAF11 WILD-TYPE 
              7             369 
  TAF11 MUTATED TAF11 WILD-TYPE 
              7             369 
[1] "BCL2L1 MUTATION ANALYSIS"
[1] 3
  BCL2L1 MUTATED BCL2L1 WILD-TYPE 
               3              373 
  BCL2L1 MUTATED BCL2L1 WILD-TYPE 
               3              373 
[1] "TRERF1 MUTATION ANALYSIS"
[1] 3
  TRERF1 MUTATED TRERF1 WILD-TYPE 
              21              355 
  TRERF1 MUTATED TRERF1 WILD-TYPE 
              21              355 
[1] "CHD2 MUTATION ANALYSIS"
[1] 3
  CHD2 MUTATED CHD2 WILD-TYPE 
            25            351 
  CHD2 MUTATED CHD2 WILD-TYPE 
            25            351 
[1] "USP28 MUTATION ANALYSIS"
[1] 3
  USP28 MUTATED USP28 WILD-TYPE 
             13             363 
  USP28 MUTATED USP28 WILD-TYPE 
             13             363 
[1] "GPS2 MUTATION ANALYSIS"
[1] 3
  GPS2 MUTATED GPS2 WILD-TYPE 
            10            366 
  GPS2 MUTATED GPS2 WILD-TYPE 
            10            366 
[1] "F7 MUTATION ANALYSIS"
[1] 3
  F7 MUTATED F7 WILD-TYPE 
           7          369 
  F7 MUTATED F7 WILD-TYPE 
           7          369 
[1] "IRX4 MUTATION ANALYSIS"
[1] 3
  IRX4 MUTATED IRX4 WILD-TYPE 
             8            368 
  IRX4 MUTATED IRX4 WILD-TYPE 
             8            368 
[1] "HSP90AA1 MUTATION ANALYSIS"
[1] 3
  HSP90AA1 MUTATED HSP90AA1 WILD-TYPE 
                22                354 
  HSP90AA1 MUTATED HSP90AA1 WILD-TYPE 
                22                354 
[1] "TTYH1 MUTATION ANALYSIS"
[1] 3
  TTYH1 MUTATED TTYH1 WILD-TYPE 
              7             369 
  TTYH1 MUTATED TTYH1 WILD-TYPE 
              7             369 
[1] "IL10RB MUTATION ANALYSIS"
[1] 3
  IL10RB MUTATED IL10RB WILD-TYPE 
               7              369 
  IL10RB MUTATED IL10RB WILD-TYPE 
               7              369 
[1] "THSD4 MUTATION ANALYSIS"
[1] 3
  THSD4 MUTATED THSD4 WILD-TYPE 
              9             367 
  THSD4 MUTATED THSD4 WILD-TYPE 
              9             367 
[1] "DDX3X MUTATION ANALYSIS"
[1] 3
  DDX3X MUTATED DDX3X WILD-TYPE 
             14             362 
  DDX3X MUTATED DDX3X WILD-TYPE 
             14             362 
[1] "DGKG MUTATION ANALYSIS"
[1] 3
  DGKG MUTATED DGKG WILD-TYPE 
            12            364 
  DGKG MUTATED DGKG WILD-TYPE 
            12            364 
[1] "TAS2R9 MUTATION ANALYSIS"
[1] 3
  TAS2R9 MUTATED TAS2R9 WILD-TYPE 
               5              371 
  TAS2R9 MUTATED TAS2R9 WILD-TYPE 
               5              371 
[1] "COL7A1 MUTATION ANALYSIS"
[1] 3
  COL7A1 MUTATED COL7A1 WILD-TYPE 
              30              346 
  COL7A1 MUTATED COL7A1 WILD-TYPE 
              30              346 
[1] "ZNF513 MUTATION ANALYSIS"
[1] 3
  ZNF513 MUTATED ZNF513 WILD-TYPE 
              11              365 
  ZNF513 MUTATED ZNF513 WILD-TYPE 
              11              365 
[1] "ACSL5 MUTATION ANALYSIS"
[1] 3
  ACSL5 MUTATED ACSL5 WILD-TYPE 
              6             370 
  ACSL5 MUTATED ACSL5 WILD-TYPE 
              6             370 
[1] "C18ORF8 MUTATION ANALYSIS"
[1] 3
  C18ORF8 MUTATED C18ORF8 WILD-TYPE 
                6               370 
  C18ORF8 MUTATED C18ORF8 WILD-TYPE 
                6               370 
[1] "PRB2 MUTATION ANALYSIS"
[1] 3
  PRB2 MUTATED PRB2 WILD-TYPE 
             7            369 
  PRB2 MUTATED PRB2 WILD-TYPE 
             7            369 
[1] "POU3F1 MUTATION ANALYSIS"
[1] 3
  POU3F1 MUTATED POU3F1 WILD-TYPE 
               3              373 
  POU3F1 MUTATED POU3F1 WILD-TYPE 
               3              373 
[1] "EZR MUTATION ANALYSIS"
[1] 3
  EZR MUTATED EZR WILD-TYPE 
           11           365 
  EZR MUTATED EZR WILD-TYPE 
           11           365 
[1] "ZEB2 MUTATION ANALYSIS"
[1] 3
  ZEB2 MUTATED ZEB2 WILD-TYPE 
            13            363 
  ZEB2 MUTATED ZEB2 WILD-TYPE 
            13            363 
[1] "C12ORF43 MUTATION ANALYSIS"
[1] 3
  C12ORF43 MUTATED C12ORF43 WILD-TYPE 
                 7                369 
  C12ORF43 MUTATED C12ORF43 WILD-TYPE 
                 7                369 
[1] "NAP1L1 MUTATION ANALYSIS"
[1] 3
  NAP1L1 MUTATED NAP1L1 WILD-TYPE 
              10              366 
  NAP1L1 MUTATED NAP1L1 WILD-TYPE 
              10              366 
[1] "NAALADL1 MUTATION ANALYSIS"
[1] 3
  NAALADL1 MUTATED NAALADL1 WILD-TYPE 
                 7                369 
  NAALADL1 MUTATED NAALADL1 WILD-TYPE 
                 7                369 
[1] "DENND5B MUTATION ANALYSIS"
[1] 3
  DENND5B MUTATED DENND5B WILD-TYPE 
               19               357 
  DENND5B MUTATED DENND5B WILD-TYPE 
               19               357 
[1] "SF3B3 MUTATION ANALYSIS"
[1] 3
  SF3B3 MUTATED SF3B3 WILD-TYPE 
             19             357 
  SF3B3 MUTATED SF3B3 WILD-TYPE 
             19             357 
[1] "KIAA1522 MUTATION ANALYSIS"
[1] 3
  KIAA1522 MUTATED KIAA1522 WILD-TYPE 
                15                361 
  KIAA1522 MUTATED KIAA1522 WILD-TYPE 
                15                361 
[1] "GTF2I MUTATION ANALYSIS"
[1] 3
  GTF2I MUTATED GTF2I WILD-TYPE 
             15             361 
  GTF2I MUTATED GTF2I WILD-TYPE 
             15             361 
[1] "MOAP1 MUTATION ANALYSIS"
[1] 3
  MOAP1 MUTATED MOAP1 WILD-TYPE 
              7             369 
  MOAP1 MUTATED MOAP1 WILD-TYPE 
              7             369 
[1] "GAR1 MUTATION ANALYSIS"
[1] 3
  GAR1 MUTATED GAR1 WILD-TYPE 
             4            372 
  GAR1 MUTATED GAR1 WILD-TYPE 
             4            372 
[1] "RFTN2 MUTATION ANALYSIS"
[1] 3
  RFTN2 MUTATED RFTN2 WILD-TYPE 
             11             365 
  RFTN2 MUTATED RFTN2 WILD-TYPE 
             11             365 
[1] "ZFP36L2 MUTATION ANALYSIS"
[1] 3
  ZFP36L2 MUTATED ZFP36L2 WILD-TYPE 
               15               361 
  ZFP36L2 MUTATED ZFP36L2 WILD-TYPE 
               15               361 
[1] "GUCY2C MUTATION ANALYSIS"
[1] 3
  GUCY2C MUTATED GUCY2C WILD-TYPE 
              11              365 
  GUCY2C MUTATED GUCY2C WILD-TYPE 
              11              365 
[1] "COPZ2 MUTATION ANALYSIS"
[1] 3
  COPZ2 MUTATED COPZ2 WILD-TYPE 
              3             373 
  COPZ2 MUTATED COPZ2 WILD-TYPE 
              3             373 
[1] "ZNF791 MUTATION ANALYSIS"
[1] 3
  ZNF791 MUTATED ZNF791 WILD-TYPE 
               9              367 
  ZNF791 MUTATED ZNF791 WILD-TYPE 
               9              367 
[1] "BUD13 MUTATION ANALYSIS"
[1] 3
  BUD13 MUTATED BUD13 WILD-TYPE 
             11             365 
  BUD13 MUTATED BUD13 WILD-TYPE 
             11             365 
[1] "HES1 MUTATION ANALYSIS"
[1] 3
  HES1 MUTATED HES1 WILD-TYPE 
            10            366 
  HES1 MUTATED HES1 WILD-TYPE 
            10            366 
[1] "HORMAD1 MUTATION ANALYSIS"
[1] 3
  HORMAD1 MUTATED HORMAD1 WILD-TYPE 
               11               365 
  HORMAD1 MUTATED HORMAD1 WILD-TYPE 
               11               365 
[1] "SND1 MUTATION ANALYSIS"
[1] 3
  SND1 MUTATED SND1 WILD-TYPE 
             8            368 
  SND1 MUTATED SND1 WILD-TYPE 
             8            368 
[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] "KARNOFSKY_PERFORMANCE_SCORE"           
[16] "HISTOLOGICAL_TYPE"                     
[17] "RADIATIONS_RADIATION_REGIMENINDICATION"
[18] "NUMBER_PACK_YEARS_SMOKED"              
[19] "NUMBER_OF_LYMPH_NODES"                 
[20] "RACE"                                  
[21] "ETHNICITY"                             
[22] "BATCH_NUMBER"                          

Input Data has 22 rows and 376 columns.

[1] "Batch" "22"   
[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=51,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=136,	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=245,	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=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY_T_STAGE':	nDistinctValues=11,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY_N_STAGE':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY_M_STAGE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'DCC_UPLOAD_DATE':	nDistinctValues=3,	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=15,	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=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "DAYS_TO_LAST_KNOWN_ALIVE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 14:'RADIATION_THERAPY':	nDistinctValues=1,	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:'KARNOFSKY_PERFORMANCE_SCORE':	nDistinctValues=8,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 16:'HISTOLOGICAL_TYPE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "HISTOLOGICAL_TYPE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 17:'RADIATIONS_RADIATION_REGIMENINDICATION':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "RADIATIONS_RADIATION_REGIMENINDICATION is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 18:'NUMBER_PACK_YEARS_SMOKED':	nDistinctValues=69,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 19:'NUMBER_OF_LYMPH_NODES':	nDistinctValues=21,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 20:'RACE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 21:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 22:'BATCH_NUMBER':	nDistinctValues=28,	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 376 columns, 1 survival variables, and 11 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
 [1] "YEARS_TO_BIRTH"              "NEOPLASM_DISEASESTAGE"      
 [3] "PATHOLOGY_T_STAGE"           "PATHOLOGY_N_STAGE"          
 [5] "PATHOLOGY_M_STAGE"           "GENDER"                     
 [7] "KARNOFSKY_PERFORMANCE_SCORE" "NUMBER_PACK_YEARS_SMOKED"   
 [9] "NUMBER_OF_LYMPH_NODES"       "RACE"                       
[11] "ETHNICITY"                  
YEARS_TO_BIRTH, nv=51, binary=FALSE, numeric=TRUE
NEOPLASM_DISEASESTAGE, nv=4, binary=FALSE, numeric=FALSE
PATHOLOGY_T_STAGE, nv=5, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
 T0  T1  T2  T3  T4 
  2   3 109 179  52 
[1] "table(vv)"
vv
T0+T1+T2       T3       T4 
     114      179       52 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
 T0  T1  T2  T3  T4 
  2   3 109 179  52 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


T0+T1+T2       T3       T4 
     114      179       52 
PATHOLOGY_N_STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
 N0  N1  N2  N3 
213  41  75   8 
[1] "table(vv)"
vv
 N0  N1  N2  N3 
213  41  75   8 
$ClinVariableName
[1] "PATHOLOGY_N_STAGE"

$Table
vv
 N0  N1  N2  N3 
213  41  75   8 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 N0  N1  N2  N3 
213  41  75   8 
PATHOLOGY_M_STAGE, nv=2, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
KARNOFSKY_PERFORMANCE_SCORE, nv=8, binary=FALSE, numeric=TRUE
NUMBER_PACK_YEARS_SMOKED, nv=69, binary=FALSE, numeric=TRUE
NUMBER_OF_LYMPH_NODES, nv=21, binary=FALSE, numeric=TRUE
RACE, nv=3, binary=FALSE, numeric=FALSE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = TP53 MUTATION ANALYSIS
D1V1, survival
                sevent
clus2              0   1
  TP53 MUTATED   107  80
  TP53 WILD-TYPE 112  71
  TP53 MUTATED TP53 WILD-TYPE 
           187            183 
  TP53 MUTATED TP53 WILD-TYPE 
            80             71 
$`TP53 MUTATED`
TCGA-2F-A9KP TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7W TCGA-4Z-AA80 
       11.97        16.27        16.77        17.16        27.62         0.62 
TCGA-4Z-AA84 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A20J 
       15.12        10.22        47.80         2.66         6.74        19.04 
TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20X TCGA-BT-A2LA 
       32.84        12.16         5.06        14.96         8.25        17.16 
TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A42F TCGA-C4-A0EZ 
       16.18        20.48         4.67        12.82        28.41         8.98 
TCGA-C4-A0F7 TCGA-CF-A1HS TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CU-A3KJ TCGA-DK-A1A3 
        2.04         0.43        12.26        13.12         5.46        21.86 
TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A2I1 
        2.14        66.41        16.70       130.88       112.44        10.59 
TCGA-DK-A2I2 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN 
        7.79        87.32         2.20        13.58         7.82         8.22 
TCGA-DK-A3IS TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6B6 
       50.27        23.21         9.67        48.00        17.98        30.67 
TCGA-DK-AA6L TCGA-DK-AA6Q TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA74 
       38.24        13.58        10.49         8.65         7.53        43.50 
TCGA-DK-AA77 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A6ME TCGA-E7-A7DU 
       10.62        43.59        15.35        38.83        12.99         0.92 
TCGA-E7-A7DV TCGA-E7-A97Q TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 
        1.22         8.09        33.04         4.01        12.62        22.52 
TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SR 
       60.66        24.30        23.41         5.52        25.74        19.79 
TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A5BR TCGA-FD-A5BV TCGA-FD-A62N 
       12.85        22.98        27.35        26.73         5.36         2.70 
TCGA-FD-A62S TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TK 
       13.35         6.15        12.69        12.36         2.27        10.85 
TCGA-FJ-A3Z7 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-G2-A2EJ TCGA-G2-A2EL TCGA-G2-A2EO 
       31.07        10.65        17.23        30.61        26.93        35.24 
TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3D 
       33.01         7.23        20.12        17.62        66.02        64.44 
TCGA-G2-AA3F TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3WC TCGA-GC-A3YS 
       19.46        15.81         4.50        15.91        17.75        24.92 
TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42P 
        8.94        13.91         7.73        20.98         2.20        10.92 
TCGA-GU-A42Q TCGA-GU-A762 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATO 
       11.31         7.63        20.05         5.62         4.73        10.65 
TCGA-GU-AATP TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QH TCGA-GV-A40G 
       32.98        21.34        19.10        19.82         8.48        19.07 
TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R 
        3.06         9.01         8.22         2.76         9.14        27.68 
TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-AAQO 
        9.07        11.70         1.74         1.81        15.42        11.80 
TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-UY-A78K TCGA-UY-A78L 
       15.32        15.58        12.23        16.67        17.62        37.05 
TCGA-UY-A78M TCGA-UY-A78N TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A9PA TCGA-UY-A9PB 
       22.68        86.83        76.01        65.75        35.24        29.56 
TCGA-UY-A9PD TCGA-UY-A9PE TCGA-XF-A8HH TCGA-XF-A9SI TCGA-XF-A9SX TCGA-XF-A9SY 
       17.82         4.54         1.87        79.66        23.64        21.04 
TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T3 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-AAMF 
       28.24        26.27         2.24        66.64         2.10        10.82 
TCGA-XF-AAMG TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMT TCGA-XF-AAMW 
      110.60        54.90         7.63        71.57         2.96         8.32 
TCGA-XF-AAMX TCGA-XF-AAN0 TCGA-XF-AAN3 TCGA-XF-AAN7 TCGA-YF-AA3M TCGA-ZF-A9R0 
        6.77        56.48        86.30        18.81        13.64        18.64 
TCGA-ZF-A9R4 TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RG 
       30.28        74.56        13.41         3.48        52.73        52.60 
TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4T TCGA-ZF-AA4W 
       82.49        47.84        20.22         2.89        19.69        60.16 
TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA58 
       63.02        38.73        35.41        57.90        19.40        47.15 
TCGA-ZF-AA5H 
       19.17 

$`TP53 WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW TCGA-4Z-AA7N 
       22.29        91.63       103.50       105.70         8.35        44.94 
TCGA-4Z-AA7O TCGA-4Z-AA7S TCGA-4Z-AA7Y TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 
       16.83        34.98        49.12        41.75        51.16        66.54 
TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX 
       33.83        40.08         7.33        12.39         6.58        13.15 
TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20T TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A3PK 
       17.88        19.50        14.89         5.06         8.35         9.96 
TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-C4-A0F6 
       17.56        28.70        24.26         1.94         2.93        23.01 
TCGA-CF-A1HR TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W 
        0.46         0.69        10.95        12.66        12.46        12.10 
TCGA-CF-A47X TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A0YN 
       12.62        12.00        12.10        11.87        13.08        12.92 
TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E 
        4.90         7.20         5.19        16.31         1.84        13.58 
TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX 
       18.41        19.00        16.14        17.62        15.62         1.81 
TCGA-DK-A2I4 TCGA-DK-A3IQ TCGA-DK-A3IT TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY 
      123.85        17.72        21.30        20.81        10.55       140.81 
TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 
       64.18        41.56        76.60        67.36        15.68        41.06 
TCGA-DK-AA6P TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA71 TCGA-DK-AA76 TCGA-E7-A3X6 
       15.02       166.03        12.36        13.64        12.03        24.66 
TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KE 
        0.10         0.49         2.24        16.70        17.39         0.56 
TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MF TCGA-E7-A7PW TCGA-E7-A7XN 
        0.66        14.56        13.97        14.33        13.68        14.07 
TCGA-E7-A85H TCGA-E7-A97P TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3N6 
       12.95        14.37        32.02        16.77         8.94        27.98 
TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SQ TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X 
       17.98        29.16        46.78        14.96        20.91         3.62 
TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ 
       53.88        11.01        19.33         5.69         8.25        27.45 
TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A6TA TCGA-FD-A6TB 
       18.08        58.92         7.10         6.28        62.86        18.81 
TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3Z9 TCGA-FJ-A871 TCGA-FT-A3EE 
        3.06         4.31         9.67         7.13         8.94         3.25 
TCGA-FT-A61P TCGA-G2-A2EC TCGA-G2-A2EF TCGA-G2-A2EK TCGA-G2-AA3C TCGA-GC-A3BM 
        6.48        22.88        61.94        15.95         6.94        21.40 
TCGA-GC-A3I6 TCGA-GC-A3RD TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A76B TCGA-GU-A42R 
        2.24        14.07         2.10         3.12         7.36        11.31 
TCGA-GU-A763 TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3QF TCGA-GV-A3QI TCGA-GV-A3QK 
       27.09         7.00        14.27        20.28        10.59        27.35 
TCGA-GV-A40E TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-K4-A3WS 
        8.58        22.72         1.51        19.40        38.60        25.02 
TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A83P TCGA-MV-A51V TCGA-R3-A69X TCGA-S5-A6DX 
        3.45        21.24         6.38        13.48        14.24         1.84 
TCGA-S5-AA26 TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A9PF TCGA-XF-A8HI TCGA-XF-A9SG 
        3.75        12.43        31.56         1.64        17.88        48.62 
TCGA-XF-A9SH TCGA-XF-A9SJ TCGA-XF-A9SL TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9T2 
       64.80         3.22        66.41        12.76        11.90        18.90 
TCGA-XF-A9T4 TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMH TCGA-XF-AAMR TCGA-XF-AAMY 
       16.27        13.74        92.98        11.31        91.73        98.99 
TCGA-XF-AAMZ TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN8 
       44.32        30.94        61.45        27.06        75.39         3.88 
TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R3 
        9.63         0.66        11.97         7.36        21.11        24.13 
TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-AA4R TCGA-ZF-AA4U TCGA-ZF-AA4V 
       27.19        21.86        28.41        34.06         8.61        59.38 
TCGA-ZF-AA56 TCGA-ZF-AA5N TCGA-ZF-AA5P 
        8.52         5.52        10.13 

  TP53 MUTATED TP53 WILD-TYPE 
          0.43           0.10 
  TP53 MUTATED TP53 WILD-TYPE 
        130.88         166.03 
  TP53 MUTATED TP53 WILD-TYPE 
         16.67          14.56 
[1] "0.4 - 130.9 (16.7)" "0.1 - 166.0 (14.6)"
[1] "hr=" "1.1"
D1V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  TP53 MUTATED         1       57        56       71
  TP53 WILD-TYPE       3       60        66       57
D1V3, multiclass
           clus
vv          TP53 MUTATED TP53 WILD-TYPE
  STAGE I              1              3
  STAGE II            57             60
  STAGE III           56             66
  STAGE IV            71             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"
                vv
clus             T0+T1+T2 T3 T4
  TP53 MUTATED         51 92 25
  TP53 WILD-TYPE       63 87 27
D1V4, multiclass
          clus
vv         TP53 MUTATED TP53 WILD-TYPE
  T0+T1+T2           51             63
  T3                 92             87
  T4                 25             27
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  TP53 MUTATED    92  22  42   7
  TP53 WILD-TYPE 121  19  33   1
D1V5, multiclass
    clus
vv   TP53 MUTATED TP53 WILD-TYPE
  N0           92            121
  N1           22             19
  N2           42             33
  N3            7              1
[1] 4 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
  TP53 MUTATED    75   5
  TP53 WILD-TYPE 107   5
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED     75    5
  TP53 WILD-TYPE  107    5
   clus
vv  TP53 MUTATED TP53 WILD-TYPE
  0           75            107
  1            5              5
[1] 2 2
[1] FALSE
D1V7, binary
                cls
clus               0   1
  TP53 MUTATED    49 138
  TP53 WILD-TYPE  47 142
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED     49  138
  TP53 WILD-TYPE   47  142
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  FEMALE           49             47
  MALE            138            142
[1] 2 2
[1] FALSE
D1V8, continuous
D1V9, continuous
D1V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TP53 MUTATED       9                        10   160
  TP53 WILD-TYPE    29                        11   141
D1V11, multiclass
                           clus
vv                          TP53 MUTATED TP53 WILD-TYPE
  ASIAN                                9             29
  BLACK OR AFRICAN AMERICAN           10             11
  WHITE                              160            141
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V12, binary
                cls
clus               0   1
  TP53 MUTATED     4 166
  TP53 WILD-TYPE   4 172
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED      4  166
  TP53 WILD-TYPE    4  172
                        clus
vv                       TP53 MUTATED TP53 WILD-TYPE
  HISPANIC OR LATINO                4              4
  NOT HISPANIC OR LATINO          166            172
[1] 2 2
[1] FALSE

Clustering(2) Variable = PIK3CA MUTATION ANALYSIS
D2V1, survival
                  sevent
clus2                0   1
  PIK3CA MUTATED    55  30
  PIK3CA WILD-TYPE 164 121
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              85              285 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              30              121 
$`PIK3CA MUTATED`
TCGA-2F-A9KO TCGA-2F-A9KR TCGA-2F-A9KW TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA84 
       22.29       103.50         8.35        27.62        49.12        15.12 
TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-BT-A20O TCGA-BT-A20Q TCGA-BT-A20R TCGA-CF-A5UA 
       47.80        33.83        12.16        19.50         5.06        12.00 
TCGA-CF-A9FF TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1AB 
       11.87         1.84        13.58         2.14        66.41        16.70 
TCGA-DK-A1AC TCGA-DK-A1AG TCGA-DK-A3WW TCGA-DK-A3X1 TCGA-DK-A6AW TCGA-DK-A6B2 
      130.88        15.62        20.81        48.00        41.56        15.68 
TCGA-DK-A6B5 TCGA-DK-AA6Q TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA76 TCGA-DK-AA77 
       41.06        13.58         7.53        13.64        12.03        10.62 
TCGA-E5-A2PC TCGA-E7-A4IJ TCGA-E7-A7DU TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3NA 
       43.59         0.49         0.92         8.94        33.04        60.66 
TCGA-FD-A3SJ TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A43N TCGA-FD-A5BX TCGA-FD-A5C1 
       24.30        29.16         5.52        22.98         5.69        58.92 
TCGA-FD-A62P TCGA-FD-A6TD TCGA-G2-A2EJ TCGA-G2-A2EO TCGA-G2-A3VY TCGA-G2-AA3B 
        6.28        12.69        30.61        35.24        17.62        66.02 
TCGA-G2-AA3C TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3WC TCGA-GC-A6I3 TCGA-GD-A3OP 
        6.94         2.24        15.81        17.75        13.91         2.10 
TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-AATO TCGA-GU-AATQ TCGA-GV-A3JX TCGA-H4-A2HO 
        2.20         7.36        10.65         7.00        19.10         1.51 
TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A4AB TCGA-K4-A54R TCGA-K4-A83P TCGA-SY-A9G5 
        8.22        25.02         2.76        27.68         6.38        31.56 
TCGA-UY-A78M TCGA-XF-A8HI TCGA-XF-A9T0 TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMG 
       22.68        17.88        26.27        13.74        92.98       110.60 
TCGA-XF-AAN0 TCGA-XF-AAN2 TCGA-ZF-A9R2 TCGA-ZF-A9RE TCGA-ZF-A9RG TCGA-ZF-A9RL 
       56.48        61.45        21.11         3.48        52.60        82.49 
TCGA-ZF-AA4N TCGA-ZF-AA4U TCGA-ZF-AA4X TCGA-ZF-AA52 TCGA-ZF-AA53 TCGA-ZF-AA56 
        2.89         8.61        63.02        35.41        57.90         8.52 
TCGA-ZF-AA5P 
       10.13 

$`PIK3CA WILD-TYPE`
TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA7N TCGA-4Z-AA7O 
       11.97        91.63       105.70        16.27        44.94        16.83 
TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 
       16.77        17.16        34.98         0.62        41.75        51.16 
TCGA-4Z-AA83 TCGA-4Z-AA86 TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM 
       66.54        10.22        40.08         7.33         2.66         6.74 
TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20P 
       12.39         6.58        13.15        19.04        32.84        17.88 
TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA 
       14.89        14.96         5.06         8.35         8.25        17.16 
TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B 
       16.18        20.48         4.67        12.82         9.96        17.56 
TCGA-BT-A42C TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F1 
       28.70        24.26        28.41         8.98         1.94         2.93 
TCGA-C4-A0F6 TCGA-C4-A0F7 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47S 
       23.01         2.04         0.46         0.43         0.69        10.95 
TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 
       12.66        12.46        12.10        12.62        12.26        13.12 
TCGA-CF-A7I0 TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ 
       12.10        13.08        12.92         4.90         7.20         5.46 
TCGA-CU-A3QU TCGA-CU-A3YL TCGA-DK-A1A3 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AD 
        5.19        16.31        21.86        18.41        19.00       112.44 
TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 
       16.14        17.62         1.81        10.59         7.79       123.85 
TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ 
       87.32         2.20        13.58         7.82         8.22        17.72 
TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WX TCGA-DK-A3WY 
       50.27        21.30        23.21         9.67        10.55       140.81 
TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B6 TCGA-DK-AA6L 
       17.98        64.18        76.60        67.36        30.67        38.24 
TCGA-DK-AA6P TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA74 
       15.02       166.03        12.36        10.49         8.65        43.50 
TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A519 
       15.35        38.83        24.66         0.10         2.24        16.70 
TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME 
       17.39         0.56         0.66        14.56        13.97        12.99 
TCGA-E7-A6MF TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A97P 
       14.33         1.22        13.68        14.07        12.95        14.37 
TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 
        8.09        32.02        16.77         4.01        12.62        22.52 
TCGA-FD-A3N6 TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR 
       27.98        23.41        17.98        25.74        46.78        19.79 
TCGA-FD-A3SS TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BR 
       12.85        27.35        14.96        20.91         3.62        26.73 
TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BY TCGA-FD-A5BZ 
       53.88        11.01        19.33         5.36         8.25        27.45 
TCGA-FD-A5C0 TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB 
       18.08         2.70         7.10        13.35        62.86        18.81 
TCGA-FD-A6TC TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI 
        6.15        12.36         2.27         3.06         4.31         9.67 
TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FJ-A871 
       10.85        31.07         7.13        10.65        17.23         8.94 
TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EC TCGA-G2-A2EF TCGA-G2-A2EK TCGA-G2-A2EL 
        3.25         6.48        22.88        61.94        15.95        26.93 
TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3BM 
       33.01         7.23        20.12        64.44        19.46        21.40 
TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GD-A2C5 
        4.50        15.91        14.07        24.92         8.94         7.73 
TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 
        3.12        20.98        10.92        11.31        11.31         7.63 
TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATP TCGA-GV-A3JV 
       27.09        20.05         5.62         4.73        32.98        14.27 
TCGA-GV-A3JW TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK 
       21.34        19.82        20.28         8.48        10.59        27.35 
TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF 
        8.58        19.07        22.72        19.40        38.60         3.06 
TCGA-HQ-A5ND TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AC TCGA-K4-A5RH TCGA-K4-A5RI 
        9.01         3.45        21.24         9.14         9.07        11.70 
TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-AAQO TCGA-LC-A66R TCGA-LT-A5Z6 
        1.74         1.81        15.42        11.80        15.32        15.58 
TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 
       13.48        12.23        16.67        14.24         1.84         3.75 
TCGA-SY-A9G0 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78N TCGA-UY-A78O TCGA-UY-A8OB 
       12.43        17.62        37.05        86.83        76.01        65.75 
TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HH 
       35.24        29.56        17.82         4.54         1.64         1.87 
TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SL TCGA-XF-A9SV 
       48.62        64.80        79.66         3.22        66.41        12.76 
TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T2 TCGA-XF-A9T3 
       11.90        23.64        21.04        28.24        18.90         2.24 
TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMJ 
       16.27        66.64         2.10        10.82        11.31        54.90 
TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX 
        7.63        71.57        91.73         2.96         8.32         6.77 
TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN1 TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN5 
       98.99        44.32        30.94        86.30        27.06        75.39 
TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-YF-AA3M 
       18.81         3.88         9.63         0.66        11.97        13.64 
TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R7 
       18.64         7.36        24.13        30.28        27.19        21.86 
TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RF TCGA-ZF-A9RM TCGA-ZF-A9RN 
       28.41        74.56        13.41        52.73        47.84        20.22 
TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA51 TCGA-ZF-AA54 
       34.06        19.69        59.38        60.16        38.73        19.40 
TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N 
       47.15        19.17         5.52 

  PIK3CA MUTATED PIK3CA WILD-TYPE 
            0.49             0.10 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
          130.88           166.03 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
           16.70            15.35 
[1] "0.5 - 130.9 (16.7)" "0.1 - 166.0 (15.3)"
[1] "hr=" "1.3"
D2V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  PIK3CA MUTATED         0       28        32       25
  PIK3CA WILD-TYPE       4       89        90      103
D2V3, multiclass
           clus
vv          PIK3CA MUTATED PIK3CA WILD-TYPE
  STAGE I                0                4
  STAGE II              28               89
  STAGE III             32               90
  STAGE IV              25              103
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1+T2  T3  T4
  PIK3CA MUTATED         28  35  15
  PIK3CA WILD-TYPE       86 144  37
D2V4, multiclass
          clus
vv         PIK3CA MUTATED PIK3CA WILD-TYPE
  T0+T1+T2             28               86
  T3                   35              144
  T4                   15               37
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  PIK3CA MUTATED    52  12  12   0
  PIK3CA WILD-TYPE 161  29  63   8
D2V5, multiclass
    clus
vv   PIK3CA MUTATED PIK3CA WILD-TYPE
  N0             52              161
  N1             12               29
  N2             12               63
  N3              0                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"
D2V6, binary
                  cls
clus                 0   1
  PIK3CA MUTATED    42   1
  PIK3CA WILD-TYPE 140   9
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3CA MUTATED     42    1
  PIK3CA WILD-TYPE  140    9
   clus
vv  PIK3CA MUTATED PIK3CA WILD-TYPE
  0             42              140
  1              1                9
[1] 2 2
[1] FALSE
D2V7, binary
                  cls
clus                 0   1
  PIK3CA MUTATED    21  64
  PIK3CA WILD-TYPE  75 216
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3CA MUTATED     21   64
  PIK3CA WILD-TYPE   75  216
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  FEMALE             21               75
  MALE               64              216
[1] 2 2
[1] FALSE
D2V8, continuous
D2V9, continuous
D2V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PIK3CA MUTATED       5                         3    75
  PIK3CA WILD-TYPE    33                        18   226
D2V11, multiclass
                           clus
vv                          PIK3CA MUTATED PIK3CA WILD-TYPE
  ASIAN                                  5               33
  BLACK OR AFRICAN AMERICAN              3               18
  WHITE                                 75              226
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V12, binary
                  cls
clus                 0   1
  PIK3CA MUTATED     2  74
  PIK3CA WILD-TYPE   6 264
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3CA MUTATED      2   74
  PIK3CA WILD-TYPE    6  264
                        clus
vv                       PIK3CA MUTATED PIK3CA WILD-TYPE
  HISPANIC OR LATINO                  2                6
  NOT HISPANIC OR LATINO             74              264
[1] 2 2
[1] FALSE

Clustering(3) Variable = RB1 MUTATION ANALYSIS
D3V1, survival
               sevent
clus2             0   1
  RB1 MUTATED    32  33
  RB1 WILD-TYPE 187 118
  RB1 MUTATED RB1 WILD-TYPE 
           65           305 
  RB1 MUTATED RB1 WILD-TYPE 
           33           118 
$`RB1 MUTATED`
TCGA-4Z-AA81 TCGA-4Z-AA86 TCGA-BL-A3JM TCGA-BT-A20R TCGA-BT-A2LA TCGA-BT-A3PH 
       41.75        10.22         6.74         5.06        17.16         4.67 
TCGA-BT-A3PJ TCGA-C4-A0F0 TCGA-CU-A0YN TCGA-DK-A3IL TCGA-DK-A3IN TCGA-DK-A3IV 
       12.82         1.94        12.92        13.58         8.22         9.67 
TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-AA6T TCGA-E5-A4TZ TCGA-E7-A6ME TCGA-E7-A7PW 
       48.00        17.98        12.36        15.35        12.99        13.68 
TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3N5 TCGA-FD-A3SL TCGA-FD-A3SO TCGA-FD-A43P 
       33.04         4.01        22.52        23.41         5.52        27.35 
TCGA-FD-A5C0 TCGA-FD-A62N TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF 
       18.08         2.70         6.15        12.69        12.36         2.27 
TCGA-FD-A6TH TCGA-G2-A2EL TCGA-GC-A3YS TCGA-GU-AATO TCGA-GV-A3JX TCGA-GV-A40G 
        4.31        26.93        24.92        10.65        19.10        19.07 
TCGA-K4-A54R TCGA-K4-A5RH TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-LC-A66R TCGA-MV-A51V 
       27.68         9.07         1.74         1.81        15.32        13.48 
TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-UY-A78L TCGA-XF-A9SG TCGA-XF-A9SI TCGA-XF-A9SJ 
       12.23        16.67        37.05        48.62        79.66         3.22 
TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SZ TCGA-XF-A9T3 TCGA-XF-A9T6 TCGA-XF-A9T8 
       11.90        23.64        28.24         2.24         2.10        13.74 
TCGA-XF-AAMF TCGA-XF-AAML TCGA-XF-AAN0 TCGA-XF-AAN2 TCGA-XF-AAN7 TCGA-ZF-A9RF 
       10.82         7.63        56.48        61.45        18.81        52.73 
TCGA-ZF-AA4T TCGA-ZF-AA4V TCGA-ZF-AA4X TCGA-ZF-AA58 TCGA-ZF-AA5H 
       19.69        59.38        63.02        47.15        19.17 

$`RB1 WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        91.63       103.50       105.70         8.35 
TCGA-4Z-AA7M TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7S 
       16.27        44.94        16.83        16.77        17.16        34.98 
TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA84 
       27.62        49.12         0.62        51.16        66.54        15.12 
TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A5ZZ 
       47.80        33.83        40.08         7.33         2.66        12.39 
TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P 
        6.58        13.15        19.04        32.84        12.16        17.88 
TCGA-BT-A20Q TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X 
       19.50        14.89        14.96         5.06         8.35         8.25 
TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E 
       16.18        20.48         9.96        17.56        28.70        24.26 
TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F1 TCGA-C4-A0F6 TCGA-C4-A0F7 TCGA-CF-A1HR 
       28.41         8.98         2.93        23.01         2.04         0.46 
TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W 
        0.43         0.69        10.95        12.66        12.46        12.10 
TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A9FF 
       12.62        12.26        13.12        12.00        12.10        11.87 
TCGA-CF-A9FM TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL 
       13.08         4.90         7.20         5.46         5.19        16.31 
TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 
        1.84        13.58        21.86         2.14        66.41        18.41 
TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF 
       19.00        16.70       130.88       112.44        16.14        17.62 
TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A2I6 
       15.62         1.81        10.59         7.79       123.85        87.32 
TCGA-DK-A3IK TCGA-DK-A3IM TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU 
        2.20         7.82        17.72        50.27        21.30        23.21 
TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 
       20.81        10.55       140.81        64.18        41.56        76.60 
TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6P 
       67.36        15.68        41.06        30.67        38.24        15.02 
TCGA-DK-AA6Q TCGA-DK-AA6S TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA71 
       13.58       166.03        10.49         8.65         7.53        13.64 
TCGA-DK-AA74 TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A2PC TCGA-E5-A4U1 TCGA-E7-A3X6 
       43.50        12.03        10.62        43.59        38.83        24.66 
TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KE 
        0.10         0.49         2.24        16.70        17.39         0.56 
TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7DV 
        0.66        14.56        13.97        14.33         0.92         1.22 
TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 
       14.07        12.95        14.37         8.09        32.02        16.77 
TCGA-FD-A3B5 TCGA-FD-A3B8 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SM 
        8.94        12.62        27.98        60.66        24.30        17.98 
TCGA-FD-A3SN TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N 
       29.16        25.74        46.78        19.79        12.85        22.98 
TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT 
       14.96        20.91         3.62        26.73        53.88        11.01 
TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C1 
       19.33         5.36         5.69         8.25        27.45        58.92 
TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TG 
        7.10         6.28        13.35        62.86        18.81         3.06 
TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF 
        9.67        10.85        31.07         7.13        10.65        17.23 
TCGA-FJ-A871 TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EC TCGA-G2-A2EF TCGA-G2-A2EJ 
        8.94         3.25         6.48        22.88        61.94        30.61 
TCGA-G2-A2EK TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY 
       15.95        35.24        33.01         7.23        20.12        17.62 
TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 
       66.02         6.94        64.44        19.46        21.40         2.24 
TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A6I1 
       15.81         4.50        15.91        14.07        17.75         8.94 
TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 
       13.91         7.73         2.10         3.12        20.98         2.20 
TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 
        7.36        10.92        11.31        11.31         7.63        27.09 
TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATP TCGA-GU-AATQ TCGA-GV-A3JV 
       20.05         5.62         4.73        32.98         7.00        14.27 
TCGA-GV-A3JW TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK 
       21.34        19.82        20.28         8.48        10.59        27.35 
TCGA-GV-A40E TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF 
        8.58        22.72         1.51        19.40        38.60         3.06 
TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB 
        9.01         8.22        25.02         3.45        21.24         2.76 
TCGA-K4-A4AC TCGA-K4-A5RI TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO TCGA-LT-A5Z6 
        9.14        11.70        15.42         6.38        11.80        15.58 
TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78K 
       14.24         1.84         3.75        12.43        31.56        17.62 
TCGA-UY-A78M TCGA-UY-A78N TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A9PA TCGA-UY-A9PB 
       22.68        86.83        76.01        65.75        35.24        29.56 
TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SH 
       17.82         4.54         1.64         1.87        17.88        64.80 
TCGA-XF-A9SL TCGA-XF-A9SV TCGA-XF-A9SY TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T4 
       66.41        12.76        21.04        26.27        18.90        16.27 
TCGA-XF-A9T5 TCGA-XF-AAME TCGA-XF-AAMG TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAMQ 
       66.64        92.98       110.60        11.31        54.90        71.57 
TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAMZ 
       91.73         2.96         8.32         6.77        98.99        44.32 
TCGA-XF-AAN1 TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN8 TCGA-YC-A8S6 
       30.94        86.30        27.06        75.39         3.88         9.63 
TCGA-YC-A9TC TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R2 
        0.66        11.97        13.64        18.64         7.36        21.11 
TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RC 
       24.13        30.28        27.19        21.86        28.41        74.56 
TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-A9RN 
       13.41         3.48        52.60        82.49        47.84        20.22 
TCGA-ZF-AA4N TCGA-ZF-AA4R TCGA-ZF-AA4U TCGA-ZF-AA4W TCGA-ZF-AA51 TCGA-ZF-AA52 
        2.89        34.06         8.61        60.16        38.73        35.41 
TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA5N TCGA-ZF-AA5P 
       57.90        19.40         8.52         5.52        10.13 

  RB1 MUTATED RB1 WILD-TYPE 
         1.74          0.10 
  RB1 MUTATED RB1 WILD-TYPE 
        79.66        166.03 
  RB1 MUTATED RB1 WILD-TYPE 
        13.68         15.95 
[1] "1.7 - 79.7 (13.7)"  "0.1 - 166.0 (15.9)"
[1] "hr=" "1.5"
D3V2, continuous
               vv
clus            STAGE I STAGE II STAGE III STAGE IV
  RB1 MUTATED         0       18        19       28
  RB1 WILD-TYPE       4       99       103      100
D3V3, multiclass
           clus
vv          RB1 MUTATED RB1 WILD-TYPE
  STAGE I             0             4
  STAGE II           18            99
  STAGE III          19           103
  STAGE IV           28           100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            T0+T1+T2  T3  T4
  RB1 MUTATED         16  36   9
  RB1 WILD-TYPE       98 143  43
D3V4, multiclass
          clus
vv         RB1 MUTATED RB1 WILD-TYPE
  T0+T1+T2          16            98
  T3                36           143
  T4                 9            43
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             N0  N1  N2  N3
  RB1 MUTATED    32   6  21   1
  RB1 WILD-TYPE 181  35  54   7
D3V5, multiclass
    clus
vv   RB1 MUTATED RB1 WILD-TYPE
  N0          32           181
  N1           6            35
  N2          21            54
  N3           1             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"
D3V6, binary
               cls
clus              0   1
  RB1 MUTATED    23   2
  RB1 WILD-TYPE 159   8
[1] "tbl2"
               cls
clus            [,1] [,2]
  RB1 MUTATED     23    2
  RB1 WILD-TYPE  159    8
   clus
vv  RB1 MUTATED RB1 WILD-TYPE
  0          23           159
  1           2             8
[1] 2 2
[1] FALSE
D3V7, binary
               cls
clus              0   1
  RB1 MUTATED    13  52
  RB1 WILD-TYPE  83 228
[1] "tbl2"
               cls
clus            [,1] [,2]
  RB1 MUTATED     13   52
  RB1 WILD-TYPE   83  228
        clus
vv       RB1 MUTATED RB1 WILD-TYPE
  FEMALE          13            83
  MALE            52           228
[1] 2 2
[1] FALSE
D3V8, continuous
D3V9, continuous
D3V10, continuous
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RB1 MUTATED       4                         4    55
  RB1 WILD-TYPE    34                        17   246
D3V11, multiclass
                           clus
vv                          RB1 MUTATED RB1 WILD-TYPE
  ASIAN                               4            34
  BLACK OR AFRICAN AMERICAN           4            17
  WHITE                              55           246
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V12, binary
               cls
clus              0   1
  RB1 MUTATED     1  61
  RB1 WILD-TYPE   7 277
[1] "tbl2"
               cls
clus            [,1] [,2]
  RB1 MUTATED      1   61
  RB1 WILD-TYPE    7  277
                        clus
vv                       RB1 MUTATED RB1 WILD-TYPE
  HISPANIC OR LATINO               1             7
  NOT HISPANIC OR LATINO          61           277
[1] 2 2
[1] FALSE

Clustering(4) Variable = FGFR3 MUTATION ANALYSIS
D4V1, survival
                 sevent
clus2               0   1
  FGFR3 MUTATED    39  16
  FGFR3 WILD-TYPE 180 135
  FGFR3 MUTATED FGFR3 WILD-TYPE 
             55             315 
  FGFR3 MUTATED FGFR3 WILD-TYPE 
             16             135 
$`FGFR3 MUTATED`
TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-4Z-AA7Y TCGA-4Z-AA81 TCGA-4Z-AA83 
       91.63       103.50       105.70        49.12        41.75        66.54 
TCGA-4Z-AA89 TCGA-BT-A0S7 TCGA-BT-A20T TCGA-BT-A42C TCGA-CF-A27C TCGA-CF-A47V 
       33.83         6.58        14.89        28.70         0.69        12.46 
TCGA-CF-A47W TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A7I0 TCGA-CF-A9FF TCGA-CF-A9FM 
       12.10        12.26        13.12        12.10        11.87        13.08 
TCGA-CU-A72E TCGA-DK-A1AG TCGA-DK-A3IS TCGA-DK-A6B0 TCGA-DK-AA6P TCGA-DK-AA71 
       13.58        15.62        50.27        76.60        15.02        13.64 
TCGA-DK-AA77 TCGA-E5-A2PC TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A519 TCGA-E7-A5KF 
       10.62        43.59        24.66         0.10        16.70         0.66 
TCGA-E7-A678 TCGA-E7-A7DU TCGA-E7-A7DV TCGA-FD-A3SM TCGA-FD-A43X TCGA-FJ-A3ZE 
       13.97         0.92         1.22        17.98         3.62        10.65 
TCGA-FJ-A3ZF TCGA-G2-A2EO TCGA-GC-A3BM TCGA-GU-A42R TCGA-GU-A763 TCGA-GU-AATQ 
       17.23        35.24        21.40        11.31        27.09         7.00 
TCGA-H4-A2HQ TCGA-UY-A78N TCGA-XF-A8HI TCGA-XF-A9SJ TCGA-XF-A9SL TCGA-XF-A9SV 
       19.40        86.83        17.88         3.22        66.41        12.76 
TCGA-XF-AAN1 TCGA-ZF-A9R2 TCGA-ZF-A9R5 TCGA-ZF-A9RE TCGA-ZF-A9RG TCGA-ZF-A9RL 
       30.94        21.11        27.19         3.48        52.60        82.49 
TCGA-ZF-AA4U 
        8.61 

$`FGFR3 WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KW TCGA-4Z-AA7M TCGA-4Z-AA7N TCGA-4Z-AA7O 
       22.29        11.97         8.35        16.27        44.94        16.83 
TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7W TCGA-4Z-AA80 TCGA-4Z-AA82 
       16.77        17.16        34.98        27.62         0.62        51.16 
TCGA-4Z-AA84 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J 
       15.12        10.22        47.80        40.08         7.33         2.66 
TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O 
        6.74        12.39        13.15        19.04        32.84        12.16 
TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20W 
       17.88        19.50         5.06        14.96         5.06         8.35 
TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PJ 
        8.25        17.16        16.18        20.48         4.67        12.82 
TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 
        9.96        17.56        24.26        28.41         8.98         1.94 
TCGA-C4-A0F1 TCGA-C4-A0F6 TCGA-C4-A0F7 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A47S 
        2.93        23.01         2.04         0.46         0.43        10.95 
TCGA-CF-A47T TCGA-CF-A47X TCGA-CF-A5UA TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR 
       12.66        12.62        12.00        12.92         4.90         7.20 
TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-DK-A1A3 TCGA-DK-A1A5 
        5.46         5.19        16.31         1.84        21.86         2.14 
TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD 
       66.41        18.41        19.00        16.70       130.88       112.44 
TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 
       16.14        17.62         1.81        10.59         7.79       123.85 
TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ 
       87.32         2.20        13.58         7.82         8.22        17.72 
TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY 
       21.30        23.21         9.67        20.81        10.55       140.81 
TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B1 TCGA-DK-A6B2 
       48.00        17.98        64.18        41.56        67.36        15.68 
TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6Q TCGA-DK-AA6S TCGA-DK-AA6T 
       41.06        30.67        38.24        13.58       166.03        12.36 
TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA74 TCGA-DK-AA76 TCGA-E5-A4TZ 
       10.49         8.65         7.53        43.50        12.03        15.35 
TCGA-E5-A4U1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A677 
       38.83         0.49         2.24        17.39         0.56        14.56 
TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A97P 
       12.99        14.33        13.68        14.07        12.95        14.37 
TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 
        8.09        32.02        16.77         8.94        33.04         4.01 
TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL 
       12.62        22.52        27.98        60.66        24.30        23.41 
TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS 
       29.16         5.52        25.74        46.78        19.79        12.85 
TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A5BR TCGA-FD-A5BS 
       22.98        27.35        14.96        20.91        26.73        53.88 
TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ 
       11.01        19.33         5.36         5.69         8.25        27.45 
TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S 
       18.08        58.92         2.70         7.10         6.28        13.35 
TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF 
       62.86        18.81         6.15        12.69        12.36         2.27 
TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 
        3.06         4.31         9.67        10.85        31.07         7.13 
TCGA-FJ-A871 TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EC TCGA-G2-A2EF TCGA-G2-A2EJ 
        8.94         3.25         6.48        22.88        61.94        30.61 
TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY 
       15.95        26.93        33.01         7.23        20.12        17.62 
TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3I6 TCGA-GC-A3OO 
       66.02         6.94        64.44        19.46         2.24        15.81 
TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A6I1 
        4.50        15.91        14.07        17.75        24.92         8.94 
TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 
       13.91         7.73         2.10         3.12        20.98         2.20 
TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A762 TCGA-GU-A764 TCGA-GU-A766 
        7.36        10.92        11.31         7.63        20.05         5.62 
TCGA-GU-A767 TCGA-GU-AATO TCGA-GU-AATP TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX 
        4.73        10.65        32.98        14.27        21.34        19.10 
TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E 
       19.82        20.28         8.48        10.59        27.35         8.58 
TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND 
       19.07        22.72         1.51        38.60         3.06         9.01 
TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC 
        8.22        25.02         3.45        21.24         2.76         9.14 
TCGA-K4-A54R TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB 
       27.68         9.07        11.70         1.74         1.81        15.42 
TCGA-K4-A83P TCGA-K4-AAQO TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI 
        6.38        11.80        15.32        15.58        13.48        12.23 
TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 TCGA-SY-A9G0 TCGA-SY-A9G5 
       16.67        14.24         1.84         3.75        12.43        31.56 
TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A9PA 
       17.62        37.05        22.68        76.01        65.75        35.24 
TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HH TCGA-XF-A9SG 
       29.56        17.82         4.54         1.64         1.87        48.62 
TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ 
       64.80        79.66        11.90        23.64        21.04        28.24 
TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 
       26.27        18.90         2.24        16.27        66.64         2.10 
TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMG TCGA-XF-AAMH TCGA-XF-AAMJ 
       13.74        92.98        10.82       110.60        11.31        54.90 
TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX 
        7.63        71.57        91.73         2.96         8.32         6.77 
TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN0 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN4 
       98.99        44.32        56.48        61.45        86.30        27.06 
TCGA-XF-AAN5 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L 
       75.39        18.81         3.88         9.63         0.66        11.97 
TCGA-YF-AA3M TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R7 
       13.64        18.64         7.36        24.13        30.28        21.86 
TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RF TCGA-ZF-A9RM TCGA-ZF-A9RN 
       28.41        74.56        13.41        52.73        47.84        20.22 
TCGA-ZF-AA4N TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA4X 
        2.89        34.06        19.69        59.38        60.16        63.02 
TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 
       38.73        35.41        57.90        19.40         8.52        47.15 
TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-ZF-AA5P 
       19.17         5.52        10.13 

  FGFR3 MUTATED FGFR3 WILD-TYPE 
           0.10            0.43 
  FGFR3 MUTATED FGFR3 WILD-TYPE 
         105.70          166.03 
  FGFR3 MUTATED FGFR3 WILD-TYPE 
          15.62           15.68 
[1] "0.1 - 105.7 (15.6)" "0.4 - 166.0 (15.7)"
[1] "hr=" "1.7"
D4V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  FGFR3 MUTATED         1       26        14       14
  FGFR3 WILD-TYPE       3       91       108      114
D4V3, multiclass
           clus
vv          FGFR3 MUTATED FGFR3 WILD-TYPE
  STAGE I               1               3
  STAGE II             26              91
  STAGE III            14             108
  STAGE IV             14             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"
                 vv
clus              T0+T1+T2  T3  T4
  FGFR3 MUTATED         25  15   8
  FGFR3 WILD-TYPE       89 164  44
D4V4, multiclass
          clus
vv         FGFR3 MUTATED FGFR3 WILD-TYPE
  T0+T1+T2            25              89
  T3                  15             164
  T4                   8              44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  FGFR3 MUTATED    38   3   7   2
  FGFR3 WILD-TYPE 175  38  68   6
D4V5, multiclass
    clus
vv   FGFR3 MUTATED FGFR3 WILD-TYPE
  N0            38             175
  N1             3              38
  N2             7              68
  N3             2               6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V6, binary
                 cls
clus                0   1
  FGFR3 MUTATED    38   4
  FGFR3 WILD-TYPE 144   6
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FGFR3 MUTATED     38    4
  FGFR3 WILD-TYPE  144    6
   clus
vv  FGFR3 MUTATED FGFR3 WILD-TYPE
  0            38             144
  1             4               6
[1] 2 2
[1] FALSE
D4V7, binary
                 cls
clus                0   1
  FGFR3 MUTATED     8  48
  FGFR3 WILD-TYPE  88 232
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FGFR3 MUTATED      8   48
  FGFR3 WILD-TYPE   88  232
        clus
vv       FGFR3 MUTATED FGFR3 WILD-TYPE
  FEMALE             8              88
  MALE              48             232
[1] 2 2
[1] FALSE
D4V8, continuous
D4V9, continuous
D4V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  FGFR3 MUTATED      11                         1    42
  FGFR3 WILD-TYPE    27                        20   259
D4V11, multiclass
                           clus
vv                          FGFR3 MUTATED FGFR3 WILD-TYPE
  ASIAN                                11              27
  BLACK OR AFRICAN AMERICAN             1              20
  WHITE                                42             259
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V12, binary
                 cls
clus                0   1
  FGFR3 MUTATED     0  51
  FGFR3 WILD-TYPE   8 287
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FGFR3 MUTATED      0   51
  FGFR3 WILD-TYPE    8  287
                        clus
vv                       FGFR3 MUTATED FGFR3 WILD-TYPE
  HISPANIC OR LATINO                 0               8
  NOT HISPANIC OR LATINO            51             287
[1] 2 2
[1] FALSE

Clustering(5) Variable = CDKN2A MUTATION ANALYSIS
D5V1, survival
                  sevent
clus2                0   1
  CDKN2A MUTATED    14  11
  CDKN2A WILD-TYPE 205 140
  CDKN2A MUTATED CDKN2A WILD-TYPE 
              25              345 
  CDKN2A MUTATED CDKN2A WILD-TYPE 
              11              140 
$`CDKN2A MUTATED`
TCGA-4Z-AA7R TCGA-4Z-AA84 TCGA-DK-A3X1 TCGA-DK-A6B6 TCGA-DK-AA6Q TCGA-DK-AA6S 
       17.16        15.12        48.00        30.67        13.58       166.03 
TCGA-E7-A677 TCGA-E7-A7XN TCGA-FD-A5BV TCGA-FD-A6TI TCGA-G2-A2EO TCGA-G2-A2ES 
       14.56        14.07         5.36         9.67        35.24        33.01 
TCGA-G2-A3VY TCGA-GC-A3BM TCGA-GC-A6I1 TCGA-GD-A3OS TCGA-GU-A42Q TCGA-GV-A40E 
       17.62        21.40         8.94        20.98        11.31         8.58 
TCGA-K4-A54R TCGA-XF-A9SY TCGA-XF-AAN3 TCGA-ZF-A9R4 TCGA-ZF-A9RD TCGA-ZF-AA4N 
       27.68        21.04        86.30        30.28        13.41         2.89 
TCGA-ZF-AA4W 
       60.16 

$`CDKN2A WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        91.63       103.50       105.70         8.35 
TCGA-4Z-AA7M TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7S TCGA-4Z-AA7W 
       16.27        44.94        16.83        16.77        34.98        27.62 
TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA86 
       49.12         0.62        41.75        51.16        66.54        10.22 
TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM 
       47.80        33.83        40.08         7.33         2.66         6.74 
TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O 
       12.39         6.58        13.15        19.04        32.84        12.16 
TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20V 
       17.88        19.50         5.06        14.89        14.96         5.06 
TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH 
        8.35         8.25        17.16        16.18        20.48         4.67 
TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E TCGA-BT-A42F 
       12.82         9.96        17.56        28.70        24.26        28.41 
TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-C4-A0F6 TCGA-C4-A0F7 TCGA-CF-A1HR 
        8.98         1.94         2.93        23.01         2.04         0.46 
TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W 
        0.43         0.69        10.95        12.66        12.46        12.10 
TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A9FF 
       12.62        12.26        13.12        12.00        12.10        11.87 
TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3QU 
       13.08        12.92         4.90         7.20         5.46         5.19 
TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 
       16.31         1.84        13.58        21.86         2.14        66.41 
TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE 
       18.41        19.00        16.70       130.88       112.44        16.14 
TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 
       17.62        15.62         1.81        10.59         7.79       123.85 
TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ 
       87.32         2.20        13.58         7.82         8.22        17.72 
TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX 
       50.27        21.30        23.21         9.67        20.81        10.55 
TCGA-DK-A3WY TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 
      140.81        17.98        64.18        41.56        76.60        67.36 
TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-AA6L TCGA-DK-AA6P TCGA-DK-AA6T TCGA-DK-AA6U 
       15.68        41.06        38.24        15.02        12.36        10.49 
TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA76 TCGA-DK-AA77 
        8.65         7.53        13.64        43.50        12.03        10.62 
TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ 
       43.59        15.35        38.83        24.66         0.10         0.49 
TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A678 
        2.24        16.70        17.39         0.56         0.66        13.97 
TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A85H 
       12.99        14.33         0.92         1.22        13.68        12.95 
TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 
       14.37         8.09        32.02        16.77         8.94        33.04 
TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ 
        4.01        12.62        22.52        27.98        60.66        24.30 
TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ 
       23.41        17.98        29.16         5.52        25.74        46.78 
TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U 
       19.79        12.85        22.98        27.35        14.96        20.91 
TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BX 
        3.62        26.73        53.88        11.01        19.33         5.69 
TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O 
        8.25        27.45        18.08        58.92         2.70         7.10 
TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD 
        6.28        13.35        62.86        18.81         6.15        12.69 
TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TK TCGA-FJ-A3Z7 
       12.36         2.27         3.06         4.31        10.85        31.07 
TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FJ-A871 TCGA-FT-A3EE TCGA-FT-A61P 
        7.13        10.65        17.23         8.94         3.25         6.48 
TCGA-G2-A2EC TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A3IB 
       22.88        61.94        30.61        15.95        26.93         7.23 
TCGA-G2-A3IE TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3I6 
       20.12        66.02         6.94        64.44        19.46         2.24 
TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS 
       15.81         4.50        15.91        14.07        17.75        24.92 
TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A6C6 TCGA-GD-A76B 
       13.91         7.73         2.10         3.12         2.20         7.36 
TCGA-GU-A42P TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 
       10.92        11.31         7.63        27.09        20.05         5.62 
TCGA-GU-A767 TCGA-GU-AATO TCGA-GU-AATP TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW 
        4.73        10.65        32.98         7.00        14.27        21.34 
TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK 
       19.10        19.82        20.28         8.48        10.59        27.35 
TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF 
       19.07        22.72         1.51        19.40        38.60         3.06 
TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB 
        9.01         8.22        25.02         3.45        21.24         2.76 
TCGA-K4-A4AC TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB 
        9.14         9.07        11.70         1.74         1.81        15.42 
TCGA-K4-A83P TCGA-K4-AAQO TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI 
        6.38        11.80        15.32        15.58        13.48        12.23 
TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 TCGA-SY-A9G0 TCGA-SY-A9G5 
       16.67        14.24         1.84         3.75        12.43        31.56 
TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78N TCGA-UY-A78O TCGA-UY-A8OB 
       17.62        37.05        22.68        86.83        76.01        65.75 
TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HH 
       35.24        29.56        17.82         4.54         1.64         1.87 
TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SL 
       17.88        48.62        64.80        79.66         3.22        66.41 
TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 
       12.76        11.90        23.64        28.24        26.27        18.90 
TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAME 
        2.24        16.27        66.64         2.10        13.74        92.98 
TCGA-XF-AAMF TCGA-XF-AAMG TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ 
       10.82       110.60        11.31        54.90         7.63        71.57 
TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAMZ 
       91.73         2.96         8.32         6.77        98.99        44.32 
TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN7 
       56.48        30.94        61.45        27.06        75.39        18.81 
TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R0 
        3.88         9.63         0.66        11.97        13.64        18.64 
TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 
        7.36        21.11        24.13        27.19        21.86        28.41 
TCGA-ZF-A9RC TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-A9RM 
       74.56         3.48        52.73        52.60        82.49        47.84 
TCGA-ZF-A9RN TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4X 
       20.22        34.06        19.69         8.61        59.38        63.02 
TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 
       38.73        35.41        57.90        19.40         8.52        47.15 
TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-ZF-AA5P 
       19.17         5.52        10.13 

  CDKN2A MUTATED CDKN2A WILD-TYPE 
            2.89             0.10 
  CDKN2A MUTATED CDKN2A WILD-TYPE 
          166.03           140.81 
  CDKN2A MUTATED CDKN2A WILD-TYPE 
           17.62            15.58 
[1] "2.9 - 166.0 (17.6)" "0.1 - 140.8 (15.6)"
[1] "hr=" "1.1"
D5V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  CDKN2A MUTATED         0       11         7        7
  CDKN2A WILD-TYPE       4      106       115      121
D5V3, multiclass
           clus
vv          CDKN2A MUTATED CDKN2A WILD-TYPE
  STAGE I                0                4
  STAGE II              11              106
  STAGE III              7              115
  STAGE IV               7              121
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1+T2  T3  T4
  CDKN2A MUTATED          5  13   2
  CDKN2A WILD-TYPE      109 166  50
D5V4, multiclass
          clus
vv         CDKN2A MUTATED CDKN2A WILD-TYPE
  T0+T1+T2              5              109
  T3                   13              166
  T4                    2               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"
                  vv
clus                N0  N1  N2  N3
  CDKN2A MUTATED    13   2   4   0
  CDKN2A WILD-TYPE 200  39  71   8
D5V5, multiclass
    clus
vv   CDKN2A MUTATED CDKN2A WILD-TYPE
  N0             13              200
  N1              2               39
  N2              4               71
  N3              0                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"
D5V6, binary
                  cls
clus                 0   1
  CDKN2A MUTATED    11   1
  CDKN2A WILD-TYPE 171   9
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CDKN2A MUTATED     11    1
  CDKN2A WILD-TYPE  171    9
   clus
vv  CDKN2A MUTATED CDKN2A WILD-TYPE
  0             11              171
  1              1                9
[1] 2 2
[1] FALSE
D5V7, binary
                  cls
clus                 0   1
  CDKN2A MUTATED     7  18
  CDKN2A WILD-TYPE  89 262
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CDKN2A MUTATED      7   18
  CDKN2A WILD-TYPE   89  262
        clus
vv       CDKN2A MUTATED CDKN2A WILD-TYPE
  FEMALE              7               89
  MALE               18              262
[1] 2 2
[1] FALSE
D5V8, continuous
D5V9, continuous
D5V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CDKN2A MUTATED       3                         1    21
  CDKN2A WILD-TYPE    35                        20   280
D5V11, multiclass
                           clus
vv                          CDKN2A MUTATED CDKN2A WILD-TYPE
  ASIAN                                  3               35
  BLACK OR AFRICAN AMERICAN              1               20
  WHITE                                 21              280
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V12, binary
                  cls
clus                 0   1
  CDKN2A MUTATED     0  23
  CDKN2A WILD-TYPE   8 315
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CDKN2A MUTATED      0   23
  CDKN2A WILD-TYPE    8  315
                        clus
vv                       CDKN2A MUTATED CDKN2A WILD-TYPE
  HISPANIC OR LATINO                  0                8
  NOT HISPANIC OR LATINO             23              315
[1] 2 2
[1] FALSE

Clustering(6) Variable = RHOB MUTATION ANALYSIS
D6V1, survival
                sevent
clus2              0   1
  RHOB MUTATED    13  11
  RHOB WILD-TYPE 206 140
  RHOB MUTATED RHOB WILD-TYPE 
            24            346 
  RHOB MUTATED RHOB WILD-TYPE 
            11            140 
$`RHOB MUTATED`
TCGA-4Z-AA7O TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-BT-A20N TCGA-BT-A3PJ TCGA-DK-A3IL 
       16.83        10.22        47.80        32.84        12.82        13.58 
TCGA-DK-A3X1 TCGA-E5-A2PC TCGA-E7-A5KF TCGA-E7-A97Q TCGA-FD-A3SL TCGA-FD-A6TB 
       48.00        43.59         0.66         8.09        23.41        18.81 
TCGA-FJ-A3ZF TCGA-G2-AA3F TCGA-HQ-A5ND TCGA-K4-A4AC TCGA-UY-A78M TCGA-UY-A9PF 
       17.23        19.46         9.01         9.14        22.68         1.64 
TCGA-ZF-A9R0 TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-AA4U TCGA-ZF-AA4W TCGA-ZF-AA52 
       18.64        24.13        30.28         8.61        60.16        35.41 

$`RHOB WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        91.63       103.50       105.70         8.35 
TCGA-4Z-AA7M TCGA-4Z-AA7N TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7W 
       16.27        44.94        16.77        17.16        34.98        27.62 
TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA84 
       49.12         0.62        41.75        51.16        66.54        15.12 
TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ 
       33.83        40.08         7.33         2.66         6.74        12.39 
TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q 
        6.58        13.15        19.04        12.16        17.88        19.50 
TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X 
        5.06        14.89        14.96         5.06         8.35         8.25 
TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PK TCGA-BT-A42B 
       17.16        16.18        20.48         4.67         9.96        17.56 
TCGA-BT-A42C TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F1 
       28.70        24.26        28.41         8.98         1.94         2.93 
TCGA-C4-A0F6 TCGA-C4-A0F7 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47S 
       23.01         2.04         0.46         0.43         0.69        10.95 
TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 
       12.66        12.46        12.10        12.62        12.26        13.12 
TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YO 
       12.00        12.10        11.87        13.08        12.92         4.90 
TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E 
        7.20         5.46         5.19        16.31         1.84        13.58 
TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB 
       21.86         2.14        66.41        18.41        19.00        16.70 
TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX 
      130.88       112.44        16.14        17.62        15.62         1.81 
TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IM 
       10.59         7.79       123.85        87.32         2.20         7.82 
TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV 
        8.22        17.72        50.27        21.30        23.21         9.67 
TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW 
       20.81        10.55       140.81        17.98        64.18        41.56 
TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L 
       76.60        67.36        15.68        41.06        30.67        38.24 
TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6W 
       15.02        13.58       166.03        12.36        10.49         8.65 
TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A4TZ 
        7.53        13.64        43.50        12.03        10.62        15.35 
TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 
       38.83        24.66         0.10         0.49         2.24        16.70 
TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF 
       17.39         0.56        14.56        13.97        12.99        14.33 
TCGA-E7-A7DU TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A97P 
        0.92         1.22        13.68        14.07        12.95        14.37 
TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 
       32.02        16.77         8.94        33.04         4.01        12.62 
TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SM TCGA-FD-A3SN 
       22.52        27.98        60.66        24.30        17.98        29.16 
TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N 
        5.52        25.74        46.78        19.79        12.85        22.98 
TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS 
       27.35        14.96        20.91         3.62        26.73        53.88 
TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ 
       11.01        19.33         5.36         5.69         8.25        27.45 
TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S 
       18.08        58.92         2.70         7.10         6.28        13.35 
TCGA-FD-A6TA TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TG 
       62.86         6.15        12.69        12.36         2.27         3.06 
TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE 
        4.31         9.67        10.85        31.07         7.13        10.65 
TCGA-FJ-A871 TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EC TCGA-G2-A2EF TCGA-G2-A2EJ 
        8.94         3.25         6.48        22.88        61.94        30.61 
TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE 
       15.95        26.93        35.24        33.01         7.23        20.12 
TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3D TCGA-GC-A3BM TCGA-GC-A3I6 
       17.62        66.02         6.94        64.44        21.40         2.24 
TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS 
       15.81         4.50        15.91        14.07        17.75        24.92 
TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS 
        8.94        13.91         7.73         2.10         3.12        20.98 
TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 
        2.20         7.36        10.92        11.31        11.31         7.63 
TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATO TCGA-GU-AATP 
       27.09        20.05         5.62         4.73        10.65        32.98 
TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF 
        7.00        14.27        21.34        19.10        19.82        20.28 
TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA 
        8.48        10.59        27.35         8.58        19.07        22.72 
TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5NE TCGA-K4-A3WS 
        1.51        19.40        38.60         3.06         8.22        25.02 
TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A54R TCGA-K4-A5RH TCGA-K4-A5RI 
        3.45        21.24         2.76        27.68         9.07        11.70 
TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO TCGA-LC-A66R 
        1.74         1.81        15.42         6.38        11.80        15.32 
TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX 
       15.58        13.48        12.23        16.67        14.24         1.84 
TCGA-S5-AA26 TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78N 
        3.75        12.43        31.56        17.62        37.05        86.83 
TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE 
       76.01        65.75        35.24        29.56        17.82         4.54 
TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SJ 
        1.87        17.88        48.62        64.80        79.66         3.22 
TCGA-XF-A9SL TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ 
       66.41        12.76        11.90        23.64        21.04        28.24 
TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 
       26.27        18.90         2.24        16.27        66.64         2.10 
TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMG TCGA-XF-AAMH TCGA-XF-AAMJ 
       13.74        92.98        10.82       110.60        11.31        54.90 
TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX 
        7.63        71.57        91.73         2.96         8.32         6.77 
TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 
       98.99        44.32        56.48        30.94        61.45        86.30 
TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YC-A9TC 
       27.06        75.39        18.81         3.88         9.63         0.66 
TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R5 TCGA-ZF-A9R7 
       11.97        13.64         7.36        21.11        27.19        21.86 
TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RG 
       28.41        74.56        13.41         3.48        52.73        52.60 
TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4R TCGA-ZF-AA4T 
       82.49        47.84        20.22         2.89        34.06        19.69 
TCGA-ZF-AA4V TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA56 
       59.38        63.02        38.73        57.90        19.40         8.52 
TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-ZF-AA5P 
       47.15        19.17         5.52        10.13 

  RHOB MUTATED RHOB WILD-TYPE 
          0.66           0.10 
  RHOB MUTATED RHOB WILD-TYPE 
         60.16         166.03 
  RHOB MUTATED RHOB WILD-TYPE 
        18.725         15.385 
[1] "0.7 - 60.2 (18.7)"  "0.1 - 166.0 (15.4)"
[1] "hr=" "1.1"
D6V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  RHOB MUTATED         0        5        10        9
  RHOB WILD-TYPE       4      112       112      119
D6V3, multiclass
           clus
vv          RHOB MUTATED RHOB WILD-TYPE
  STAGE I              0              4
  STAGE II             5            112
  STAGE III           10            112
  STAGE IV             9            119
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1+T2  T3  T4
  RHOB MUTATED          7  12   4
  RHOB WILD-TYPE      107 167  48
D6V4, multiclass
          clus
vv         RHOB MUTATED RHOB WILD-TYPE
  T0+T1+T2            7            107
  T3                 12            167
  T4                  4             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"
                vv
clus              N0  N1  N2  N3
  RHOB MUTATED     9   4   4   2
  RHOB WILD-TYPE 204  37  71   6
D6V5, multiclass
    clus
vv   RHOB MUTATED RHOB WILD-TYPE
  N0            9            204
  N1            4             37
  N2            4             71
  N3            2              6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V6, binary
                cls
clus               0   1
  RHOB MUTATED    13   1
  RHOB WILD-TYPE 169   9
[1] "tbl2"
                cls
clus             [,1] [,2]
  RHOB MUTATED     13    1
  RHOB WILD-TYPE  169    9
   clus
vv  RHOB MUTATED RHOB WILD-TYPE
  0           13            169
  1            1              9
[1] 2 2
[1] FALSE
D6V7, binary
                cls
clus               0   1
  RHOB MUTATED     6  18
  RHOB WILD-TYPE  90 262
[1] "tbl2"
                cls
clus             [,1] [,2]
  RHOB MUTATED      6   18
  RHOB WILD-TYPE   90  262
        clus
vv       RHOB MUTATED RHOB WILD-TYPE
  FEMALE            6             90
  MALE             18            262
[1] 2 2
[1] FALSE
D6V8, continuous
[1] "Remove cluster labels:" "RHOB MUTATED"          
clus
  RHOB MUTATED RHOB WILD-TYPE 
             2            118 
    TCGA-2F-A9KO     TCGA-2F-A9KP     TCGA-2F-A9KQ     TCGA-2F-A9KR 
"RHOB WILD-TYPE" "RHOB WILD-TYPE" "RHOB WILD-TYPE" "RHOB WILD-TYPE" 
    TCGA-2F-A9KT     TCGA-2F-A9KW     TCGA-CF-A1HS     TCGA-CF-A27C 
"RHOB WILD-TYPE" "RHOB WILD-TYPE" "RHOB WILD-TYPE" "RHOB WILD-TYPE" 
    TCGA-CF-A3MF     TCGA-CF-A3MG     TCGA-CF-A3MH     TCGA-CF-A3MI 
"RHOB WILD-TYPE" "RHOB WILD-TYPE" "RHOB WILD-TYPE" "RHOB WILD-TYPE" 
    TCGA-CF-A47S     TCGA-CF-A47T     TCGA-CF-A47V     TCGA-CF-A47W 
"RHOB WILD-TYPE" "RHOB WILD-TYPE" "RHOB WILD-TYPE" "RHOB WILD-TYPE" 
    TCGA-CF-A47X     TCGA-CF-A47Y     TCGA-CF-A5U8     TCGA-CF-A5UA 
"RHOB WILD-TYPE" "RHOB WILD-TYPE" "RHOB WILD-TYPE" "RHOB WILD-TYPE" 
    TCGA-CF-A7I0     TCGA-DK-A2HX     TCGA-DK-A3IN     TCGA-DK-A3IV 
"RHOB WILD-TYPE" "RHOB WILD-TYPE" "RHOB WILD-TYPE" "RHOB WILD-TYPE" 
    TCGA-DK-A3WX     TCGA-DK-A3X2     TCGA-DK-A6B2     TCGA-DK-A6B5 
"RHOB WILD-TYPE" "RHOB WILD-TYPE" "RHOB WILD-TYPE" "RHOB WILD-TYPE" 
    TCGA-DK-A6B6     TCGA-DK-AA6P     TCGA-DK-AA6S     TCGA-DK-AA6U 
"RHOB WILD-TYPE" "RHOB WILD-TYPE" "RHOB WILD-TYPE" "RHOB WILD-TYPE" 
    TCGA-DK-AA6W     TCGA-DK-AA76     TCGA-E5-A4TZ     TCGA-E5-A4U1 
"RHOB WILD-TYPE" "RHOB WILD-TYPE" "RHOB WILD-TYPE" "RHOB WILD-TYPE" 
    TCGA-E7-A519     TCGA-E7-A541     TCGA-E7-A7DU     TCGA-E7-A7DV 
"RHOB WILD-TYPE" "RHOB WILD-TYPE" "RHOB WILD-TYPE" "RHOB WILD-TYPE" 
    TCGA-FT-A61P     TCGA-G2-A2EC     TCGA-G2-A2EF     TCGA-G2-A2EJ 
"RHOB WILD-TYPE" "RHOB WILD-TYPE" "RHOB WILD-TYPE" "RHOB WILD-TYPE" 
    TCGA-G2-A2EK     TCGA-G2-A2EL     TCGA-G2-A2EO     TCGA-G2-A2ES 
"RHOB WILD-TYPE" "RHOB WILD-TYPE" "RHOB WILD-TYPE" "RHOB WILD-TYPE" 
    TCGA-G2-A3IB     TCGA-G2-A3IE     TCGA-G2-A3VY     TCGA-GC-A3BM 
"RHOB WILD-TYPE" "RHOB WILD-TYPE" "RHOB WILD-TYPE" "RHOB WILD-TYPE" 
    TCGA-GC-A3I6     TCGA-GC-A3OO     TCGA-GC-A3RC     TCGA-GC-A3RD 
"RHOB WILD-TYPE" "RHOB WILD-TYPE" "RHOB WILD-TYPE" "RHOB WILD-TYPE" 
    TCGA-GC-A3YS     TCGA-GC-A6I1     TCGA-GC-A6I3     TCGA-GD-A3OS 
"RHOB WILD-TYPE" "RHOB WILD-TYPE" "RHOB WILD-TYPE" "RHOB WILD-TYPE" 
    TCGA-GD-A6C6     TCGA-GV-A3JV     TCGA-GV-A3JW     TCGA-GV-A3JX 
"RHOB WILD-TYPE" "RHOB WILD-TYPE" "RHOB WILD-TYPE" "RHOB WILD-TYPE" 
    TCGA-GV-A3JZ     TCGA-GV-A3QF     TCGA-GV-A3QH     TCGA-GV-A3QI 
"RHOB WILD-TYPE" "RHOB WILD-TYPE" "RHOB WILD-TYPE" "RHOB WILD-TYPE" 
    TCGA-GV-A3QK     TCGA-GV-A40E     TCGA-GV-A40G     TCGA-GV-A6ZA 
"RHOB WILD-TYPE" "RHOB WILD-TYPE" "RHOB WILD-TYPE" "RHOB WILD-TYPE" 
    TCGA-SY-A9G0     TCGA-SY-A9G5     TCGA-UY-A78L     TCGA-UY-A78N 
"RHOB WILD-TYPE" "RHOB WILD-TYPE" "RHOB WILD-TYPE" "RHOB WILD-TYPE" 
    TCGA-XF-A8HH     TCGA-XF-A8HI     TCGA-XF-A9SG     TCGA-XF-A9SH 
"RHOB WILD-TYPE" "RHOB WILD-TYPE" "RHOB WILD-TYPE" "RHOB WILD-TYPE" 
    TCGA-XF-A9SI     TCGA-XF-A9SJ     TCGA-XF-A9SL     TCGA-XF-A9SV 
"RHOB WILD-TYPE" "RHOB WILD-TYPE" "RHOB WILD-TYPE" "RHOB WILD-TYPE" 
    TCGA-XF-A9SW     TCGA-XF-A9SX     TCGA-XF-A9SY     TCGA-XF-A9SZ 
"RHOB WILD-TYPE" "RHOB WILD-TYPE" "RHOB WILD-TYPE" "RHOB WILD-TYPE" 
    TCGA-XF-A9T0     TCGA-XF-A9T2     TCGA-XF-A9T3     TCGA-XF-A9T4 
"RHOB WILD-TYPE" "RHOB WILD-TYPE" "RHOB WILD-TYPE" "RHOB WILD-TYPE" 
    TCGA-XF-A9T5     TCGA-XF-A9T6     TCGA-XF-A9T8     TCGA-XF-AAME 
"RHOB WILD-TYPE" "RHOB WILD-TYPE" "RHOB WILD-TYPE" "RHOB WILD-TYPE" 
    TCGA-XF-AAMF     TCGA-XF-AAMG     TCGA-XF-AAMH     TCGA-XF-AAMJ 
"RHOB WILD-TYPE" "RHOB WILD-TYPE" "RHOB WILD-TYPE" "RHOB WILD-TYPE" 
    TCGA-XF-AAML     TCGA-XF-AAMQ     TCGA-XF-AAMR     TCGA-XF-AAMT 
"RHOB WILD-TYPE" "RHOB WILD-TYPE" "RHOB WILD-TYPE" "RHOB WILD-TYPE" 
    TCGA-XF-AAMW     TCGA-XF-AAMX     TCGA-XF-AAMY     TCGA-XF-AAMZ 
"RHOB WILD-TYPE" "RHOB WILD-TYPE" "RHOB WILD-TYPE" "RHOB WILD-TYPE" 
    TCGA-XF-AAN0     TCGA-XF-AAN1     TCGA-XF-AAN2     TCGA-XF-AAN3 
"RHOB WILD-TYPE" "RHOB WILD-TYPE" "RHOB WILD-TYPE" "RHOB WILD-TYPE" 
    TCGA-XF-AAN4     TCGA-XF-AAN5     TCGA-XF-AAN7     TCGA-XF-AAN8 
"RHOB WILD-TYPE" "RHOB WILD-TYPE" "RHOB WILD-TYPE" "RHOB WILD-TYPE" 
    TCGA-YF-AA3L     TCGA-YF-AA3M 
"RHOB WILD-TYPE" "RHOB WILD-TYPE" 
D6V9, continuous
D6V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RHOB MUTATED       2                         3    17
  RHOB WILD-TYPE    36                        18   284
D6V11, multiclass
                           clus
vv                          RHOB MUTATED RHOB WILD-TYPE
  ASIAN                                2             36
  BLACK OR AFRICAN AMERICAN            3             18
  WHITE                               17            284
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V12, binary
                cls
clus               0   1
  RHOB MUTATED     0  19
  RHOB WILD-TYPE   8 319
[1] "tbl2"
                cls
clus             [,1] [,2]
  RHOB MUTATED      0   19
  RHOB WILD-TYPE    8  319
                        clus
vv                       RHOB MUTATED RHOB WILD-TYPE
  HISPANIC OR LATINO                0              8
  NOT HISPANIC OR LATINO           19            319
[1] 2 2
[1] FALSE

Clustering(7) Variable = ELF3 MUTATION ANALYSIS
D7V1, survival
                sevent
clus2              0   1
  ELF3 MUTATED    28  13
  ELF3 WILD-TYPE 191 138
  ELF3 MUTATED ELF3 WILD-TYPE 
            41            329 
  ELF3 MUTATED ELF3 WILD-TYPE 
            13            138 
$`ELF3 MUTATED`
TCGA-2F-A9KT TCGA-BT-A20Q TCGA-CF-A1HS TCGA-CF-A47X TCGA-CU-A0YR TCGA-CU-A3YL 
      105.70        19.50         0.43        12.62         7.20        16.31 
TCGA-CU-A72E TCGA-DK-AA6L TCGA-E5-A2PC TCGA-E5-A4U1 TCGA-E7-A5KF TCGA-E7-A97Q 
       13.58        38.24        43.59        38.83         0.66         8.09 
TCGA-FD-A3SQ TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A62O TCGA-FD-A6TB TCGA-FD-A6TC 
       46.78        22.98        27.35         7.10        18.81         6.15 
TCGA-FD-A6TI TCGA-FJ-A3ZF TCGA-G2-A2EO TCGA-GC-A3RC TCGA-GC-A6I1 TCGA-GD-A2C5 
        9.67        17.23        35.24        15.91         8.94         7.73 
TCGA-GD-A3OP TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-AATP TCGA-GV-A3JV TCGA-R3-A69X 
        2.10         2.20         7.36        32.98        14.27        14.24 
TCGA-UY-A78O TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-ZF-A9R0 TCGA-ZF-A9R4 TCGA-ZF-A9R7 
       76.01        30.94        61.45        18.64        30.28        21.86 
TCGA-ZF-A9RG TCGA-ZF-A9RM TCGA-ZF-AA4X TCGA-ZF-AA56 TCGA-ZF-AA5N 
       52.60        47.84        63.02         8.52         5.52 

$`ELF3 WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KW TCGA-4Z-AA7M 
       22.29        11.97        91.63       103.50         8.35        16.27 
TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7W 
       44.94        16.83        16.77        17.16        34.98        27.62 
TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA84 
       49.12         0.62        41.75        51.16        66.54        15.12 
TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J 
       10.22        47.80        33.83        40.08         7.33         2.66 
TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N 
        6.74        12.39         6.58        13.15        19.04        32.84 
TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20V 
       12.16        17.88         5.06        14.89        14.96         5.06 
TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH 
        8.35         8.25        17.16        16.18        20.48         4.67 
TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E TCGA-BT-A42F 
       12.82         9.96        17.56        28.70        24.26        28.41 
TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-C4-A0F6 TCGA-C4-A0F7 TCGA-CF-A1HR 
        8.98         1.94         2.93        23.01         2.04         0.46 
TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47Y 
        0.69        10.95        12.66        12.46        12.10        12.26 
TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A0YN 
       13.12        12.00        12.10        11.87        13.08        12.92 
TCGA-CU-A0YO TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A5W6 TCGA-DK-A1A3 TCGA-DK-A1A5 
        4.90         5.46         5.19         1.84        21.86         2.14 
TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD 
       66.41        18.41        19.00        16.70       130.88       112.44 
TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 
       16.14        17.62        15.62         1.81        10.59         7.79 
TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN 
      123.85        87.32         2.20        13.58         7.82         8.22 
TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW 
       17.72        50.27        21.30        23.21         9.67        20.81 
TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW 
       10.55       140.81        48.00        17.98        64.18        41.56 
TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6P 
       76.60        67.36        15.68        41.06        30.67        15.02 
TCGA-DK-AA6Q TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA6X 
       13.58       166.03        12.36        10.49         8.65         7.53 
TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A4TZ TCGA-E7-A3X6 
       13.64        43.50        12.03        10.62        15.35        24.66 
TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KE 
        0.10         0.49         2.24        16.70        17.39         0.56 
TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7DV 
       14.56        13.97        12.99        14.33         0.92         1.22 
TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A97P TCGA-FD-A3B3 TCGA-FD-A3B4 
       13.68        14.07        12.95        14.37        32.02        16.77 
TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 
        8.94        33.04         4.01        12.62        22.52        27.98 
TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO 
       60.66        24.30        23.41        17.98        29.16         5.52 
TCGA-FD-A3SP TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X 
       25.74        19.79        12.85        14.96        20.91         3.62 
TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX 
       26.73        53.88        11.01        19.33         5.36         5.69 
TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62P 
        8.25        27.45        18.08        58.92         2.70         6.28 
TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TG 
       13.35        62.86        12.69        12.36         2.27         3.06 
TCGA-FD-A6TH TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A871 
        4.31        10.85        31.07         7.13        10.65         8.94 
TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EC TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK 
        3.25         6.48        22.88        61.94        30.61        15.95 
TCGA-G2-A2EL TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B 
       26.93        33.01         7.23        20.12        17.62        66.02 
TCGA-G2-AA3C TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO 
        6.94        64.44        19.46        21.40         2.24        15.81 
TCGA-GC-A3RB TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A6I3 TCGA-GD-A3OQ 
        4.50        14.07        17.75        24.92        13.91         3.12 
TCGA-GD-A3OS TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 
       20.98        10.92        11.31        11.31         7.63        27.09 
TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATO TCGA-GU-AATQ TCGA-GV-A3JW 
       20.05         5.62         4.73        10.65         7.00        21.34 
TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK 
       19.10        19.82        20.28         8.48        10.59        27.35 
TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE 
        8.58        19.07        22.72         1.51        19.40        38.60 
TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV 
        3.06         9.01         8.22        25.02         3.45        21.24 
TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ 
        2.76         9.14        27.68         9.07        11.70         1.74 
TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO TCGA-LC-A66R TCGA-LT-A5Z6 
        1.81        15.42         6.38        11.80        15.32        15.58 
TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-S5-A6DX TCGA-S5-AA26 TCGA-SY-A9G0 
       13.48        12.23        16.67         1.84         3.75        12.43 
TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78N TCGA-UY-A8OB 
       31.56        17.62        37.05        22.68        86.83        65.75 
TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HH 
       35.24        29.56        17.82         4.54         1.64         1.87 
TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SL 
       17.88        48.62        64.80        79.66         3.22        66.41 
TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T0 
       12.76        11.90        23.64        21.04        28.24        26.27 
TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 
       18.90         2.24        16.27        66.64         2.10        13.74 
TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMG TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML 
       92.98        10.82       110.60        11.31        54.90         7.63 
TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAMY 
       71.57        91.73         2.96         8.32         6.77        98.99 
TCGA-XF-AAMZ TCGA-XF-AAN0 TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN7 
       44.32        56.48        86.30        27.06        75.39        18.81 
TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R1 
        3.88         9.63         0.66        11.97        13.64         7.36 
TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RD 
       21.11        24.13        27.19        28.41        74.56        13.41 
TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RL TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4R 
        3.48        52.73        82.49        20.22         2.89        34.06 
TCGA-ZF-AA4T TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA51 TCGA-ZF-AA52 
       19.69         8.61        59.38        60.16        38.73        35.41 
TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5P 
       57.90        19.40        47.15        19.17        10.13 

  ELF3 MUTATED ELF3 WILD-TYPE 
          0.43           0.10 
  ELF3 MUTATED ELF3 WILD-TYPE 
        105.70         166.03 
  ELF3 MUTATED ELF3 WILD-TYPE 
         17.23          15.42 
[1] "0.4 - 105.7 (17.2)" "0.1 - 166.0 (15.4)"
[1] "hr=" "1.4"
D7V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  ELF3 MUTATED         0       14        12       13
  ELF3 WILD-TYPE       4      103       110      115
D7V3, multiclass
           clus
vv          ELF3 MUTATED ELF3 WILD-TYPE
  STAGE I              0              4
  STAGE II            14            103
  STAGE III           12            110
  STAGE IV            13            115
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1+T2  T3  T4
  ELF3 MUTATED         17  15   7
  ELF3 WILD-TYPE       97 164  45
D7V4, multiclass
          clus
vv         ELF3 MUTATED ELF3 WILD-TYPE
  T0+T1+T2           17             97
  T3                 15            164
  T4                  7             45
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  ELF3 MUTATED    23   4   8   1
  ELF3 WILD-TYPE 190  37  67   7
D7V5, multiclass
    clus
vv   ELF3 MUTATED ELF3 WILD-TYPE
  N0           23            190
  N1            4             37
  N2            8             67
  N3            1              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"
D7V6, binary
                cls
clus               0   1
  ELF3 MUTATED    18   1
  ELF3 WILD-TYPE 164   9
[1] "tbl2"
                cls
clus             [,1] [,2]
  ELF3 MUTATED     18    1
  ELF3 WILD-TYPE  164    9
   clus
vv  ELF3 MUTATED ELF3 WILD-TYPE
  0           18            164
  1            1              9
[1] 2 2
[1] FALSE
D7V7, binary
                cls
clus               0   1
  ELF3 MUTATED    14  27
  ELF3 WILD-TYPE  82 253
[1] "tbl2"
                cls
clus             [,1] [,2]
  ELF3 MUTATED     14   27
  ELF3 WILD-TYPE   82  253
        clus
vv       ELF3 MUTATED ELF3 WILD-TYPE
  FEMALE           14             82
  MALE             27            253
[1] 2 2
[1] FALSE
D7V8, continuous
D7V9, continuous
D7V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ELF3 MUTATED       3                         1    35
  ELF3 WILD-TYPE    35                        20   266
D7V11, multiclass
                           clus
vv                          ELF3 MUTATED ELF3 WILD-TYPE
  ASIAN                                3             35
  BLACK OR AFRICAN AMERICAN            1             20
  WHITE                               35            266
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V12, binary
                cls
clus               0   1
  ELF3 MUTATED     0  41
  ELF3 WILD-TYPE   8 297
[1] "tbl2"
                cls
clus             [,1] [,2]
  ELF3 MUTATED      0   41
  ELF3 WILD-TYPE    8  297
                        clus
vv                       ELF3 MUTATED ELF3 WILD-TYPE
  HISPANIC OR LATINO                0              8
  NOT HISPANIC OR LATINO           41            297
[1] 2 2
[1] FALSE

Clustering(8) Variable = TSC1 MUTATION ANALYSIS
D8V1, survival
                sevent
clus2              0   1
  TSC1 MUTATED    19   9
  TSC1 WILD-TYPE 200 142
  TSC1 MUTATED TSC1 WILD-TYPE 
            28            342 
  TSC1 MUTATED TSC1 WILD-TYPE 
             9            142 
$`TSC1 MUTATED`
TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA83 TCGA-BT-A20P TCGA-BT-A42C TCGA-CF-A1HR 
       49.12         0.62        66.54        17.88        28.70         0.46 
TCGA-CF-A9FF TCGA-DK-A1A3 TCGA-DK-A3WW TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SQ 
       11.87        21.86        20.81        17.98        29.16        46.78 
TCGA-FD-A5BU TCGA-FD-A6TB TCGA-FD-A6TF TCGA-FD-A6TI TCGA-G2-A2EO TCGA-G2-AA3B 
       19.33        18.81         2.27         9.67        35.24        66.02 
TCGA-GD-A2C5 TCGA-GU-A766 TCGA-GU-AATP TCGA-GV-A3QF TCGA-XF-AAMR TCGA-ZF-A9R3 
        7.73         5.62        32.98        20.28        91.73        24.13 
TCGA-ZF-A9RL TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA5H 
       82.49        57.90        19.40        19.17 

$`TSC1 WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        91.63       103.50       105.70         8.35 
TCGA-4Z-AA7M TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7S 
       16.27        44.94        16.83        16.77        17.16        34.98 
TCGA-4Z-AA7W TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA84 TCGA-4Z-AA86 TCGA-4Z-AA87 
       27.62        41.75        51.16        15.12        10.22        47.80 
TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ 
       33.83        40.08         7.33         2.66         6.74        12.39 
TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20Q 
        6.58        13.15        19.04        32.84        12.16        19.50 
TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X 
        5.06        14.89        14.96         5.06         8.35         8.25 
TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK 
       17.16        16.18        20.48         4.67        12.82         9.96 
TCGA-BT-A42B TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F1 
       17.56        24.26        28.41         8.98         1.94         2.93 
TCGA-C4-A0F6 TCGA-C4-A0F7 TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T 
       23.01         2.04         0.43         0.69        10.95        12.66 
TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA 
       12.46        12.10        12.62        12.26        13.12        12.00 
TCGA-CF-A7I0 TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ 
       12.10        13.08        12.92         4.90         7.20         5.46 
TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1A6 
        5.19        16.31         1.84        13.58         2.14        66.41 
TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE 
       18.41        19.00        16.70       130.88       112.44        16.14 
TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 
       17.62        15.62         1.81        10.59         7.79       123.85 
TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ 
       87.32         2.20        13.58         7.82         8.22        17.72 
TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WX TCGA-DK-A3WY 
       50.27        21.30        23.21         9.67        10.55       140.81 
TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 
       48.00        17.98        64.18        41.56        76.60        67.36 
TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6P TCGA-DK-AA6Q 
       15.68        41.06        30.67        38.24        15.02        13.58 
TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA71 
      166.03        12.36        10.49         8.65         7.53        13.64 
TCGA-DK-AA74 TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E5-A4U1 
       43.50        12.03        10.62        43.59        15.35        38.83 
TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 
       24.66         0.10         0.49         2.24        16.70        17.39 
TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF 
        0.56         0.66        14.56        13.97        12.99        14.33 
TCGA-E7-A7DU TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A97P 
        0.92         1.22        13.68        14.07        12.95        14.37 
TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 
        8.09        32.02        16.77         8.94        33.04         4.01 
TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL 
       12.62        22.52        27.98        60.66        24.30        23.41 
TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P 
        5.52        25.74        19.79        12.85        22.98        27.35 
TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT 
       14.96        20.91         3.62        26.73        53.88        11.01 
TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 
        5.36         5.69         8.25        27.45        18.08        58.92 
TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TC 
        2.70         7.10         6.28        13.35        62.86         6.15 
TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TK TCGA-FJ-A3Z7 
       12.69        12.36         3.06         4.31        10.85        31.07 
TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FJ-A871 TCGA-FT-A3EE TCGA-FT-A61P 
        7.13        10.65        17.23         8.94         3.25         6.48 
TCGA-G2-A2EC TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2ES 
       22.88        61.94        30.61        15.95        26.93        33.01 
TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3C TCGA-G2-AA3D TCGA-G2-AA3F 
        7.23        20.12        17.62         6.94        64.44        19.46 
TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD 
       21.40         2.24        15.81         4.50        15.91        14.07 
TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A3OP TCGA-GD-A3OQ 
       17.75        24.92         8.94        13.91         2.10         3.12 
TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R 
       20.98         2.20         7.36        10.92        11.31        11.31 
TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A767 TCGA-GU-AATO TCGA-GU-AATQ 
        7.63        27.09        20.05         4.73        10.65         7.00 
TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QH TCGA-GV-A3QI 
       14.27        21.34        19.10        19.82         8.48        10.59 
TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-H4-A2HQ 
       27.35         8.58        19.07        22.72         1.51        19.40 
TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU 
       38.60         3.06         9.01         8.22        25.02         3.45 
TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RH TCGA-K4-A5RI 
       21.24         2.76         9.14        27.68         9.07        11.70 
TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO TCGA-LC-A66R 
        1.74         1.81        15.42         6.38        11.80        15.32 
TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX 
       15.58        13.48        12.23        16.67        14.24         1.84 
TCGA-S5-AA26 TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M 
        3.75        12.43        31.56        17.62        37.05        22.68 
TCGA-UY-A78N TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD 
       86.83        76.01        65.75        35.24        29.56        17.82 
TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH 
        4.54         1.64         1.87        17.88        48.62        64.80 
TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SL TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SX 
       79.66         3.22        66.41        12.76        11.90        23.64 
TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 
       21.04        28.24        26.27        18.90         2.24        16.27 
TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMG 
       66.64         2.10        13.74        92.98        10.82       110.60 
TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMT TCGA-XF-AAMW 
       11.31        54.90         7.63        71.57         2.96         8.32 
TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN2 
        6.77        98.99        44.32        56.48        30.94        61.45 
TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 
       86.30        27.06        75.39        18.81         3.88         9.63 
TCGA-YC-A9TC TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R2 
        0.66        11.97        13.64        18.64         7.36        21.11 
TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RD 
       30.28        27.19        21.86        28.41        74.56        13.41 
TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N 
        3.48        52.73        52.60        47.84        20.22         2.89 
TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA4X 
       34.06        19.69         8.61        59.38        60.16        63.02 
TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5N TCGA-ZF-AA5P 
       38.73        35.41         8.52        47.15         5.52        10.13 

  TSC1 MUTATED TSC1 WILD-TYPE 
          0.46           0.10 
  TSC1 MUTATED TSC1 WILD-TYPE 
         91.73         166.03 
  TSC1 MUTATED TSC1 WILD-TYPE 
        20.545         14.990 
[1] "0.5 - 91.7 (20.5)"  "0.1 - 166.0 (15.0)"
[1] "hr=" "1.7"
D8V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  TSC1 MUTATED         0       13         7        9
  TSC1 WILD-TYPE       4      104       115      119
D8V3, multiclass
           clus
vv          TSC1 MUTATED TSC1 WILD-TYPE
  STAGE I              0              4
  STAGE II            13            104
  STAGE III            7            115
  STAGE IV             9            119
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1+T2  T3  T4
  TSC1 MUTATED         12  15   1
  TSC1 WILD-TYPE      102 164  51
D8V4, multiclass
          clus
vv         TSC1 MUTATED TSC1 WILD-TYPE
  T0+T1+T2           12            102
  T3                 15            164
  T4                  1             51
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  TSC1 MUTATED    17   1   8   0
  TSC1 WILD-TYPE 196  40  67   8
D8V5, multiclass
    clus
vv   TSC1 MUTATED TSC1 WILD-TYPE
  N0           17            196
  N1            1             40
  N2            8             67
  N3            0              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"
D8V6, binary
                cls
clus               0   1
  TSC1 MUTATED    16   2
  TSC1 WILD-TYPE 166   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  TSC1 MUTATED     16    2
  TSC1 WILD-TYPE  166    8
   clus
vv  TSC1 MUTATED TSC1 WILD-TYPE
  0           16            166
  1            2              8
[1] 2 2
[1] FALSE
D8V7, binary
                cls
clus               0   1
  TSC1 MUTATED     7  23
  TSC1 WILD-TYPE  89 257
[1] "tbl2"
                cls
clus             [,1] [,2]
  TSC1 MUTATED      7   23
  TSC1 WILD-TYPE   89  257
        clus
vv       TSC1 MUTATED TSC1 WILD-TYPE
  FEMALE            7             89
  MALE             23            257
[1] 2 2
[1] FALSE
D8V8, continuous
D8V9, continuous
D8V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TSC1 MUTATED       4                         1    25
  TSC1 WILD-TYPE    34                        20   276
D8V11, multiclass
                           clus
vv                          TSC1 MUTATED TSC1 WILD-TYPE
  ASIAN                                4             34
  BLACK OR AFRICAN AMERICAN            1             20
  WHITE                               25            276
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V12, binary
                cls
clus               0   1
  TSC1 MUTATED     1  26
  TSC1 WILD-TYPE   7 312
[1] "tbl2"
                cls
clus             [,1] [,2]
  TSC1 MUTATED      1   26
  TSC1 WILD-TYPE    7  312
                        clus
vv                       TSC1 MUTATED TSC1 WILD-TYPE
  HISPANIC OR LATINO                1              7
  NOT HISPANIC OR LATINO           26            312
[1] 2 2
[1] FALSE

Clustering(9) Variable = KDM6A MUTATION ANALYSIS
D9V1, survival
                 sevent
clus2               0   1
  KDM6A MUTATED    59  39
  KDM6A WILD-TYPE 160 112
  KDM6A MUTATED KDM6A WILD-TYPE 
             98             272 
  KDM6A MUTATED KDM6A WILD-TYPE 
             39             112 
$`KDM6A MUTATED`
TCGA-2F-A9KP TCGA-4Z-AA7Q TCGA-4Z-AA7W TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA84 
       11.97        16.77        27.62        51.16        66.54        15.12 
TCGA-4Z-AA89 TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A20T TCGA-BT-A2LB TCGA-BT-A2LD 
       33.83        12.39         6.58        14.89        16.18        20.48 
TCGA-BT-A3PH TCGA-CF-A1HS TCGA-CF-A47W TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CU-A3KJ 
        4.67         0.43        12.10        12.26        13.12         5.46 
TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC 
       21.86        66.41        18.41        19.00        16.70       130.88 
TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I2 TCGA-DK-A2I6 TCGA-DK-A3IS TCGA-DK-A6B0 
       17.62        15.62         7.79        87.32        50.27        76.60 
TCGA-DK-A6B5 TCGA-DK-AA6P TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA77 TCGA-E5-A2PC 
       41.06        15.02         8.65         7.53        10.62        43.59 
TCGA-E7-A519 TCGA-E7-A5KF TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A7DU TCGA-E7-A7PW 
       16.70         0.66        13.97        12.99         0.92        13.68 
TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A97Q TCGA-FD-A3B5 TCGA-FD-A3N5 TCGA-FD-A3SJ 
       14.07        12.95         8.09         8.94        22.52        24.30 
TCGA-FD-A3SL TCGA-FD-A43P TCGA-FD-A43X TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5C0 
       23.41        27.35         3.62         5.36         5.69        18.08 
TCGA-FD-A6TA TCGA-FD-A6TC TCGA-FJ-A3ZE TCGA-FJ-A871 TCGA-G2-A2EK TCGA-G2-A2EL 
       62.86         6.15        10.65         8.94        15.95        26.93 
TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3D TCGA-GC-A3RC 
       35.24        33.01        66.02         6.94        64.44        15.91 
TCGA-GD-A2C5 TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42R TCGA-GU-AATP 
        7.73         2.20         7.36        10.92        11.31        32.98 
TCGA-GU-AATQ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A6ZA TCGA-K4-A4AB TCGA-UY-A9PD 
        7.00        20.28         8.48        22.72         2.76        17.82 
TCGA-UY-A9PF TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SJ TCGA-XF-A9T0 
        1.64         1.87        17.88        64.80         3.22        26.27 
TCGA-XF-AAMG TCGA-XF-AAMX TCGA-XF-AAN0 TCGA-XF-AAN2 TCGA-ZF-A9R0 TCGA-ZF-A9R2 
      110.60         6.77        56.48        61.45        18.64        21.11 
TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RG TCGA-ZF-AA51 
       24.13        27.19        13.41         3.48        52.60        38.73 
TCGA-ZF-AA53 TCGA-ZF-AA56 
       57.90         8.52 

$`KDM6A WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW TCGA-4Z-AA7M 
       22.29        91.63       103.50       105.70         8.35        16.27 
TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7Y TCGA-4Z-AA80 
       44.94        16.83        17.16        34.98        49.12         0.62 
TCGA-4Z-AA81 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J 
       41.75        10.22        47.80        40.08         7.33         2.66 
TCGA-BL-A3JM TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P 
        6.74        13.15        19.04        32.84        12.16        17.88 
TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X 
       19.50         5.06        14.96         5.06         8.35         8.25 
TCGA-BT-A2LA TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E 
       17.16        12.82         9.96        17.56        28.70        24.26 
TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-C4-A0F6 TCGA-C4-A0F7 
       28.41         8.98         1.94         2.93        23.01         2.04 
TCGA-CF-A1HR TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47X 
        0.46         0.69        10.95        12.66        12.46        12.62 
TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YO 
       12.00        12.10        11.87        13.08        12.92         4.90 
TCGA-CU-A0YR TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A5 
        7.20         5.19        16.31         1.84        13.58         2.14 
TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I4 TCGA-DK-A3IK 
      112.44        16.14         1.81        10.59       123.85         2.20 
TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IT TCGA-DK-A3IU 
       13.58         7.82         8.22        17.72        21.30        23.21 
TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A3X2 
        9.67        20.81        10.55       140.81        48.00        17.98 
TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B6 TCGA-DK-AA6L 
       64.18        41.56        67.36        15.68        30.67        38.24 
TCGA-DK-AA6Q TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA71 TCGA-DK-AA74 
       13.58       166.03        12.36        10.49        13.64        43.50 
TCGA-DK-AA76 TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ 
       12.03        15.35        38.83        24.66         0.10         0.49 
TCGA-E7-A4XJ TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A677 TCGA-E7-A6MF TCGA-E7-A7DV 
        2.24        17.39         0.56        14.56        14.33         1.22 
TCGA-E7-A97P TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 
       14.37        32.02        16.77        33.04         4.01        12.62 
TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP 
       27.98        60.66        17.98        29.16         5.52        25.74 
TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43S TCGA-FD-A43U 
       46.78        19.79        12.85        22.98        14.96        20.91 
TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BY TCGA-FD-A5BZ 
       26.73        53.88        11.01        19.33         8.25        27.45 
TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TB 
       58.92         2.70         7.10         6.28        13.35        18.81 
TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI 
       12.69        12.36         2.27         3.06         4.31         9.67 
TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZF TCGA-FT-A3EE TCGA-FT-A61P 
       10.85        31.07         7.13        17.23         3.25         6.48 
TCGA-G2-A2EC TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY 
       22.88        61.94        30.61         7.23        20.12        17.62 
TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RD 
       19.46        21.40         2.24        15.81         4.50        14.07 
TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A3OP TCGA-GD-A3OQ 
       17.75        24.92         8.94        13.91         2.10         3.12 
TCGA-GD-A3OS TCGA-GU-A42Q TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 
       20.98        11.31         7.63        27.09        20.05         5.62 
TCGA-GU-A767 TCGA-GU-AATO TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ 
        4.73        10.65        14.27        21.34        19.10        19.82 
TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-H4-A2HO TCGA-H4-A2HQ 
       10.59        27.35         8.58        19.07         1.51        19.40 
TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU 
       38.60         3.06         9.01         8.22        25.02         3.45 
TCGA-K4-A3WV TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ 
       21.24         9.14        27.68         9.07        11.70         1.74 
TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO TCGA-LC-A66R TCGA-LT-A5Z6 
        1.81        15.42         6.38        11.80        15.32        15.58 
TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 
       13.48        12.23        16.67        14.24         1.84         3.75 
TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78N 
       12.43        31.56        17.62        37.05        22.68        86.83 
TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PE TCGA-XF-A9SG 
       76.01        65.75        35.24        29.56         4.54        48.62 
TCGA-XF-A9SI TCGA-XF-A9SL TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY 
       79.66        66.41        12.76        11.90        23.64        21.04 
TCGA-XF-A9SZ TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 
       28.24        18.90         2.24        16.27        66.64         2.10 
TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML 
       13.74        92.98        10.82        11.31        54.90         7.63 
TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMY TCGA-XF-AAMZ 
       71.57        91.73         2.96         8.32        98.99        44.32 
TCGA-XF-AAN1 TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN7 TCGA-XF-AAN8 
       30.94        86.30        27.06        75.39        18.81         3.88 
TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R1 TCGA-ZF-A9R4 
        9.63         0.66        11.97        13.64         7.36        30.28 
TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RF TCGA-ZF-A9RL TCGA-ZF-A9RM 
       21.86        28.41        74.56        52.73        82.49        47.84 
TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4U TCGA-ZF-AA4V 
       20.22         2.89        34.06        19.69         8.61        59.38 
TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA52 TCGA-ZF-AA54 TCGA-ZF-AA58 TCGA-ZF-AA5H 
       60.16        63.02        35.41        19.40        47.15        19.17 
TCGA-ZF-AA5N TCGA-ZF-AA5P 
        5.52        10.13 

  KDM6A MUTATED KDM6A WILD-TYPE 
           0.43            0.10 
  KDM6A MUTATED KDM6A WILD-TYPE 
         130.88          166.03 
  KDM6A MUTATED KDM6A WILD-TYPE 
          15.93           15.50 
[1] "0.4 - 130.9 (15.9)" "0.1 - 166.0 (15.5)"
[1] "hr=" "1.1"
D9V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  KDM6A MUTATED         0       32        28       37
  KDM6A WILD-TYPE       4       85        94       91
D9V3, multiclass
           clus
vv          KDM6A MUTATED KDM6A WILD-TYPE
  STAGE I               0               4
  STAGE II             32              85
  STAGE III            28              94
  STAGE IV             37              91
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1+T2  T3  T4
  KDM6A MUTATED         33  45  13
  KDM6A WILD-TYPE       81 134  39
D9V4, multiclass
          clus
vv         KDM6A MUTATED KDM6A WILD-TYPE
  T0+T1+T2            33              81
  T3                  45             134
  T4                  13              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"
                 vv
clus               N0  N1  N2  N3
  KDM6A MUTATED    51  10  23   3
  KDM6A WILD-TYPE 162  31  52   5
D9V5, multiclass
    clus
vv   KDM6A MUTATED KDM6A WILD-TYPE
  N0            51             162
  N1            10              31
  N2            23              52
  N3             3               5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V6, binary
                 cls
clus                0   1
  KDM6A MUTATED    56   3
  KDM6A WILD-TYPE 126   7
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KDM6A MUTATED     56    3
  KDM6A WILD-TYPE  126    7
   clus
vv  KDM6A MUTATED KDM6A WILD-TYPE
  0            56             126
  1             3               7
[1] 2 2
[1] FALSE
D9V7, binary
                 cls
clus                0   1
  KDM6A MUTATED    26  72
  KDM6A WILD-TYPE  70 208
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KDM6A MUTATED     26   72
  KDM6A WILD-TYPE   70  208
        clus
vv       KDM6A MUTATED KDM6A WILD-TYPE
  FEMALE            26              70
  MALE              72             208
[1] 2 2
[1] FALSE
D9V8, continuous
D9V9, continuous
D9V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  KDM6A MUTATED      11                         5    82
  KDM6A WILD-TYPE    27                        16   219
D9V11, multiclass
                           clus
vv                          KDM6A MUTATED KDM6A WILD-TYPE
  ASIAN                                11              27
  BLACK OR AFRICAN AMERICAN             5              16
  WHITE                                82             219
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V12, binary
                 cls
clus                0   1
  KDM6A MUTATED     1  89
  KDM6A WILD-TYPE   7 249
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KDM6A MUTATED      1   89
  KDM6A WILD-TYPE    7  249
                        clus
vv                       KDM6A MUTATED KDM6A WILD-TYPE
  HISPANIC OR LATINO                 1               7
  NOT HISPANIC OR LATINO            89             249
[1] 2 2
[1] FALSE

Clustering(10) Variable = CDKN1A MUTATION ANALYSIS
D10V1, survival
                  sevent
clus2                0   1
  CDKN1A MUTATED    20  11
  CDKN1A WILD-TYPE 199 140
  CDKN1A MUTATED CDKN1A WILD-TYPE 
              31              339 
  CDKN1A MUTATED CDKN1A WILD-TYPE 
              11              140 
$`CDKN1A MUTATED`
TCGA-2F-A9KQ TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-BT-A20T TCGA-BT-A42C TCGA-CF-A1HS 
       91.63        17.16        34.98        14.89        28.70         0.43 
TCGA-CF-A27C TCGA-CF-A7I0 TCGA-CF-A9FF TCGA-CU-A3QU TCGA-DK-A1AC TCGA-DK-A2HX 
        0.69        12.10        11.87         5.19       130.88         1.81 
TCGA-DK-A2I4 TCGA-DK-A3IN TCGA-E7-A5KF TCGA-FD-A3B7 TCGA-FD-A3SM TCGA-FD-A3SO 
      123.85         8.22         0.66         4.01        17.98         5.52 
TCGA-FD-A5C1 TCGA-FD-A6TC TCGA-G2-A3IB TCGA-GD-A3OQ TCGA-GU-AATO TCGA-GV-A3JX 
       58.92         6.15         7.23         3.12        10.65        19.10 
TCGA-GV-A40E TCGA-S5-A6DX TCGA-XF-A9SG TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R7 
        8.58         1.84        48.62         7.36        21.11        21.86 
TCGA-ZF-A9RL 
       82.49 

$`CDKN1A WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW TCGA-4Z-AA7M 
       22.29        11.97       103.50       105.70         8.35        16.27 
TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA80 
       44.94        16.83        16.77        27.62        49.12         0.62 
TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA84 TCGA-4Z-AA86 TCGA-4Z-AA87 
       41.75        51.16        66.54        15.12        10.22        47.80 
TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ 
       33.83        40.08         7.33         2.66         6.74        12.39 
TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P 
        6.58        13.15        19.04        32.84        12.16        17.88 
TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X 
       19.50         5.06        14.96         5.06         8.35         8.25 
TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK 
       17.16        16.18        20.48         4.67        12.82         9.96 
TCGA-BT-A42B TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F1 
       17.56        24.26        28.41         8.98         1.94         2.93 
TCGA-C4-A0F6 TCGA-C4-A0F7 TCGA-CF-A1HR TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V 
       23.01         2.04         0.46        10.95        12.66        12.46 
TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A9FM 
       12.10        12.62        12.26        13.12        12.00        13.08 
TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3YL TCGA-CU-A5W6 
       12.92         4.90         7.20         5.46        16.31         1.84 
TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA 
       13.58        21.86         2.14        66.41        18.41        19.00 
TCGA-DK-A1AB TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I1 
       16.70       112.44        16.14        17.62        15.62        10.59 
TCGA-DK-A2I2 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IQ 
        7.79        87.32         2.20        13.58         7.82        17.72 
TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX 
       50.27        21.30        23.21         9.67        20.81        10.55 
TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 
      140.81        48.00        17.98        64.18        41.56        76.60 
TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6P 
       67.36        15.68        41.06        30.67        38.24        15.02 
TCGA-DK-AA6Q TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA6X 
       13.58       166.03        12.36        10.49         8.65         7.53 
TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A2PC TCGA-E5-A4TZ 
       13.64        43.50        12.03        10.62        43.59        15.35 
TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 
       38.83        24.66         0.10         0.49         2.24        16.70 
TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF 
       17.39         0.56        14.56        13.97        12.99        14.33 
TCGA-E7-A7DU TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A97P 
        0.92         1.22        13.68        14.07        12.95        14.37 
TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B8 
        8.09        32.02        16.77         8.94        33.04        12.62 
TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SN 
       22.52        27.98        60.66        24.30        23.41        29.16 
TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P 
       25.74        46.78        19.79        12.85        22.98        27.35 
TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT 
       14.96        20.91         3.62        26.73        53.88        11.01 
TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 
       19.33         5.36         5.69         8.25        27.45        18.08 
TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB 
        2.70         7.10         6.28        13.35        62.86        18.81 
TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI 
       12.69        12.36         2.27         3.06         4.31         9.67 
TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FJ-A871 
       10.85        31.07         7.13        10.65        17.23         8.94 
TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EC TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK 
        3.25         6.48        22.88        61.94        30.61        15.95 
TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B 
       26.93        35.24        33.01        20.12        17.62        66.02 
TCGA-G2-AA3C TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO 
        6.94        64.44        19.46        21.40         2.24        15.81 
TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A6I1 
        4.50        15.91        14.07        17.75        24.92         8.94 
TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GD-A76B 
       13.91         7.73         2.10        20.98         2.20         7.36 
TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A764 
       10.92        11.31        11.31         7.63        27.09        20.05 
TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATP TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW 
        5.62         4.73        32.98         7.00        14.27        21.34 
TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40G 
       19.82        20.28         8.48        10.59        27.35        19.07 
TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND 
       22.72         1.51        19.40        38.60         3.06         9.01 
TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC 
        8.22        25.02         3.45        21.24         2.76         9.14 
TCGA-K4-A54R TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB 
       27.68         9.07        11.70         1.74         1.81        15.42 
TCGA-K4-A83P TCGA-K4-AAQO TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI 
        6.38        11.80        15.32        15.58        13.48        12.23 
TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-AA26 TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78K 
       16.67        14.24         3.75        12.43        31.56        17.62 
TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78N TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A9PA 
       37.05        22.68        86.83        76.01        65.75        35.24 
TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HH TCGA-XF-A8HI 
       29.56        17.82         4.54         1.64         1.87        17.88 
TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SL TCGA-XF-A9SV TCGA-XF-A9SW 
       64.80        79.66         3.22        66.41        12.76        11.90 
TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 
       23.64        21.04        28.24        26.27        18.90         2.24 
TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMF 
       16.27        66.64         2.10        13.74        92.98        10.82 
TCGA-XF-AAMG TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR 
      110.60        11.31        54.90         7.63        71.57        91.73 
TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN0 
        2.96         8.32         6.77        98.99        44.32        56.48 
TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN7 
       30.94        61.45        86.30        27.06        75.39        18.81 
TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R0 
        3.88         9.63         0.66        11.97        13.64        18.64 
TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RD 
       24.13        30.28        27.19        28.41        74.56        13.41 
TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N 
        3.48        52.73        52.60        47.84        20.22         2.89 
TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA4X 
       34.06        19.69         8.61        59.38        60.16        63.02 
TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 
       38.73        35.41        57.90        19.40         8.52        47.15 
TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-ZF-AA5P 
       19.17         5.52        10.13 

  CDKN1A MUTATED CDKN1A WILD-TYPE 
            0.43             0.10 
  CDKN1A MUTATED CDKN1A WILD-TYPE 
          130.88           166.03 
  CDKN1A MUTATED CDKN1A WILD-TYPE 
           11.87            15.91 
[1] "0.4 - 130.9 (11.9)" "0.1 - 166.0 (15.9)"
[1] "hr=" "1.1"
D10V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  CDKN1A MUTATED         0       11        10       10
  CDKN1A WILD-TYPE       4      106       112      118
D10V3, multiclass
           clus
vv          CDKN1A MUTATED CDKN1A WILD-TYPE
  STAGE I                0                4
  STAGE II              11              106
  STAGE III             10              112
  STAGE IV              10              118
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1+T2  T3  T4
  CDKN1A MUTATED          7  14   7
  CDKN1A WILD-TYPE      107 165  45
D10V4, multiclass
          clus
vv         CDKN1A MUTATED CDKN1A WILD-TYPE
  T0+T1+T2              7              107
  T3                   14              165
  T4                    7               45
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  CDKN1A MUTATED    20   5   4   0
  CDKN1A WILD-TYPE 193  36  71   8
D10V5, multiclass
    clus
vv   CDKN1A MUTATED CDKN1A WILD-TYPE
  N0             20              193
  N1              5               36
  N2              4               71
  N3              0                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"
D10V6, binary
                  cls
clus                 0   1
  CDKN1A MUTATED    20   1
  CDKN1A WILD-TYPE 162   9
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CDKN1A MUTATED     20    1
  CDKN1A WILD-TYPE  162    9
   clus
vv  CDKN1A MUTATED CDKN1A WILD-TYPE
  0             20              162
  1              1                9
[1] 2 2
[1] FALSE
D10V7, binary
                  cls
clus                 0   1
  CDKN1A MUTATED     5  28
  CDKN1A WILD-TYPE  91 252
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CDKN1A MUTATED      5   28
  CDKN1A WILD-TYPE   91  252
        clus
vv       CDKN1A MUTATED CDKN1A WILD-TYPE
  FEMALE              5               91
  MALE               28              252
[1] 2 2
[1] FALSE
D10V8, continuous
D10V9, continuous
D10V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CDKN1A MUTATED       7                         4    21
  CDKN1A WILD-TYPE    31                        17   280
D10V11, multiclass
                           clus
vv                          CDKN1A MUTATED CDKN1A WILD-TYPE
  ASIAN                                  7               31
  BLACK OR AFRICAN AMERICAN              4               17
  WHITE                                 21              280
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V12, binary
                  cls
clus                 0   1
  CDKN1A MUTATED     1  29
  CDKN1A WILD-TYPE   7 309
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CDKN1A MUTATED      1   29
  CDKN1A WILD-TYPE    7  309
                        clus
vv                       CDKN1A MUTATED CDKN1A WILD-TYPE
  HISPANIC OR LATINO                  1                7
  NOT HISPANIC OR LATINO             29              309
[1] 2 2
[1] FALSE

Clustering(11) Variable = EP300 MUTATION ANALYSIS
D11V1, survival
                 sevent
clus2               0   1
  EP300 MUTATED    40  18
  EP300 WILD-TYPE 179 133
  EP300 MUTATED EP300 WILD-TYPE 
             58             312 
  EP300 MUTATED EP300 WILD-TYPE 
             18             133 
$`EP300 MUTATED`
TCGA-2F-A9KR TCGA-2F-A9KW TCGA-4Z-AA7Y TCGA-4Z-AA81 TCGA-BT-A20X TCGA-BT-A2LB 
      103.50         8.35        49.12        41.75         8.25        16.18 
TCGA-BT-A3PH TCGA-BT-A3PK TCGA-CF-A47Y TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-DK-A1A5 
        4.67         9.96        12.26         7.20         5.46         2.14 
TCGA-DK-A1A7 TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A6AW 
       18.41       123.85        87.32        20.81        10.55        41.56 
TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA71 TCGA-DK-AA77 TCGA-E7-A678 TCGA-E7-A7DV 
       10.49         8.65        13.64        10.62        13.97         1.22 
TCGA-E7-A7XN TCGA-E7-A97Q TCGA-FD-A3B8 TCGA-FD-A3SM TCGA-FD-A3SO TCGA-FD-A5C0 
       14.07         8.09        12.62        17.98         5.52        18.08 
TCGA-FD-A62S TCGA-FD-A6TE TCGA-FD-A6TG TCGA-FJ-A3ZF TCGA-FT-A61P TCGA-G2-A2EJ 
       13.35        12.36         3.06        17.23         6.48        30.61 
TCGA-G2-A2EL TCGA-GC-A3BM TCGA-GC-A3RB TCGA-GD-A3OQ TCGA-GU-AATP TCGA-GV-A3JX 
       26.93        21.40         4.50         3.12        32.98        19.10 
TCGA-GV-A3JZ TCGA-K4-A54R TCGA-R3-A69X TCGA-UY-A9PB TCGA-UY-A9PE TCGA-XF-A9SI 
       19.82        27.68        14.24        29.56         4.54        79.66 
TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9T5 TCGA-XF-AAN2 TCGA-ZF-A9R4 TCGA-ZF-A9R5 
       23.64        21.04        66.64        61.45        30.28        27.19 
TCGA-ZF-A9RC TCGA-ZF-AA4V TCGA-ZF-AA51 TCGA-ZF-AA58 
       74.56        59.38        38.73        47.15 

$`EP300 WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA7N 
       22.29        11.97        91.63       105.70        16.27        44.94 
TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7W TCGA-4Z-AA80 
       16.83        16.77        17.16        34.98        27.62         0.62 
TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA84 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-4Z-AA89 
       51.16        66.54        15.12        10.22        47.80        33.83 
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 
       40.08         7.33         2.66         6.74        12.39         6.58 
TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q 
       13.15        19.04        32.84        12.16        17.88        19.50 
TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A2LA 
        5.06        14.89        14.96         5.06         8.35        17.16 
TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E TCGA-BT-A42F 
       20.48        12.82        17.56        28.70        24.26        28.41 
TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-C4-A0F6 TCGA-C4-A0F7 TCGA-CF-A1HR 
        8.98         1.94         2.93        23.01         2.04         0.46 
TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W 
        0.43         0.69        10.95        12.66        12.46        12.10 
TCGA-CF-A47X TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A9FF TCGA-CF-A9FM 
       12.62        13.12        12.00        12.10        11.87        13.08 
TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E 
       12.92         4.90         5.19        16.31         1.84        13.58 
TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD 
       21.86        66.41        19.00        16.70       130.88       112.44 
TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 
       16.14        17.62        15.62         1.81        10.59         7.79 
TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS 
        2.20        13.58         7.82         8.22        17.72        50.27 
TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A3X2 
       21.30        23.21         9.67       140.81        48.00        17.98 
TCGA-DK-A6AV TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 
       64.18        76.60        67.36        15.68        41.06        30.67 
TCGA-DK-AA6L TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6X 
       38.24        15.02        13.58       166.03        12.36         7.53 
TCGA-DK-AA74 TCGA-DK-AA76 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 
       43.50        12.03        43.59        15.35        38.83        24.66 
TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KE 
        0.10         0.49         2.24        16.70        17.39         0.56 
TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7PW 
        0.66        14.56        12.99        14.33         0.92        13.68 
TCGA-E7-A85H TCGA-E7-A97P TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 
       12.95        14.37        32.02        16.77         8.94        33.04 
TCGA-FD-A3B7 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL 
        4.01        22.52        27.98        60.66        24.30        23.41 
TCGA-FD-A3SN TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N 
       29.16        25.74        46.78        19.79        12.85        22.98 
TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS 
       27.35        14.96        20.91         3.62        26.73        53.88 
TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ 
       11.01        19.33         5.36         5.69         8.25        27.45 
TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A6TA TCGA-FD-A6TB 
       58.92         2.70         7.10         6.28        62.86        18.81 
TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TF TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FD-A6TK 
        6.15        12.69         2.27         4.31         9.67        10.85 
TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A871 TCGA-FT-A3EE TCGA-G2-A2EC 
       31.07         7.13        10.65         8.94         3.25        22.88 
TCGA-G2-A2EF TCGA-G2-A2EK TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE 
       61.94        15.95        35.24        33.01         7.23        20.12 
TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3I6 
       17.62        66.02         6.94        64.44        19.46         2.24 
TCGA-GC-A3OO TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A6I1 
       15.81        15.91        14.07        17.75        24.92         8.94 
TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GD-A76B 
       13.91         7.73         2.10        20.98         2.20         7.36 
TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A764 
       10.92        11.31        11.31         7.63        27.09        20.05 
TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATO TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW 
        5.62         4.73        10.65         7.00        14.27        21.34 
TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G 
       20.28         8.48        10.59        27.35         8.58        19.07 
TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND 
       22.72         1.51        19.40        38.60         3.06         9.01 
TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC 
        8.22        25.02         3.45        21.24         2.76         9.14 
TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P 
        9.07        11.70         1.74         1.81        15.42         6.38 
TCGA-K4-AAQO TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN 
       11.80        15.32        15.58        13.48        12.23        16.67 
TCGA-S5-A6DX TCGA-S5-AA26 TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L 
        1.84         3.75        12.43        31.56        17.62        37.05 
TCGA-UY-A78M TCGA-UY-A78N TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A9PA TCGA-UY-A9PD 
       22.68        86.83        76.01        65.75        35.24        17.82 
TCGA-UY-A9PF TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SJ 
        1.64         1.87        17.88        48.62        64.80         3.22 
TCGA-XF-A9SL TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 
       66.41        12.76        11.90        28.24        26.27        18.90 
TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMF 
        2.24        16.27         2.10        13.74        92.98        10.82 
TCGA-XF-AAMG TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR 
      110.60        11.31        54.90         7.63        71.57        91.73 
TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN0 
        2.96         8.32         6.77        98.99        44.32        56.48 
TCGA-XF-AAN1 TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN7 TCGA-XF-AAN8 
       30.94        86.30        27.06        75.39        18.81         3.88 
TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R0 TCGA-ZF-A9R1 
        9.63         0.66        11.97        13.64        18.64         7.36 
TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RD TCGA-ZF-A9RE 
       21.11        24.13        21.86        28.41        13.41         3.48 
TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N 
       52.73        52.60        82.49        47.84        20.22         2.89 
TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4U TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA52 
       34.06        19.69         8.61        60.16        63.02        35.41 
TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-ZF-AA5P 
       57.90        19.40         8.52        19.17         5.52        10.13 

  EP300 MUTATED EP300 WILD-TYPE 
           1.22            0.10 
  EP300 MUTATED EP300 WILD-TYPE 
         123.85          166.03 
  EP300 MUTATED EP300 WILD-TYPE 
         17.605          15.500 
[1] "1.2 - 123.8 (17.6)" "0.1 - 166.0 (15.5)"
[1] "hr=" "1.5"
D11V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  EP300 MUTATED         1       18        18       21
  EP300 WILD-TYPE       3       99       104      107
D11V3, multiclass
           clus
vv          EP300 MUTATED EP300 WILD-TYPE
  STAGE I               1               3
  STAGE II             18              99
  STAGE III            18             104
  STAGE IV             21             107
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1+T2  T3  T4
  EP300 MUTATED         20  29   5
  EP300 WILD-TYPE       94 150  47
D11V4, multiclass
          clus
vv         EP300 MUTATED EP300 WILD-TYPE
  T0+T1+T2            20              94
  T3                  29             150
  T4                   5              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"
                 vv
clus               N0  N1  N2  N3
  EP300 MUTATED    35   4  14   3
  EP300 WILD-TYPE 178  37  61   5
D11V5, multiclass
    clus
vv   EP300 MUTATED EP300 WILD-TYPE
  N0            35             178
  N1             4              37
  N2            14              61
  N3             3               5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V6, binary
                 cls
clus                0   1
  EP300 MUTATED    31   1
  EP300 WILD-TYPE 151   9
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EP300 MUTATED     31    1
  EP300 WILD-TYPE  151    9
   clus
vv  EP300 MUTATED EP300 WILD-TYPE
  0            31             151
  1             1               9
[1] 2 2
[1] FALSE
D11V7, binary
                 cls
clus                0   1
  EP300 MUTATED    14  44
  EP300 WILD-TYPE  82 236
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EP300 MUTATED     14   44
  EP300 WILD-TYPE   82  236
        clus
vv       EP300 MUTATED EP300 WILD-TYPE
  FEMALE            14              82
  MALE              44             236
[1] 2 2
[1] FALSE
D11V8, continuous
D11V9, continuous
D11V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  EP300 MUTATED       4                         1    52
  EP300 WILD-TYPE    34                        20   249
D11V11, multiclass
                           clus
vv                          EP300 MUTATED EP300 WILD-TYPE
  ASIAN                                 4              34
  BLACK OR AFRICAN AMERICAN             1              20
  WHITE                                52             249
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V12, binary
                 cls
clus                0   1
  EP300 MUTATED     1  54
  EP300 WILD-TYPE   7 284
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EP300 MUTATED      1   54
  EP300 WILD-TYPE    7  284
                        clus
vv                       EP300 MUTATED EP300 WILD-TYPE
  HISPANIC OR LATINO                 1               7
  NOT HISPANIC OR LATINO            54             284
[1] 2 2
[1] FALSE

Clustering(12) Variable = ARID1A MUTATION ANALYSIS
D12V1, survival
                  sevent
clus2                0   1
  ARID1A MUTATED    56  36
  ARID1A WILD-TYPE 163 115
  ARID1A MUTATED ARID1A WILD-TYPE 
              92              278 
  ARID1A MUTATED ARID1A WILD-TYPE 
              36              115 
$`ARID1A MUTATED`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KW TCGA-4Z-AA7O TCGA-4Z-AA84 TCGA-BL-A0C8 
       22.29        11.97         8.35        16.83        15.12        40.08 
TCGA-BL-A13I TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0YX TCGA-BT-A20Q TCGA-BT-A20R 
        7.33         6.74        12.39        13.15        19.50         5.06 
TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-CF-A1HR TCGA-CU-A0YO TCGA-CU-A3KJ 
       20.48         4.67        12.82         0.46         4.90         5.46 
TCGA-CU-A5W6 TCGA-DK-A1AD TCGA-DK-A2HX TCGA-DK-A3IK TCGA-DK-A3IM TCGA-DK-A3IN 
        1.84       112.44         1.81         2.20         7.82         8.22 
TCGA-DK-A3IU TCGA-DK-A3X2 TCGA-DK-A6AW TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-AA6P 
       23.21        17.98        41.56        15.68        41.06        15.02 
TCGA-DK-AA6W TCGA-DK-AA71 TCGA-DK-AA76 TCGA-E5-A4TZ TCGA-E7-A4XJ TCGA-E7-A519 
        8.65        13.64        12.03        15.35         2.24        16.70 
TCGA-E7-A541 TCGA-E7-A7DU TCGA-E7-A85H TCGA-FD-A3B3 TCGA-FD-A3SN TCGA-FD-A3SP 
       17.39         0.92        12.95        32.02        29.16        25.74 
TCGA-FD-A3SR TCGA-FD-A43N TCGA-FD-A5C1 TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A6TG 
       19.79        22.98        58.92         7.10         6.28         3.06 
TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A3ZF TCGA-FJ-A871 TCGA-G2-A2EK 
        9.67        10.85         7.13        17.23         8.94        15.95 
TCGA-G2-A2EL TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3RC TCGA-GD-A2C5 TCGA-GD-A76B 
       26.93        64.44        19.46        15.91         7.73         7.36 
TCGA-GU-A42P TCGA-GU-A42R TCGA-GU-A766 TCGA-GV-A3JV TCGA-GV-A3QK TCGA-GV-A6ZA 
       10.92        11.31         5.62        14.27        27.35        22.72 
TCGA-H4-A2HO TCGA-K4-A3WV TCGA-K4-A54R TCGA-K4-A83P TCGA-LC-A66R TCGA-MV-A51V 
        1.51        21.24        27.68         6.38        15.32        13.48 
TCGA-SY-A9G5 TCGA-UY-A9PF TCGA-XF-A9SW TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 
       31.56         1.64        11.90        28.24        26.27        18.90 
TCGA-XF-A9T5 TCGA-XF-A9T8 TCGA-XF-AAML TCGA-XF-AAN0 TCGA-XF-AAN2 TCGA-YC-A8S6 
       66.64        13.74         7.63        56.48        61.45         9.63 
TCGA-YF-AA3M TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RF TCGA-ZF-AA4X 
       13.64        21.86        28.41        74.56        52.73        63.02 
TCGA-ZF-AA51 TCGA-ZF-AA5N 
       38.73         5.52 

$`ARID1A WILD-TYPE`
TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA7N TCGA-4Z-AA7Q 
       91.63       103.50       105.70        16.27        44.94        16.77 
TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 
       17.16        34.98        27.62        49.12         0.62        41.75 
TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-BL-A13J 
       51.16        66.54        10.22        47.80        33.83         2.66 
TCGA-BT-A0S7 TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20T 
        6.58        19.04        32.84        12.16        17.88        14.89 
TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB 
       14.96         5.06         8.35         8.25        17.16        16.18 
TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ 
        9.96        17.56        28.70        24.26        28.41         8.98 
TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-C4-A0F6 TCGA-C4-A0F7 TCGA-CF-A1HS TCGA-CF-A27C 
        1.94         2.93        23.01         2.04         0.43         0.69 
TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y 
       10.95        12.66        12.46        12.10        12.62        12.26 
TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A0YN 
       13.12        12.00        12.10        11.87        13.08        12.92 
TCGA-CU-A0YR TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 
        7.20         5.19        16.31        13.58        21.86         2.14 
TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AE 
       66.41        18.41        19.00        16.70       130.88        16.14 
TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A2I6 
       17.62        15.62        10.59         7.79       123.85        87.32 
TCGA-DK-A3IL TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IV TCGA-DK-A3WW 
       13.58        17.72        50.27        21.30         9.67        20.81 
TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A6AV TCGA-DK-A6B0 TCGA-DK-A6B1 
       10.55       140.81        48.00        64.18        76.60        67.36 
TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6Q TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6U 
       30.67        38.24        13.58       166.03        12.36        10.49 
TCGA-DK-AA6X TCGA-DK-AA74 TCGA-DK-AA77 TCGA-E5-A2PC TCGA-E5-A4U1 TCGA-E7-A3X6 
        7.53        43.50        10.62        43.59        38.83        24.66 
TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 
        0.10         0.49         0.56         0.66        14.56        13.97 
TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A97P 
       12.99        14.33         1.22        13.68        14.07        14.37 
TCGA-E7-A97Q TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 
        8.09        16.77         8.94        33.04         4.01        12.62 
TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM 
       22.52        27.98        60.66        24.30        23.41        17.98 
TCGA-FD-A3SO TCGA-FD-A3SQ TCGA-FD-A3SS TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U 
        5.52        46.78        12.85        27.35        14.96        20.91 
TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV 
        3.62        26.73        53.88        11.01        19.33         5.36 
TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A62N TCGA-FD-A62S 
        5.69         8.25        27.45        18.08         2.70        13.35 
TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF 
       62.86        18.81         6.15        12.69        12.36         2.27 
TCGA-FD-A6TH TCGA-FJ-A3Z7 TCGA-FJ-A3ZE TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EC 
        4.31        31.07        10.65         3.25         6.48        22.88 
TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE 
       61.94        30.61        35.24        33.01         7.23        20.12 
TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3C TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO 
       17.62        66.02         6.94        21.40         2.24        15.81 
TCGA-GC-A3RB TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GC-A6I3 
        4.50        14.07        17.75        24.92         8.94        13.91 
TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A762 
        2.10         3.12        20.98         2.20        11.31         7.63 
TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A767 TCGA-GU-AATO TCGA-GU-AATP TCGA-GU-AATQ 
       27.09        20.05         4.73        10.65        32.98         7.00 
TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI 
       21.34        19.10        19.82        20.28         8.48        10.59 
TCGA-GV-A40E TCGA-GV-A40G TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND 
        8.58        19.07        19.40        38.60         3.06         9.01 
TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A5RH 
        8.22        25.02         3.45         2.76         9.14         9.07 
TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-AAQO TCGA-LT-A5Z6 
       11.70         1.74         1.81        15.42        11.80        15.58 
TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 TCGA-SY-A9G0 
       12.23        16.67        14.24         1.84         3.75        12.43 
TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78N TCGA-UY-A78O TCGA-UY-A8OB 
       17.62        37.05        22.68        86.83        76.01        65.75 
TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE TCGA-XF-A8HH TCGA-XF-A8HI 
       35.24        29.56        17.82         4.54         1.87        17.88 
TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SL TCGA-XF-A9SV 
       48.62        64.80        79.66         3.22        66.41        12.76 
TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T6 TCGA-XF-AAME 
       23.64        21.04         2.24        16.27         2.10        92.98 
TCGA-XF-AAMF TCGA-XF-AAMG TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAMQ TCGA-XF-AAMR 
       10.82       110.60        11.31        54.90        71.57        91.73 
TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN1 
        2.96         8.32         6.77        98.99        44.32        30.94 
TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A9TC 
       86.30        27.06        75.39        18.81         3.88         0.66 
TCGA-YF-AA3L TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R4 
       11.97        18.64         7.36        21.11        24.13        30.28 
TCGA-ZF-A9R5 TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-A9RM 
       27.19        13.41         3.48        52.60        82.49        47.84 
TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4U TCGA-ZF-AA4V 
       20.22         2.89        34.06        19.69         8.61        59.38 
TCGA-ZF-AA4W TCGA-ZF-AA52 TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 
       60.16        35.41        57.90        19.40         8.52        47.15 
TCGA-ZF-AA5H TCGA-ZF-AA5P 
       19.17        10.13 

  ARID1A MUTATED ARID1A WILD-TYPE 
            0.46             0.10 
  ARID1A MUTATED ARID1A WILD-TYPE 
          112.44           166.03 
  ARID1A MUTATED ARID1A WILD-TYPE 
          14.645           16.270 
[1] "0.5 - 112.4 (14.6)" "0.1 - 166.0 (16.3)"
[1] "hr=" "1.1"
D12V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  ARID1A MUTATED         2       28        27       35
  ARID1A WILD-TYPE       2       89        95       93
D12V3, multiclass
           clus
vv          ARID1A MUTATED ARID1A WILD-TYPE
  STAGE I                2                2
  STAGE II              28               89
  STAGE III             27               95
  STAGE IV              35               93
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1+T2  T3  T4
  ARID1A MUTATED         26  47  14
  ARID1A WILD-TYPE       88 132  38
D12V4, multiclass
          clus
vv         ARID1A MUTATED ARID1A WILD-TYPE
  T0+T1+T2             26               88
  T3                   47              132
  T4                   14               38
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  ARID1A MUTATED    49  10  24   1
  ARID1A WILD-TYPE 164  31  51   7
D12V5, multiclass
    clus
vv   ARID1A MUTATED ARID1A WILD-TYPE
  N0             49              164
  N1             10               31
  N2             24               51
  N3              1                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"
D12V6, binary
                  cls
clus                 0   1
  ARID1A MUTATED    48   2
  ARID1A WILD-TYPE 134   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID1A MUTATED     48    2
  ARID1A WILD-TYPE  134    8
   clus
vv  ARID1A MUTATED ARID1A WILD-TYPE
  0             48              134
  1              2                8
[1] 2 2
[1] FALSE
D12V7, binary
                  cls
clus                 0   1
  ARID1A MUTATED    19  74
  ARID1A WILD-TYPE  77 206
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID1A MUTATED     19   74
  ARID1A WILD-TYPE   77  206
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  FEMALE             19               77
  MALE               74              206
[1] 2 2
[1] FALSE
D12V8, continuous
D12V9, continuous
D12V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ARID1A MUTATED       4                         1    87
  ARID1A WILD-TYPE    34                        20   214
D12V11, multiclass
                           clus
vv                          ARID1A MUTATED ARID1A WILD-TYPE
  ASIAN                                  4               34
  BLACK OR AFRICAN AMERICAN              1               20
  WHITE                                 87              214
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V12, binary
                  cls
clus                 0   1
  ARID1A MUTATED     3  87
  ARID1A WILD-TYPE   5 251
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID1A MUTATED      3   87
  ARID1A WILD-TYPE    5  251
                        clus
vv                       ARID1A MUTATED ARID1A WILD-TYPE
  HISPANIC OR LATINO                  3                5
  NOT HISPANIC OR LATINO             87              251
[1] 2 2
[1] FALSE

Clustering(13) Variable = STAG2 MUTATION ANALYSIS
D13V1, survival
                 sevent
clus2               0   1
  STAG2 MUTATED    35  16
  STAG2 WILD-TYPE 184 135
  STAG2 MUTATED STAG2 WILD-TYPE 
             51             319 
  STAG2 MUTATED STAG2 WILD-TYPE 
             16             135 
$`STAG2 MUTATED`
TCGA-4Z-AA7R TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-BL-A13J TCGA-BT-A42E TCGA-CF-A27C 
       17.16        15.12        33.83         2.66        24.26         0.69 
TCGA-CF-A47W TCGA-CF-A5U8 TCGA-CU-A72E TCGA-DK-A1AA TCGA-DK-A1AF TCGA-DK-A3IS 
       12.10        13.12        13.58        19.00        17.62        50.27 
TCGA-DK-A3X2 TCGA-DK-A6AW TCGA-DK-AA71 TCGA-E5-A2PC TCGA-E7-A3Y1 TCGA-E7-A4IJ 
       17.98        41.56        13.64        43.59         0.10         0.49 
TCGA-E7-A519 TCGA-E7-A5KF TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A7DU TCGA-E7-A7DV 
       16.70         0.66        13.97        12.99         0.92         1.22 
TCGA-E7-A97P TCGA-FD-A3B5 TCGA-FD-A3NA TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SQ 
       14.37         8.94        60.66        23.41        17.98        46.78 
TCGA-FD-A5BX TCGA-FD-A6TA TCGA-FJ-A3ZE TCGA-G2-AA3D TCGA-GD-A6C6 TCGA-H4-A2HQ 
        5.69        62.86        10.65        64.44         2.20        19.40 
TCGA-K4-A83P TCGA-MV-A51V TCGA-PQ-A6FI TCGA-R3-A69X TCGA-UY-A78M TCGA-XF-A8HI 
        6.38        13.48        12.23        14.24        22.68        17.88 
TCGA-XF-A9SI TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-AAN5 TCGA-YC-A8S6 TCGA-ZF-A9RD 
       79.66        18.90         2.24        75.39         9.63        13.41 
TCGA-ZF-A9RE TCGA-ZF-A9RG TCGA-ZF-AA53 
        3.48        52.60        57.90 

$`STAG2 WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        91.63       103.50       105.70         8.35 
TCGA-4Z-AA7M TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7S TCGA-4Z-AA7W 
       16.27        44.94        16.83        16.77        34.98        27.62 
TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA86 
       49.12         0.62        41.75        51.16        66.54        10.22 
TCGA-4Z-AA87 TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 
       47.80        40.08         7.33         6.74        12.39         6.58 
TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q 
       13.15        19.04        32.84        12.16        17.88        19.50 
TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X 
        5.06        14.89        14.96         5.06         8.35         8.25 
TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK 
       17.16        16.18        20.48         4.67        12.82         9.96 
TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F1 
       17.56        28.70        28.41         8.98         1.94         2.93 
TCGA-C4-A0F6 TCGA-C4-A0F7 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A47S TCGA-CF-A47T 
       23.01         2.04         0.46         0.43        10.95        12.66 
TCGA-CF-A47V TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A9FF 
       12.46        12.62        12.26        12.00        12.10        11.87 
TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3QU 
       13.08        12.92         4.90         7.20         5.46         5.19 
TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 
       16.31         1.84        21.86         2.14        66.41        18.41 
TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AG TCGA-DK-A2HX 
       16.70       130.88       112.44        16.14        15.62         1.81 
TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL 
       10.59         7.79       123.85        87.32         2.20        13.58 
TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV 
        7.82         8.22        17.72        21.30        23.21         9.67 
TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A6AV TCGA-DK-A6B0 
       20.81        10.55       140.81        48.00        64.18        76.60 
TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6P 
       67.36        15.68        41.06        30.67        38.24        15.02 
TCGA-DK-AA6Q TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA6X 
       13.58       166.03        12.36        10.49         8.65         7.53 
TCGA-DK-AA74 TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 
       43.50        12.03        10.62        15.35        38.83        24.66 
TCGA-E7-A4XJ TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A677 TCGA-E7-A6MF TCGA-E7-A7PW 
        2.24        17.39         0.56        14.56        14.33        13.68 
TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B6 
       14.07        12.95         8.09        32.02        16.77        33.04 
TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SJ TCGA-FD-A3SN 
        4.01        12.62        22.52        27.98        24.30        29.16 
TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P 
        5.52        25.74        19.79        12.85        22.98        27.35 
TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT 
       14.96        20.91         3.62        26.73        53.88        11.01 
TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 
       19.33         5.36         8.25        27.45        18.08        58.92 
TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TB TCGA-FD-A6TC 
        2.70         7.10         6.28        13.35        18.81         6.15 
TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI 
       12.69        12.36         2.27         3.06         4.31         9.67 
TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZF TCGA-FJ-A871 TCGA-FT-A3EE 
       10.85        31.07         7.13        17.23         8.94         3.25 
TCGA-FT-A61P TCGA-G2-A2EC TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL 
        6.48        22.88        61.94        30.61        15.95        26.93 
TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B 
       35.24        33.01         7.23        20.12        17.62        66.02 
TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB 
        6.94        19.46        21.40         2.24        15.81         4.50 
TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GC-A6I3 
       15.91        14.07        17.75        24.92         8.94        13.91 
TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A76B TCGA-GU-A42P 
        7.73         2.10         3.12        20.98         7.36        10.92 
TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 
       11.31        11.31         7.63        27.09        20.05         5.62 
TCGA-GU-A767 TCGA-GU-AATO TCGA-GU-AATP TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW 
        4.73        10.65        32.98         7.00        14.27        21.34 
TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK 
       19.10        19.82        20.28         8.48        10.59        27.35 
TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-HQ-A2OE TCGA-HQ-A2OF 
        8.58        19.07        22.72         1.51        38.60         3.06 
TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB 
        9.01         8.22        25.02         3.45        21.24         2.76 
TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ 
        9.14        27.68         9.07        11.70         1.74         1.81 
TCGA-K4-A6MB TCGA-K4-AAQO TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-PQ-A6FN TCGA-S5-A6DX 
       15.42        11.80        15.32        15.58        16.67         1.84 
TCGA-S5-AA26 TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78N 
        3.75        12.43        31.56        17.62        37.05        86.83 
TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE 
       76.01        65.75        35.24        29.56        17.82         4.54 
TCGA-UY-A9PF TCGA-XF-A8HH TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SJ TCGA-XF-A9SL 
        1.64         1.87        48.62        64.80         3.22        66.41 
TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T0 
       12.76        11.90        23.64        21.04        28.24        26.27 
TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMF 
       16.27        66.64         2.10        13.74        92.98        10.82 
TCGA-XF-AAMG TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR 
      110.60        11.31        54.90         7.63        71.57        91.73 
TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN0 
        2.96         8.32         6.77        98.99        44.32        56.48 
TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN7 TCGA-XF-AAN8 
       30.94        61.45        86.30        27.06        18.81         3.88 
TCGA-YC-A9TC TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R2 
        0.66        11.97        13.64        18.64         7.36        21.11 
TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RC 
       24.13        30.28        27.19        21.86        28.41        74.56 
TCGA-ZF-A9RF TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4R 
       52.73        82.49        47.84        20.22         2.89        34.06 
TCGA-ZF-AA4T TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA51 
       19.69         8.61        59.38        60.16        63.02        38.73 
TCGA-ZF-AA52 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N 
       35.41        19.40         8.52        47.15        19.17         5.52 
TCGA-ZF-AA5P 
       10.13 

  STAG2 MUTATED STAG2 WILD-TYPE 
           0.10            0.43 
  STAG2 MUTATED STAG2 WILD-TYPE 
          79.66          166.03 
  STAG2 MUTATED STAG2 WILD-TYPE 
          14.37           15.81 
[1] "0.1 - 79.7 (14.4)"  "0.4 - 166.0 (15.8)"
[1] "hr=" "1.3"
D13V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  STAG2 MUTATED         0       18        10       23
  STAG2 WILD-TYPE       4       99       112      105
D13V3, multiclass
           clus
vv          STAG2 MUTATED STAG2 WILD-TYPE
  STAGE I               0               4
  STAGE II             18              99
  STAGE III            10             112
  STAGE IV             23             105
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1+T2  T3  T4
  STAG2 MUTATED         20  22   6
  STAG2 WILD-TYPE       94 157  46
D13V4, multiclass
          clus
vv         STAG2 MUTATED STAG2 WILD-TYPE
  T0+T1+T2            20              94
  T3                  22             157
  T4                   6              46
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  STAG2 MUTATED    25   4  14   2
  STAG2 WILD-TYPE 188  37  61   6
D13V5, multiclass
    clus
vv   STAG2 MUTATED STAG2 WILD-TYPE
  N0            25             188
  N1             4              37
  N2            14              61
  N3             2               6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V6, binary
                 cls
clus                0   1
  STAG2 MUTATED    27   5
  STAG2 WILD-TYPE 155   5
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STAG2 MUTATED     27    5
  STAG2 WILD-TYPE  155    5
   clus
vv  STAG2 MUTATED STAG2 WILD-TYPE
  0            27             155
  1             5               5
[1] 2 2
[1] FALSE
D13V7, binary
                 cls
clus                0   1
  STAG2 MUTATED    11  41
  STAG2 WILD-TYPE  85 239
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STAG2 MUTATED     11   41
  STAG2 WILD-TYPE   85  239
        clus
vv       STAG2 MUTATED STAG2 WILD-TYPE
  FEMALE            11              85
  MALE              41             239
[1] 2 2
[1] FALSE
D13V8, continuous
D13V9, continuous
D13V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  STAG2 MUTATED      11                         3    38
  STAG2 WILD-TYPE    27                        18   263
D13V11, multiclass
                           clus
vv                          STAG2 MUTATED STAG2 WILD-TYPE
  ASIAN                                11              27
  BLACK OR AFRICAN AMERICAN             3              18
  WHITE                                38             263
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V12, binary
                 cls
clus                0   1
  STAG2 MUTATED     0  49
  STAG2 WILD-TYPE   8 289
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STAG2 MUTATED      0   49
  STAG2 WILD-TYPE    8  289
                        clus
vv                       STAG2 MUTATED STAG2 WILD-TYPE
  HISPANIC OR LATINO                 0               8
  NOT HISPANIC OR LATINO            49             289
[1] 2 2
[1] FALSE

Clustering(14) Variable = ERCC2 MUTATION ANALYSIS
D14V1, survival
                 sevent
clus2               0   1
  ERCC2 MUTATED    24  10
  ERCC2 WILD-TYPE 195 141
  ERCC2 MUTATED ERCC2 WILD-TYPE 
             34             336 
  ERCC2 MUTATED ERCC2 WILD-TYPE 
             10             141 
$`ERCC2 MUTATED`
TCGA-4Z-AA84 TCGA-4Z-AA87 TCGA-BT-A20O TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-CU-A0YR 
       15.12        47.80        12.16        12.82         9.96         7.20 
TCGA-DK-A1A3 TCGA-DK-A1A7 TCGA-DK-A1AC TCGA-DK-A2I6 TCGA-E5-A2PC TCGA-E7-A5KE 
       21.86        18.41       130.88        87.32        43.59         0.56 
TCGA-E7-A677 TCGA-E7-A85H TCGA-E7-A97P TCGA-FD-A3N5 TCGA-FD-A3SN TCGA-FT-A3EE 
       14.56        12.95        14.37        22.52        29.16         3.25 
TCGA-FT-A61P TCGA-G2-A2ES TCGA-GC-A3RC TCGA-GD-A3OQ TCGA-H4-A2HO TCGA-MV-A51V 
        6.48        33.01        15.91         3.12         1.51        13.48 
TCGA-UY-A78N TCGA-UY-A9PF TCGA-XF-A9SJ TCGA-XF-A9T0 TCGA-XF-A9T3 TCGA-XF-AAMG 
       86.83         1.64         3.22        26.27         2.24       110.60 
TCGA-ZF-A9RC TCGA-ZF-A9RG TCGA-ZF-AA4V TCGA-ZF-AA51 
       74.56        52.60        59.38        38.73 

$`ERCC2 WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        91.63       103.50       105.70         8.35 
TCGA-4Z-AA7M TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7S 
       16.27        44.94        16.83        16.77        17.16        34.98 
TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 
       27.62        49.12         0.62        41.75        51.16        66.54 
TCGA-4Z-AA86 TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM 
       10.22        33.83        40.08         7.33         2.66         6.74 
TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20P 
       12.39         6.58        13.15        19.04        32.84        17.88 
TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20W 
       19.50         5.06        14.89        14.96         5.06         8.35 
TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A42B 
        8.25        17.16        16.18        20.48         4.67        17.56 
TCGA-BT-A42C TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F1 
       28.70        24.26        28.41         8.98         1.94         2.93 
TCGA-C4-A0F6 TCGA-C4-A0F7 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47S 
       23.01         2.04         0.46         0.43         0.69        10.95 
TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 
       12.66        12.46        12.10        12.62        12.26        13.12 
TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YO 
       12.00        12.10        11.87        13.08        12.92         4.90 
TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A5 
        5.46         5.19        16.31         1.84        13.58         2.14 
TCGA-DK-A1A6 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF 
       66.41        19.00        16.70       112.44        16.14        17.62 
TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IK 
       15.62         1.81        10.59         7.79       123.85         2.20 
TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT 
       13.58         7.82         8.22        17.72        50.27        21.30 
TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 
       23.21         9.67        20.81        10.55       140.81        48.00 
TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 
       17.98        64.18        41.56        76.60        67.36        15.68 
TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6S 
       41.06        30.67        38.24        15.02        13.58       166.03 
TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA74 
       12.36        10.49         8.65         7.53        13.64        43.50 
TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 
       12.03        10.62        15.35        38.83        24.66         0.10 
TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KF TCGA-E7-A678 
        0.49         2.24        16.70        17.39         0.66        13.97 
TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A7XN 
       12.99        14.33         0.92         1.22        13.68        14.07 
TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 
        8.09        32.02        16.77         8.94        33.04         4.01 
TCGA-FD-A3B8 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM 
       12.62        27.98        60.66        24.30        23.41        17.98 
TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N 
        5.52        25.74        46.78        19.79        12.85        22.98 
TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS 
       27.35        14.96        20.91         3.62        26.73        53.88 
TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ 
       11.01        19.33         5.36         5.69         8.25        27.45 
TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S 
       18.08        58.92         2.70         7.10         6.28        13.35 
TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF 
       62.86        18.81         6.15        12.69        12.36         2.27 
TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 
        3.06         4.31         9.67        10.85        31.07         7.13 
TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FJ-A871 TCGA-G2-A2EC TCGA-G2-A2EF TCGA-G2-A2EJ 
       10.65        17.23         8.94        22.88        61.94        30.61 
TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY 
       15.95        26.93        35.24         7.23        20.12        17.62 
TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 
       66.02         6.94        64.44        19.46        21.40         2.24 
TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A6I1 
       15.81         4.50        14.07        17.75        24.92         8.94 
TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GD-A76B 
       13.91         7.73         2.10        20.98         2.20         7.36 
TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A764 
       10.92        11.31        11.31         7.63        27.09        20.05 
TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATO TCGA-GU-AATP TCGA-GU-AATQ TCGA-GV-A3JV 
        5.62         4.73        10.65        32.98         7.00        14.27 
TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI 
       21.34        19.10        19.82        20.28         8.48        10.59 
TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HQ TCGA-HQ-A2OE 
       27.35         8.58        19.07        22.72        19.40        38.60 
TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV 
        3.06         9.01         8.22        25.02         3.45        21.24 
TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ 
        2.76         9.14        27.68         9.07        11.70         1.74 
TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO TCGA-LC-A66R TCGA-LT-A5Z6 
        1.81        15.42         6.38        11.80        15.32        15.58 
TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 TCGA-SY-A9G0 
       12.23        16.67        14.24         1.84         3.75        12.43 
TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78O TCGA-UY-A8OB 
       31.56        17.62        37.05        22.68        76.01        65.75 
TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE TCGA-XF-A8HH TCGA-XF-A8HI 
       35.24        29.56        17.82         4.54         1.87        17.88 
TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SL TCGA-XF-A9SV TCGA-XF-A9SW 
       48.62        64.80        79.66        66.41        12.76        11.90 
TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T2 TCGA-XF-A9T4 TCGA-XF-A9T5 
       23.64        21.04        28.24        18.90        16.27        66.64 
TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMJ 
        2.10        13.74        92.98        10.82        11.31        54.90 
TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX 
        7.63        71.57        91.73         2.96         8.32         6.77 
TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 
       98.99        44.32        56.48        30.94        61.45        86.30 
TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YC-A9TC 
       27.06        75.39        18.81         3.88         9.63         0.66 
TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R3 
       11.97        13.64        18.64         7.36        21.11        24.13 
TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RD TCGA-ZF-A9RE 
       30.28        27.19        21.86        28.41        13.41         3.48 
TCGA-ZF-A9RF TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4R 
       52.73        82.49        47.84        20.22         2.89        34.06 
TCGA-ZF-AA4T TCGA-ZF-AA4U TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA52 TCGA-ZF-AA53 
       19.69         8.61        60.16        63.02        35.41        57.90 
TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-ZF-AA5P 
       19.40         8.52        47.15        19.17         5.52        10.13 

  ERCC2 MUTATED ERCC2 WILD-TYPE 
           0.56            0.10 
  ERCC2 MUTATED ERCC2 WILD-TYPE 
         130.88          166.03 
  ERCC2 MUTATED ERCC2 WILD-TYPE 
         15.515          15.650 
[1] "0.6 - 130.9 (15.5)" "0.1 - 166.0 (15.6)"
[1] "hr=" "1.7"
D14V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  ERCC2 MUTATED         0        8        14       12
  ERCC2 WILD-TYPE       4      109       108      116
D14V3, multiclass
           clus
vv          ERCC2 MUTATED ERCC2 WILD-TYPE
  STAGE I               0               4
  STAGE II              8             109
  STAGE III            14             108
  STAGE IV             12             116
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1+T2  T3  T4
  ERCC2 MUTATED         11  18   5
  ERCC2 WILD-TYPE      103 161  47
D14V4, multiclass
          clus
vv         ERCC2 MUTATED ERCC2 WILD-TYPE
  T0+T1+T2            11             103
  T3                  18             161
  T4                   5              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"
                 vv
clus               N0  N1  N2  N3
  ERCC2 MUTATED    19   4   8   1
  ERCC2 WILD-TYPE 194  37  67   7
D14V5, multiclass
    clus
vv   ERCC2 MUTATED ERCC2 WILD-TYPE
  N0            19             194
  N1             4              37
  N2             8              67
  N3             1               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"
D14V6, binary
                 cls
clus                0   1
  ERCC2 MUTATED    16   1
  ERCC2 WILD-TYPE 166   9
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERCC2 MUTATED     16    1
  ERCC2 WILD-TYPE  166    9
   clus
vv  ERCC2 MUTATED ERCC2 WILD-TYPE
  0            16             166
  1             1               9
[1] 2 2
[1] FALSE
D14V7, binary
                 cls
clus                0   1
  ERCC2 MUTATED     7  27
  ERCC2 WILD-TYPE  89 253
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERCC2 MUTATED      7   27
  ERCC2 WILD-TYPE   89  253
        clus
vv       ERCC2 MUTATED ERCC2 WILD-TYPE
  FEMALE             7              89
  MALE              27             253
[1] 2 2
[1] FALSE
D14V8, continuous
D14V9, continuous
D14V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ERCC2 MUTATED       4                         2    28
  ERCC2 WILD-TYPE    34                        19   273
D14V11, multiclass
                           clus
vv                          ERCC2 MUTATED ERCC2 WILD-TYPE
  ASIAN                                 4              34
  BLACK OR AFRICAN AMERICAN             2              19
  WHITE                                28             273
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V12, binary
                 cls
clus                0   1
  ERCC2 MUTATED     2  29
  ERCC2 WILD-TYPE   6 309
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERCC2 MUTATED      2   29
  ERCC2 WILD-TYPE    6  309
                        clus
vv                       ERCC2 MUTATED ERCC2 WILD-TYPE
  HISPANIC OR LATINO                 2               6
  NOT HISPANIC OR LATINO            29             309
[1] 2 2
[1] FALSE

Clustering(15) Variable = ZFP36L1 MUTATION ANALYSIS
D15V1, survival
                   sevent
clus2                 0   1
  ZFP36L1 MUTATED    18   8
  ZFP36L1 WILD-TYPE 201 143
  ZFP36L1 MUTATED ZFP36L1 WILD-TYPE 
               26               344 
  ZFP36L1 MUTATED ZFP36L1 WILD-TYPE 
                8               143 
$`ZFP36L1 MUTATED`
TCGA-4Z-AA84 TCGA-BT-A20R TCGA-CF-A47S TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A7 
       15.12         5.06        10.95        13.58        21.86        18.41 
TCGA-DK-A2I2 TCGA-DK-A3X2 TCGA-DK-A6B6 TCGA-DK-AA6P TCGA-DK-AA6T TCGA-DK-AA6U 
        7.79        17.98        30.67        15.02        12.36        10.49 
TCGA-E7-A677 TCGA-FD-A43U TCGA-FD-A6TE TCGA-G2-A2ES TCGA-G2-AA3F TCGA-GC-A3WC 
       14.56        20.91        12.36        33.01        19.46        17.75 
TCGA-GU-AATP TCGA-GV-A3QF TCGA-K4-A54R TCGA-K4-A83P TCGA-XF-A9T6 TCGA-XF-AAMR 
       32.98        20.28        27.68         6.38         2.10        91.73 
TCGA-ZF-AA4X TCGA-ZF-AA5N 
       63.02         5.52 

$`ZFP36L1 WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        91.63       103.50       105.70         8.35 
TCGA-4Z-AA7M TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7S 
       16.27        44.94        16.83        16.77        17.16        34.98 
TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 
       27.62        49.12         0.62        41.75        51.16        66.54 
TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J 
       10.22        47.80        33.83        40.08         7.33         2.66 
TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N 
        6.74        12.39         6.58        13.15        19.04        32.84 
TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20V 
       12.16        17.88        19.50        14.89        14.96         5.06 
TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH 
        8.35         8.25        17.16        16.18        20.48         4.67 
TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E TCGA-BT-A42F 
       12.82         9.96        17.56        28.70        24.26        28.41 
TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-C4-A0F6 TCGA-C4-A0F7 TCGA-CF-A1HR 
        8.98         1.94         2.93        23.01         2.04         0.46 
TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X 
        0.43         0.69        12.66        12.46        12.10        12.62 
TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A9FF TCGA-CF-A9FM 
       12.26        13.12        12.00        12.10        11.87        13.08 
TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL 
       12.92         4.90         7.20         5.46         5.19        16.31 
TCGA-CU-A5W6 TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC 
        1.84         2.14        66.41        19.00        16.70       130.88 
TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 
      112.44        16.14        17.62        15.62         1.81        10.59 
TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN 
      123.85        87.32         2.20        13.58         7.82         8.22 
TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW 
       17.72        50.27        21.30        23.21         9.67        20.81 
TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 
       10.55       140.81        48.00        64.18        41.56        76.60 
TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-AA6L TCGA-DK-AA6Q TCGA-DK-AA6S 
       67.36        15.68        41.06        38.24        13.58       166.03 
TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA76 TCGA-DK-AA77 
        8.65         7.53        13.64        43.50        12.03        10.62 
TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ 
       43.59        15.35        38.83        24.66         0.10         0.49 
TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A678 
        2.24        16.70        17.39         0.56         0.66        13.97 
TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A7XN 
       12.99        14.33         0.92         1.22        13.68        14.07 
TCGA-E7-A85H TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 
       12.95        14.37         8.09        32.02        16.77         8.94 
TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA 
       33.04         4.01        12.62        22.52        27.98        60.66 
TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP 
       24.30        23.41        17.98        29.16         5.52        25.74 
TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S 
       46.78        19.79        12.85        22.98        27.35        14.96 
TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV 
        3.62        26.73        53.88        11.01        19.33         5.36 
TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N 
        5.69         8.25        27.45        18.08        58.92         2.70 
TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC 
        7.10         6.28        13.35        62.86        18.81         6.15 
TCGA-FD-A6TD TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FD-A6TK 
       12.69         2.27         3.06         4.31         9.67        10.85 
TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FJ-A871 TCGA-FT-A3EE 
       31.07         7.13        10.65        17.23         8.94         3.25 
TCGA-FT-A61P TCGA-G2-A2EC TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL 
        6.48        22.88        61.94        30.61        15.95        26.93 
TCGA-G2-A2EO TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3C 
       35.24         7.23        20.12        17.62        66.02         6.94 
TCGA-G2-AA3D TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC 
       64.44        21.40         2.24        15.81         4.50        15.91 
TCGA-GC-A3RD TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP 
       14.07        24.92         8.94        13.91         7.73         2.10 
TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42Q 
        3.12        20.98         2.20         7.36        10.92        11.31 
TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 
       11.31         7.63        27.09        20.05         5.62         4.73 
TCGA-GU-AATO TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ 
       10.65         7.00        14.27        21.34        19.10        19.82 
TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA 
        8.48        10.59        27.35         8.58        19.07        22.72 
TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE 
        1.51        19.40        38.60         3.06         9.01         8.22 
TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A5RH 
       25.02         3.45        21.24         2.76         9.14         9.07 
TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-AAQO TCGA-LC-A66R 
       11.70         1.74         1.81        15.42        11.80        15.32 
TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX 
       15.58        13.48        12.23        16.67        14.24         1.84 
TCGA-S5-AA26 TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M 
        3.75        12.43        31.56        17.62        37.05        22.68 
TCGA-UY-A78N TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD 
       86.83        76.01        65.75        35.24        29.56        17.82 
TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH 
        4.54         1.64         1.87        17.88        48.62        64.80 
TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SL TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SX 
       79.66         3.22        66.41        12.76        11.90        23.64 
TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 
       21.04        28.24        26.27        18.90         2.24        16.27 
TCGA-XF-A9T5 TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMG TCGA-XF-AAMH 
       66.64        13.74        92.98        10.82       110.60        11.31 
TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX 
       54.90         7.63        71.57         2.96         8.32         6.77 
TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 
       98.99        44.32        56.48        30.94        61.45        86.30 
TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YC-A9TC 
       27.06        75.39        18.81         3.88         9.63         0.66 
TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R3 
       11.97        13.64        18.64         7.36        21.11        24.13 
TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RD 
       30.28        27.19        21.86        28.41        74.56        13.41 
TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-A9RN 
        3.48        52.73        52.60        82.49        47.84        20.22 
TCGA-ZF-AA4N TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W 
        2.89        34.06        19.69         8.61        59.38        60.16 
TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 
       38.73        35.41        57.90        19.40         8.52        47.15 
TCGA-ZF-AA5H TCGA-ZF-AA5P 
       19.17        10.13 

  ZFP36L1 MUTATED ZFP36L1 WILD-TYPE 
              2.1               0.1 
  ZFP36L1 MUTATED ZFP36L1 WILD-TYPE 
            91.73            166.03 
  ZFP36L1 MUTATED ZFP36L1 WILD-TYPE 
           16.435            15.650 
[1] "2.1 - 91.7 (16.4)"  "0.1 - 166.0 (15.6)"
[1] "hr=" "1.3"
D15V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  ZFP36L1 MUTATED         1        7         3       15
  ZFP36L1 WILD-TYPE       3      110       119      113
D15V3, multiclass
           clus
vv          ZFP36L1 MUTATED ZFP36L1 WILD-TYPE
  STAGE I                 1                 3
  STAGE II                7               110
  STAGE III               3               119
  STAGE IV               15               113
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1+T2  T3  T4
  ZFP36L1 MUTATED          6  14   2
  ZFP36L1 WILD-TYPE      108 165  50
D15V4, multiclass
          clus
vv         ZFP36L1 MUTATED ZFP36L1 WILD-TYPE
  T0+T1+T2               6               108
  T3                    14               165
  T4                     2                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"
                   vv
clus                 N0  N1  N2  N3
  ZFP36L1 MUTATED    10   3   9   1
  ZFP36L1 WILD-TYPE 203  38  66   7
D15V5, multiclass
    clus
vv   ZFP36L1 MUTATED ZFP36L1 WILD-TYPE
  N0              10               203
  N1               3                38
  N2               9                66
  N3               1                 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"
D15V6, binary
                   cls
clus                  0   1
  ZFP36L1 MUTATED    14   2
  ZFP36L1 WILD-TYPE 168   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZFP36L1 MUTATED     14    2
  ZFP36L1 WILD-TYPE  168    8
   clus
vv  ZFP36L1 MUTATED ZFP36L1 WILD-TYPE
  0              14               168
  1               2                 8
[1] 2 2
[1] FALSE
D15V7, binary
                   cls
clus                  0   1
  ZFP36L1 MUTATED     7  19
  ZFP36L1 WILD-TYPE  89 261
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZFP36L1 MUTATED      7   19
  ZFP36L1 WILD-TYPE   89  261
        clus
vv       ZFP36L1 MUTATED ZFP36L1 WILD-TYPE
  FEMALE               7                89
  MALE                19               261
[1] 2 2
[1] FALSE
D15V8, continuous
D15V9, continuous
D15V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ZFP36L1 MUTATED       2                         0    24
  ZFP36L1 WILD-TYPE    36                        21   277
D15V11, multiclass
                           clus
vv                          ZFP36L1 MUTATED ZFP36L1 WILD-TYPE
  ASIAN                                   2                36
  BLACK OR AFRICAN AMERICAN               0                21
  WHITE                                  24               277
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V12, binary
                   cls
clus                  0   1
  ZFP36L1 MUTATED     0  25
  ZFP36L1 WILD-TYPE   8 313
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZFP36L1 MUTATED      0   25
  ZFP36L1 WILD-TYPE    8  313
                        clus
vv                       ZFP36L1 MUTATED ZFP36L1 WILD-TYPE
  HISPANIC OR LATINO                   0                 8
  NOT HISPANIC OR LATINO              25               313
[1] 2 2
[1] FALSE

Clustering(16) Variable = FBXW7 MUTATION ANALYSIS
D16V1, survival
                 sevent
clus2               0   1
  FBXW7 MUTATED    17  14
  FBXW7 WILD-TYPE 202 137
  FBXW7 MUTATED FBXW7 WILD-TYPE 
             31             339 
  FBXW7 MUTATED FBXW7 WILD-TYPE 
             14             137 
$`FBXW7 MUTATED`
TCGA-4Z-AA7O TCGA-BL-A13I TCGA-BT-A0YX TCGA-BT-A20O TCGA-C4-A0F0 TCGA-C4-A0F1 
       16.83         7.33        13.15        12.16         1.94         2.93 
TCGA-CU-A0YR TCGA-DK-A1AC TCGA-DK-A2I2 TCGA-DK-A3IN TCGA-DK-A3IS TCGA-DK-A3WX 
        7.20       130.88         7.79         8.22        50.27        10.55 
TCGA-DK-A6AW TCGA-DK-AA6S TCGA-E7-A5KE TCGA-FD-A6TA TCGA-FD-A6TF TCGA-G2-A2ES 
       41.56       166.03         0.56        62.86         2.27        33.01 
TCGA-G2-AA3D TCGA-GC-A3RD TCGA-GU-A42Q TCGA-K4-A3WU TCGA-LT-A5Z6 TCGA-PQ-A6FN 
       64.44        14.07        11.31         3.45        15.58        16.67 
TCGA-UY-A9PF TCGA-XF-A9T2 TCGA-XF-A9T5 TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-YC-A9TC 
        1.64        18.90        66.64        30.94        61.45         0.66 
TCGA-ZF-A9R7 
       21.86 

$`FBXW7 WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        91.63       103.50       105.70         8.35 
TCGA-4Z-AA7M TCGA-4Z-AA7N TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7W 
       16.27        44.94        16.77        17.16        34.98        27.62 
TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA84 
       49.12         0.62        41.75        51.16        66.54        15.12 
TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BL-A13J TCGA-BL-A3JM 
       10.22        47.80        33.83        40.08         2.66         6.74 
TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20P TCGA-BT-A20Q 
       12.39         6.58        19.04        32.84        17.88        19.50 
TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X 
        5.06        14.89        14.96         5.06         8.35         8.25 
TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK 
       17.16        16.18        20.48         4.67        12.82         9.96 
TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F6 
       17.56        28.70        24.26        28.41         8.98        23.01 
TCGA-C4-A0F7 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T 
        2.04         0.46         0.43         0.69        10.95        12.66 
TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA 
       12.46        12.10        12.62        12.26        13.12        12.00 
TCGA-CF-A7I0 TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A3KJ 
       12.10        11.87        13.08        12.92         4.90         5.46 
TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 
        5.19        16.31         1.84        13.58        21.86         2.14 
TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AD TCGA-DK-A1AE 
       66.41        18.41        19.00        16.70       112.44        16.14 
TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I4 TCGA-DK-A2I6 
       17.62        15.62         1.81        10.59       123.85        87.32 
TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IQ TCGA-DK-A3IT TCGA-DK-A3IU 
        2.20        13.58         7.82        17.72        21.30        23.21 
TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV 
        9.67        20.81       140.81        48.00        17.98        64.18 
TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L 
       76.60        67.36        15.68        41.06        30.67        38.24 
TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA6X 
       15.02        13.58        12.36        10.49         8.65         7.53 
TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A2PC TCGA-E5-A4TZ 
       13.64        43.50        12.03        10.62        43.59        15.35 
TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 
       38.83        24.66         0.10         0.49         2.24        16.70 
TCGA-E7-A541 TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF 
       17.39         0.66        14.56        13.97        12.99        14.33 
TCGA-E7-A7DU TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A97P 
        0.92         1.22        13.68        14.07        12.95        14.37 
TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 
        8.09        32.02        16.77         8.94        33.04         4.01 
TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL 
       12.62        22.52        27.98        60.66        24.30        23.41 
TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR 
       17.98        29.16         5.52        25.74        46.78        19.79 
TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X 
       12.85        22.98        27.35        14.96        20.91         3.62 
TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX 
       26.73        53.88        11.01        19.33         5.36         5.69 
TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O 
        8.25        27.45        18.08        58.92         2.70         7.10 
TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE 
        6.28        13.35        18.81         6.15        12.69        12.36 
TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 
        3.06         4.31         9.67        10.85        31.07         7.13 
TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FJ-A871 TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EC 
       10.65        17.23         8.94         3.25         6.48        22.88 
TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A3IB 
       61.94        30.61        15.95        26.93        35.24         7.23 
TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3BM 
       20.12        17.62        66.02         6.94        19.46        21.40 
TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3WC TCGA-GC-A3YS 
        2.24        15.81         4.50        15.91        17.75        24.92 
TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS 
        8.94        13.91         7.73         2.10         3.12        20.98 
TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 
        2.20         7.36        10.92        11.31         7.63        27.09 
TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATO TCGA-GU-AATP TCGA-GU-AATQ 
       20.05         5.62         4.73        10.65        32.98         7.00 
TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH 
       14.27        21.34        19.10        19.82        20.28         8.48 
TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO 
       10.59        27.35         8.58        19.07        22.72         1.51 
TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS 
       19.40        38.60         3.06         9.01         8.22        25.02 
TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RH TCGA-K4-A5RI 
       21.24         2.76         9.14        27.68         9.07        11.70 
TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO TCGA-LC-A66R 
        1.74         1.81        15.42         6.38        11.80        15.32 
TCGA-MV-A51V TCGA-PQ-A6FI TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 TCGA-SY-A9G0 
       13.48        12.23        14.24         1.84         3.75        12.43 
TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78N TCGA-UY-A78O 
       31.56        17.62        37.05        22.68        86.83        76.01 
TCGA-UY-A8OB TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE TCGA-XF-A8HH 
       65.75        35.24        29.56        17.82         4.54         1.87 
TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SL 
       17.88        48.62        64.80        79.66         3.22        66.41 
TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T0 
       12.76        11.90        23.64        21.04        28.24        26.27 
TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMF 
        2.24        16.27         2.10        13.74        92.98        10.82 
TCGA-XF-AAMG TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR 
      110.60        11.31        54.90         7.63        71.57        91.73 
TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN0 
        2.96         8.32         6.77        98.99        44.32        56.48 
TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 
       86.30        27.06        75.39        18.81         3.88         9.63 
TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R3 
       11.97        13.64        18.64         7.36        21.11        24.13 
TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RE 
       30.28        27.19        28.41        74.56        13.41         3.48 
TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N 
       52.73        52.60        82.49        47.84        20.22         2.89 
TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA4X 
       34.06        19.69         8.61        59.38        60.16        63.02 
TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 
       38.73        35.41        57.90        19.40         8.52        47.15 
TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-ZF-AA5P 
       19.17         5.52        10.13 

  FBXW7 MUTATED FBXW7 WILD-TYPE 
           0.56            0.10 
  FBXW7 MUTATED FBXW7 WILD-TYPE 
         166.03          140.81 
  FBXW7 MUTATED FBXW7 WILD-TYPE 
          14.07           15.81 
[1] "0.6 - 166.0 (14.1)" "0.1 - 140.8 (15.8)"
[1] "hr=" "1.1"
D16V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  FBXW7 MUTATED         0        9        14        8
  FBXW7 WILD-TYPE       4      108       108      120
D16V3, multiclass
           clus
vv          FBXW7 MUTATED FBXW7 WILD-TYPE
  STAGE I               0               4
  STAGE II              9             108
  STAGE III            14             108
  STAGE IV              8             120
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1+T2  T3  T4
  FBXW7 MUTATED          7  18   3
  FBXW7 WILD-TYPE      107 161  49
D16V4, multiclass
          clus
vv         FBXW7 MUTATED FBXW7 WILD-TYPE
  T0+T1+T2             7             107
  T3                  18             161
  T4                   3              49
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  FBXW7 MUTATED    21   1   5   1
  FBXW7 WILD-TYPE 192  40  70   7
D16V5, multiclass
    clus
vv   FBXW7 MUTATED FBXW7 WILD-TYPE
  N0            21             192
  N1             1              40
  N2             5              70
  N3             1               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"
D16V6, binary
                 cls
clus                0   1
  FBXW7 MUTATED    20   2
  FBXW7 WILD-TYPE 162   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FBXW7 MUTATED     20    2
  FBXW7 WILD-TYPE  162    8
   clus
vv  FBXW7 MUTATED FBXW7 WILD-TYPE
  0            20             162
  1             2               8
[1] 2 2
[1] FALSE
D16V7, binary
                 cls
clus                0   1
  FBXW7 MUTATED    11  20
  FBXW7 WILD-TYPE  85 260
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FBXW7 MUTATED     11   20
  FBXW7 WILD-TYPE   85  260
        clus
vv       FBXW7 MUTATED FBXW7 WILD-TYPE
  FEMALE            11              85
  MALE              20             260
[1] 2 2
[1] FALSE
D16V8, continuous
D16V9, continuous
D16V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  FBXW7 MUTATED       1                         1    26
  FBXW7 WILD-TYPE    37                        20   275
D16V11, multiclass
                           clus
vv                          FBXW7 MUTATED FBXW7 WILD-TYPE
  ASIAN                                 1              37
  BLACK OR AFRICAN AMERICAN             1              20
  WHITE                                26             275
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V12, binary
                 cls
clus                0   1
  FBXW7 MUTATED     0  27
  FBXW7 WILD-TYPE   8 311
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FBXW7 MUTATED      0   27
  FBXW7 WILD-TYPE    8  311
                        clus
vv                       FBXW7 MUTATED FBXW7 WILD-TYPE
  HISPANIC OR LATINO                 0               8
  NOT HISPANIC OR LATINO            27             311
[1] 2 2
[1] FALSE

Clustering(17) Variable = HRAS MUTATION ANALYSIS
D17V1, survival
                sevent
clus2              0   1
  HRAS MUTATED     8   8
  HRAS WILD-TYPE 211 143
  HRAS MUTATED HRAS WILD-TYPE 
            16            354 
  HRAS MUTATED HRAS WILD-TYPE 
             8            143 
$`HRAS MUTATED`
TCGA-2F-A9KO TCGA-BT-A2LB TCGA-BT-A3PH TCGA-CF-A47T TCGA-DK-A1AC TCGA-E7-A677 
       22.29        16.18         4.67        12.66       130.88        14.56 
TCGA-E7-A6MF TCGA-E7-A97P TCGA-FT-A3EE TCGA-G2-A2EJ TCGA-GD-A3OQ TCGA-XF-A9T4 
       14.33        14.37         3.25        30.61         3.12        16.27 
TCGA-XF-AAMW TCGA-YC-A8S6 TCGA-ZF-AA58 TCGA-ZF-AA5N 
        8.32         9.63        47.15         5.52 

$`HRAS WILD-TYPE`
TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW TCGA-4Z-AA7M 
       11.97        91.63       103.50       105.70         8.35        16.27 
TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7W 
       44.94        16.83        16.77        17.16        34.98        27.62 
TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA84 
       49.12         0.62        41.75        51.16        66.54        15.12 
TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J 
       10.22        47.80        33.83        40.08         7.33         2.66 
TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N 
        6.74        12.39         6.58        13.15        19.04        32.84 
TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U 
       12.16        17.88        19.50         5.06        14.89        14.96 
TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LD TCGA-BT-A3PJ 
        5.06         8.35         8.25        17.16        20.48        12.82 
TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ 
        9.96        17.56        28.70        24.26        28.41         8.98 
TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-C4-A0F6 TCGA-C4-A0F7 TCGA-CF-A1HR TCGA-CF-A1HS 
        1.94         2.93        23.01         2.04         0.46         0.43 
TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y 
        0.69        10.95        12.46        12.10        12.62        12.26 
TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A0YN 
       13.12        12.00        12.10        11.87        13.08        12.92 
TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 
        4.90         7.20         5.46         5.19        16.31         1.84 
TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA 
       13.58        21.86         2.14        66.41        18.41        19.00 
TCGA-DK-A1AB TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX 
       16.70       112.44        16.14        17.62        15.62         1.81 
TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL 
       10.59         7.79       123.85        87.32         2.20        13.58 
TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU 
        7.82         8.22        17.72        50.27        21.30        23.21 
TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A3X2 
        9.67        20.81        10.55       140.81        48.00        17.98 
TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 
       64.18        41.56        76.60        67.36        15.68        41.06 
TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6S TCGA-DK-AA6T 
       30.67        38.24        15.02        13.58       166.03        12.36 
TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA76 
       10.49         8.65         7.53        13.64        43.50        12.03 
TCGA-DK-AA77 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 
       10.62        43.59        15.35        38.83        24.66         0.10 
TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF 
        0.49         2.24        16.70        17.39         0.56         0.66 
TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A7DU TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A7XN 
       13.97        12.99         0.92         1.22        13.68        14.07 
TCGA-E7-A85H TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 
       12.95         8.09        32.02        16.77         8.94        33.04 
TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ 
        4.01        12.62        22.52        27.98        60.66        24.30 
TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ 
       23.41        17.98        29.16         5.52        25.74        46.78 
TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U 
       19.79        12.85        22.98        27.35        14.96        20.91 
TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV 
        3.62        26.73        53.88        11.01        19.33         5.36 
TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N 
        5.69         8.25        27.45        18.08        58.92         2.70 
TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC 
        7.10         6.28        13.35        62.86        18.81         6.15 
TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI 
       12.69        12.36         2.27         3.06         4.31         9.67 
TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FJ-A871 
       10.85        31.07         7.13        10.65        17.23         8.94 
TCGA-FT-A61P TCGA-G2-A2EC TCGA-G2-A2EF TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO 
        6.48        22.88        61.94        15.95        26.93        35.24 
TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3C 
       33.01         7.23        20.12        17.62        66.02         6.94 
TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB 
       64.44        19.46        21.40         2.24        15.81         4.50 
TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GC-A6I3 
       15.91        14.07        17.75        24.92         8.94        13.91 
TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42P 
        7.73         2.10        20.98         2.20         7.36        10.92 
TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 
       11.31        11.31         7.63        27.09        20.05         5.62 
TCGA-GU-A767 TCGA-GU-AATO TCGA-GU-AATP TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW 
        4.73        10.65        32.98         7.00        14.27        21.34 
TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK 
       19.10        19.82        20.28         8.48        10.59        27.35 
TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE 
        8.58        19.07        22.72         1.51        19.40        38.60 
TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV 
        3.06         9.01         8.22        25.02         3.45        21.24 
TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ 
        2.76         9.14        27.68         9.07        11.70         1.74 
TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO TCGA-LC-A66R TCGA-LT-A5Z6 
        1.81        15.42         6.38        11.80        15.32        15.58 
TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 
       13.48        12.23        16.67        14.24         1.84         3.75 
TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78N 
       12.43        31.56        17.62        37.05        22.68        86.83 
TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE 
       76.01        65.75        35.24        29.56        17.82         4.54 
TCGA-UY-A9PF TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI 
        1.64         1.87        17.88        48.62        64.80        79.66 
TCGA-XF-A9SJ TCGA-XF-A9SL TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY 
        3.22        66.41        12.76        11.90        23.64        21.04 
TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T5 TCGA-XF-A9T6 
       28.24        26.27        18.90         2.24        66.64         2.10 
TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMG TCGA-XF-AAMH TCGA-XF-AAMJ 
       13.74        92.98        10.82       110.60        11.31        54.90 
TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMX TCGA-XF-AAMY 
        7.63        71.57        91.73         2.96         6.77        98.99 
TCGA-XF-AAMZ TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN4 
       44.32        56.48        30.94        61.45        86.30        27.06 
TCGA-XF-AAN5 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-YF-AA3M 
       75.39        18.81         3.88         0.66        11.97        13.64 
TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R5 
       18.64         7.36        21.11        24.13        30.28        27.19 
TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RF 
       21.86        28.41        74.56        13.41         3.48        52.73 
TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4R 
       52.60        82.49        47.84        20.22         2.89        34.06 
TCGA-ZF-AA4T TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA51 
       19.69         8.61        59.38        60.16        63.02        38.73 
TCGA-ZF-AA52 TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA5H TCGA-ZF-AA5P 
       35.41        57.90        19.40         8.52        19.17        10.13 

  HRAS MUTATED HRAS WILD-TYPE 
          3.12           0.10 
  HRAS MUTATED HRAS WILD-TYPE 
        130.88         166.03 
  HRAS MUTATED HRAS WILD-TYPE 
         14.35          15.86 
[1] "3.1 - 130.9 (14.3)" "0.1 - 166.0 (15.9)"
[1] "hr=" "1.5"
D17V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  HRAS MUTATED         0        7         3        7
  HRAS WILD-TYPE       4      110       119      121
D17V3, multiclass
           clus
vv          HRAS MUTATED HRAS WILD-TYPE
  STAGE I              0              4
  STAGE II             7            110
  STAGE III            3            119
  STAGE IV             7            121
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1+T2  T3  T4
  HRAS MUTATED          9   5   2
  HRAS WILD-TYPE      105 174  50
D17V4, multiclass
          clus
vv         HRAS MUTATED HRAS WILD-TYPE
  T0+T1+T2            9            105
  T3                  5            174
  T4                  2             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"
                vv
clus              N0  N1  N2  N3
  HRAS MUTATED     9   3   2   0
  HRAS WILD-TYPE 204  38  73   8
D17V5, multiclass
    clus
vv   HRAS MUTATED HRAS WILD-TYPE
  N0            9            204
  N1            3             38
  N2            2             73
  N3            0              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"
D17V6, binary
                cls
clus               0   1
  HRAS MUTATED     9   1
  HRAS WILD-TYPE 173   9
[1] "tbl2"
                cls
clus             [,1] [,2]
  HRAS MUTATED      9    1
  HRAS WILD-TYPE  173    9
   clus
vv  HRAS MUTATED HRAS WILD-TYPE
  0            9            173
  1            1              9
[1] 2 2
[1] FALSE
D17V7, binary
                cls
clus               0   1
  HRAS MUTATED     7  10
  HRAS WILD-TYPE  89 270
[1] "tbl2"
                cls
clus             [,1] [,2]
  HRAS MUTATED      7   10
  HRAS WILD-TYPE   89  270
        clus
vv       HRAS MUTATED HRAS WILD-TYPE
  FEMALE            7             89
  MALE             10            270
[1] 2 2
[1] FALSE
D17V8, continuous
D17V9, continuous
D17V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  HRAS MUTATED       5                         0    12
  HRAS WILD-TYPE    33                        21   289
D17V11, multiclass
                           clus
vv                          HRAS MUTATED HRAS WILD-TYPE
  ASIAN                                5             33
  BLACK OR AFRICAN AMERICAN            0             21
  WHITE                               12            289
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V12, binary
                cls
clus               0   1
  HRAS MUTATED     0  16
  HRAS WILD-TYPE   8 322
[1] "tbl2"
                cls
clus             [,1] [,2]
  HRAS MUTATED      0   16
  HRAS WILD-TYPE    8  322
                        clus
vv                       HRAS MUTATED HRAS WILD-TYPE
  HISPANIC OR LATINO                0              8
  NOT HISPANIC OR LATINO           16            322
[1] 2 2
[1] FALSE

Clustering(18) Variable = CREBBP MUTATION ANALYSIS
D18V1, survival
                  sevent
clus2                0   1
  CREBBP MUTATED    28  16
  CREBBP WILD-TYPE 191 135
  CREBBP MUTATED CREBBP WILD-TYPE 
              44              326 
  CREBBP MUTATED CREBBP WILD-TYPE 
              16              135 
$`CREBBP MUTATED`
TCGA-4Z-AA81 TCGA-4Z-AA86 TCGA-BL-A5ZZ TCGA-BT-A20O TCGA-BT-A20T TCGA-BT-A3PJ 
       41.75        10.22        12.39        12.16        14.89        12.82 
TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-CF-A47X TCGA-CU-A3YL TCGA-DK-A1A3 TCGA-DK-A1AD 
        1.94         2.93        12.62        16.31        21.86       112.44 
TCGA-DK-A2I1 TCGA-DK-A3X2 TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-AA6U TCGA-E5-A4TZ 
       10.59        17.98        41.56        76.60        10.49        15.35 
TCGA-E7-A519 TCGA-E7-A6ME TCGA-E7-A7PW TCGA-FD-A3N5 TCGA-FD-A3SL TCGA-FD-A3SM 
       16.70        12.99        13.68        22.52        23.41        17.98 
TCGA-FD-A3SP TCGA-FJ-A3Z9 TCGA-FJ-A871 TCGA-FT-A61P TCGA-G2-A2EL TCGA-G2-A2EO 
       25.74         7.13         8.94         6.48        26.93        35.24 
TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GV-A3JX TCGA-K4-A5RH TCGA-K4-AAQO TCGA-PQ-A6FI 
       15.91        14.07        19.10         9.07        11.80        12.23 
TCGA-XF-A9T3 TCGA-XF-AAMT TCGA-XF-AAN5 TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-A9RN 
        2.24         2.96        75.39        52.60        82.49        20.22 
TCGA-ZF-AA4N TCGA-ZF-AA4R 
        2.89        34.06 

$`CREBBP WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        91.63       103.50       105.70         8.35 
TCGA-4Z-AA7M TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7S 
       16.27        44.94        16.83        16.77        17.16        34.98 
TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA84 
       27.62        49.12         0.62        51.16        66.54        15.12 
TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM 
       47.80        33.83        40.08         7.33         2.66         6.74 
TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20P TCGA-BT-A20Q 
        6.58        13.15        19.04        32.84        17.88        19.50 
TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA 
        5.06        14.96         5.06         8.35         8.25        17.16 
TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C 
       16.18        20.48         4.67         9.96        17.56        28.70 
TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F6 TCGA-C4-A0F7 TCGA-CF-A1HR 
       24.26        28.41         8.98        23.01         2.04         0.46 
TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W 
        0.43         0.69        10.95        12.66        12.46        12.10 
TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A9FF TCGA-CF-A9FM 
       12.26        13.12        12.00        12.10        11.87        13.08 
TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A5W6 
       12.92         4.90         7.20         5.46         5.19         1.84 
TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB 
       13.58         2.14        66.41        18.41        19.00        16.70 
TCGA-DK-A1AC TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I2 
      130.88        16.14        17.62        15.62         1.81         7.79 
TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN 
      123.85        87.32         2.20        13.58         7.82         8.22 
TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW 
       17.72        50.27        21.30        23.21         9.67        20.81 
TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A6AV TCGA-DK-A6B1 TCGA-DK-A6B2 
       10.55       140.81        48.00        64.18        67.36        15.68 
TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6S 
       41.06        30.67        38.24        15.02        13.58       166.03 
TCGA-DK-AA6T TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA76 
       12.36         8.65         7.53        13.64        43.50        12.03 
TCGA-DK-AA77 TCGA-E5-A2PC TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ 
       10.62        43.59        38.83        24.66         0.10         0.49 
TCGA-E7-A4XJ TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 
        2.24        17.39         0.56         0.66        14.56        13.97 
TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7DV TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A97P 
       14.33         0.92         1.22        14.07        12.95        14.37 
TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 
        8.09        32.02        16.77         8.94        33.04         4.01 
TCGA-FD-A3B8 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SN TCGA-FD-A3SO 
       12.62        27.98        60.66        24.30        29.16         5.52 
TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S 
       46.78        19.79        12.85        22.98        27.35        14.96 
TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU 
       20.91         3.62        26.73        53.88        11.01        19.33 
TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 
        5.36         5.69         8.25        27.45        18.08        58.92 
TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB 
        2.70         7.10         6.28        13.35        62.86        18.81 
TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH 
        6.15        12.69        12.36         2.27         3.06         4.31 
TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FT-A3EE 
        9.67        10.85        31.07        10.65        17.23         3.25 
TCGA-G2-A2EC TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2ES TCGA-G2-A3IB 
       22.88        61.94        30.61        15.95        33.01         7.23 
TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3D TCGA-G2-AA3F 
       20.12        17.62        66.02         6.94        64.44        19.46 
TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3WC TCGA-GC-A3YS 
       21.40         2.24        15.81         4.50        17.75        24.92 
TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS 
        8.94        13.91         7.73         2.10         3.12        20.98 
TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 
        2.20         7.36        10.92        11.31        11.31         7.63 
TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATO TCGA-GU-AATP 
       27.09        20.05         5.62         4.73        10.65        32.98 
TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH 
        7.00        14.27        21.34        19.82        20.28         8.48 
TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO 
       10.59        27.35         8.58        19.07        22.72         1.51 
TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS 
       19.40        38.60         3.06         9.01         8.22        25.02 
TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RI 
        3.45        21.24         2.76         9.14        27.68        11.70 
TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-LC-A66R TCGA-LT-A5Z6 
        1.74         1.81        15.42         6.38        15.32        15.58 
TCGA-MV-A51V TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 TCGA-SY-A9G0 
       13.48        16.67        14.24         1.84         3.75        12.43 
TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78N TCGA-UY-A78O 
       31.56        17.62        37.05        22.68        86.83        76.01 
TCGA-UY-A8OB TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF 
       65.75        35.24        29.56        17.82         4.54         1.64 
TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SJ 
        1.87        17.88        48.62        64.80        79.66         3.22 
TCGA-XF-A9SL TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ 
       66.41        12.76        11.90        23.64        21.04        28.24 
TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 
       26.27        18.90        16.27        66.64         2.10        13.74 
TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMG TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML 
       92.98        10.82       110.60        11.31        54.90         7.63 
TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAMZ 
       71.57        91.73         8.32         6.77        98.99        44.32 
TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN7 
       56.48        30.94        61.45        86.30        27.06        18.81 
TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R0 
        3.88         9.63         0.66        11.97        13.64        18.64 
TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R7 
        7.36        21.11        24.13        30.28        27.19        21.86 
TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RM 
       28.41        74.56        13.41         3.48        52.73        47.84 
TCGA-ZF-AA4T TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA51 
       19.69         8.61        59.38        60.16        63.02        38.73 
TCGA-ZF-AA52 TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H 
       35.41        57.90        19.40         8.52        47.15        19.17 
TCGA-ZF-AA5N TCGA-ZF-AA5P 
        5.52        10.13 

  CREBBP MUTATED CREBBP WILD-TYPE 
            1.94             0.10 
  CREBBP MUTATED CREBBP WILD-TYPE 
          112.44           166.03 
  CREBBP MUTATED CREBBP WILD-TYPE 
          15.120           15.745 
[1] "1.9 - 112.4 (15.1)" "0.1 - 166.0 (15.7)"
[1] "hr=" "1.1"
D18V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  CREBBP MUTATED         2       14        16       13
  CREBBP WILD-TYPE       2      103       106      115
D18V3, multiclass
           clus
vv          CREBBP MUTATED CREBBP WILD-TYPE
  STAGE I                2                2
  STAGE II              14              103
  STAGE III             16              106
  STAGE IV              13              115
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1+T2  T3  T4
  CREBBP MUTATED         12  25   4
  CREBBP WILD-TYPE      102 154  48
D18V4, multiclass
          clus
vv         CREBBP MUTATED CREBBP WILD-TYPE
  T0+T1+T2             12              102
  T3                   25              154
  T4                    4               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"
                  vv
clus                N0  N1  N2  N3
  CREBBP MUTATED    24   3   9   2
  CREBBP WILD-TYPE 189  38  66   6
D18V5, multiclass
    clus
vv   CREBBP MUTATED CREBBP WILD-TYPE
  N0             24              189
  N1              3               38
  N2              9               66
  N3              2                6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V6, binary
                  cls
clus                 0   1
  CREBBP MUTATED    24   2
  CREBBP WILD-TYPE 158   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CREBBP MUTATED     24    2
  CREBBP WILD-TYPE  158    8
   clus
vv  CREBBP MUTATED CREBBP WILD-TYPE
  0             24              158
  1              2                8
[1] 2 2
[1] FALSE
D18V7, binary
                  cls
clus                 0   1
  CREBBP MUTATED     8  37
  CREBBP WILD-TYPE  88 243
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CREBBP MUTATED      8   37
  CREBBP WILD-TYPE   88  243
        clus
vv       CREBBP MUTATED CREBBP WILD-TYPE
  FEMALE              8               88
  MALE               37              243
[1] 2 2
[1] FALSE
D18V8, continuous
D18V9, continuous
D18V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CREBBP MUTATED       3                         2    38
  CREBBP WILD-TYPE    35                        19   263
D18V11, multiclass
                           clus
vv                          CREBBP MUTATED CREBBP WILD-TYPE
  ASIAN                                  3               35
  BLACK OR AFRICAN AMERICAN              2               19
  WHITE                                 38              263
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V12, binary
                  cls
clus                 0   1
  CREBBP MUTATED     0  40
  CREBBP WILD-TYPE   8 298
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CREBBP MUTATED      0   40
  CREBBP WILD-TYPE    8  298
                        clus
vv                       CREBBP MUTATED CREBBP WILD-TYPE
  HISPANIC OR LATINO                  0                8
  NOT HISPANIC OR LATINO             40              298
[1] 2 2
[1] FALSE

Clustering(19) Variable = KRAS MUTATION ANALYSIS
D19V1, survival
                sevent
clus2              0   1
  KRAS MUTATED     5   8
  KRAS WILD-TYPE 214 143
  KRAS MUTATED KRAS WILD-TYPE 
            13            357 
  KRAS MUTATED KRAS WILD-TYPE 
             8            143 
$`KRAS MUTATED`
TCGA-4Z-AA81 TCGA-CF-A47X TCGA-CF-A5UA TCGA-DK-A6AW TCGA-E7-A4XJ TCGA-FD-A5BX 
       41.75        12.62        12.00        41.56         2.24         5.69 
TCGA-FJ-A3Z9 TCGA-FJ-A871 TCGA-G2-AA3C TCGA-XF-AAMH TCGA-XF-AAN7 TCGA-ZF-A9R4 
        7.13         8.94         6.94        11.31        18.81        30.28 
TCGA-ZF-AA54 
       19.40 

$`KRAS WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        91.63       103.50       105.70         8.35 
TCGA-4Z-AA7M TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7S 
       16.27        44.94        16.83        16.77        17.16        34.98 
TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA84 
       27.62        49.12         0.62        51.16        66.54        15.12 
TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J 
       10.22        47.80        33.83        40.08         7.33         2.66 
TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N 
        6.74        12.39         6.58        13.15        19.04        32.84 
TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U 
       12.16        17.88        19.50         5.06        14.89        14.96 
TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A2LD 
        5.06         8.35         8.25        17.16        16.18        20.48 
TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E 
        4.67        12.82         9.96        17.56        28.70        24.26 
TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-C4-A0F6 TCGA-C4-A0F7 
       28.41         8.98         1.94         2.93        23.01         2.04 
TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V 
        0.46         0.43         0.69        10.95        12.66        12.46 
TCGA-CF-A47W TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A7I0 TCGA-CF-A9FF TCGA-CF-A9FM 
       12.10        12.26        13.12        12.10        11.87        13.08 
TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL 
       12.92         4.90         7.20         5.46         5.19        16.31 
TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 
        1.84        13.58        21.86         2.14        66.41        18.41 
TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF 
       19.00        16.70       130.88       112.44        16.14        17.62 
TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A2I6 
       15.62         1.81        10.59         7.79       123.85        87.32 
TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS 
        2.20        13.58         7.82         8.22        17.72        50.27 
TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY 
       21.30        23.21         9.67        20.81        10.55       140.81 
TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 
       48.00        17.98        64.18        76.60        67.36        15.68 
TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6S 
       41.06        30.67        38.24        15.02        13.58       166.03 
TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA74 
       12.36        10.49         8.65         7.53        13.64        43.50 
TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 
       12.03        10.62        43.59        15.35        38.83        24.66 
TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF 
        0.10         0.49        16.70        17.39         0.56         0.66 
TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7DV 
       14.56        13.97        12.99        14.33         0.92         1.22 
TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B3 
       13.68        14.07        12.95        14.37         8.09        32.02 
TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 
       16.77         8.94        33.04         4.01        12.62        22.52 
TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN 
       27.98        60.66        24.30        23.41        17.98        29.16 
TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N 
        5.52        25.74        46.78        19.79        12.85        22.98 
TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS 
       27.35        14.96        20.91         3.62        26.73        53.88 
TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 
       11.01        19.33         5.36         8.25        27.45        18.08 
TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA 
       58.92         2.70         7.10         6.28        13.35        62.86 
TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TG 
       18.81         6.15        12.69        12.36         2.27         3.06 
TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3ZE TCGA-FJ-A3ZF 
        4.31         9.67        10.85        31.07        10.65        17.23 
TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EC TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK 
        3.25         6.48        22.88        61.94        30.61        15.95 
TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY 
       26.93        35.24        33.01         7.23        20.12        17.62 
TCGA-G2-AA3B TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO 
       66.02        64.44        19.46        21.40         2.24        15.81 
TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A6I1 
        4.50        15.91        14.07        17.75        24.92         8.94 
TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 
       13.91         7.73         2.10         3.12        20.98         2.20 
TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 
        7.36        10.92        11.31        11.31         7.63        27.09 
TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATO TCGA-GU-AATP TCGA-GU-AATQ 
       20.05         5.62         4.73        10.65        32.98         7.00 
TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH 
       14.27        21.34        19.10        19.82        20.28         8.48 
TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO 
       10.59        27.35         8.58        19.07        22.72         1.51 
TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS 
       19.40        38.60         3.06         9.01         8.22        25.02 
TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RH 
        3.45        21.24         2.76         9.14        27.68         9.07 
TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO 
       11.70         1.74         1.81        15.42         6.38        11.80 
TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X 
       15.32        15.58        13.48        12.23        16.67        14.24 
TCGA-S5-A6DX TCGA-S5-AA26 TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L 
        1.84         3.75        12.43        31.56        17.62        37.05 
TCGA-UY-A78M TCGA-UY-A78N TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A9PA TCGA-UY-A9PB 
       22.68        86.83        76.01        65.75        35.24        29.56 
TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG 
       17.82         4.54         1.64         1.87        17.88        48.62 
TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SL TCGA-XF-A9SV TCGA-XF-A9SW 
       64.80        79.66         3.22        66.41        12.76        11.90 
TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 
       23.64        21.04        28.24        26.27        18.90         2.24 
TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMF 
       16.27        66.64         2.10        13.74        92.98        10.82 
TCGA-XF-AAMG TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMT 
      110.60        54.90         7.63        71.57        91.73         2.96 
TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN0 TCGA-XF-AAN1 
        8.32         6.77        98.99        44.32        56.48        30.94 
TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN8 TCGA-YC-A8S6 
       61.45        86.30        27.06        75.39         3.88         9.63 
TCGA-YC-A9TC TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R2 
        0.66        11.97        13.64        18.64         7.36        21.11 
TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RD 
       24.13        27.19        21.86        28.41        74.56        13.41 
TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-A9RN 
        3.48        52.73        52.60        82.49        47.84        20.22 
TCGA-ZF-AA4N TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W 
        2.89        34.06        19.69         8.61        59.38        60.16 
TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA53 TCGA-ZF-AA56 TCGA-ZF-AA58 
       63.02        38.73        35.41        57.90         8.52        47.15 
TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-ZF-AA5P 
       19.17         5.52        10.13 

  KRAS MUTATED KRAS WILD-TYPE 
          2.24           0.10 
  KRAS MUTATED KRAS WILD-TYPE 
         41.75         166.03 
  KRAS MUTATED KRAS WILD-TYPE 
         12.00          15.81 
[1] "2.2 - 41.8 (12.0)"  "0.1 - 166.0 (15.8)"
[1] "hr=" "2"  
D19V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  KRAS MUTATED         1        6         2        4
  KRAS WILD-TYPE       3      111       120      124
D19V3, multiclass
           clus
vv          KRAS MUTATED KRAS WILD-TYPE
  STAGE I              1              3
  STAGE II             6            111
  STAGE III            2            120
  STAGE IV             4            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"
                vv
clus             T0+T1+T2  T3  T4
  KRAS MUTATED          7   6   0
  KRAS WILD-TYPE      107 173  52
D19V4, multiclass
          clus
vv         KRAS MUTATED KRAS WILD-TYPE
  T0+T1+T2            7            107
  T3                  6            173
  T4                  0             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"
                vv
clus              N0  N1  N2  N3
  KRAS MUTATED     6   4   0   0
  KRAS WILD-TYPE 207  37  75   8
D19V5, multiclass
    clus
vv   KRAS MUTATED KRAS WILD-TYPE
  N0            6            207
  N1            4             37
  N2            0             75
  N3            0              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"
D19V6, binary
                cls
clus               0   1
  KRAS MUTATED     8   0
  KRAS WILD-TYPE 174  10
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRAS MUTATED      8    0
  KRAS WILD-TYPE  174   10
   clus
vv  KRAS MUTATED KRAS WILD-TYPE
  0            8            174
  1            0             10
[1] 2 2
[1] FALSE
D19V7, binary
                cls
clus               0   1
  KRAS MUTATED     0  13
  KRAS WILD-TYPE  96 267
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRAS MUTATED      0   13
  KRAS WILD-TYPE   96  267
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  FEMALE            0             96
  MALE             13            267
[1] 2 2
[1] FALSE
D19V8, continuous
D19V9, continuous
D19V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  KRAS MUTATED       3                         0    10
  KRAS WILD-TYPE    35                        21   291
D19V11, multiclass
                           clus
vv                          KRAS MUTATED KRAS WILD-TYPE
  ASIAN                                3             35
  BLACK OR AFRICAN AMERICAN            0             21
  WHITE                               10            291
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V12, binary
                cls
clus               0   1
  KRAS MUTATED     0  12
  KRAS WILD-TYPE   8 326
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRAS MUTATED      0   12
  KRAS WILD-TYPE    8  326
                        clus
vv                       KRAS MUTATED KRAS WILD-TYPE
  HISPANIC OR LATINO                0              8
  NOT HISPANIC OR LATINO           12            326
[1] 2 2
[1] FALSE

Clustering(20) Variable = NFE2L2 MUTATION ANALYSIS
D20V1, survival
                  sevent
clus2                0   1
  NFE2L2 MUTATED    12  12
  NFE2L2 WILD-TYPE 207 139
  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
              24              346 
  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
              12              139 
$`NFE2L2 MUTATED`
TCGA-BL-A13I TCGA-BT-A0YX TCGA-BT-A20U TCGA-BT-A42B TCGA-C4-A0F6 TCGA-DK-A1AE 
        7.33        13.15        14.96        17.56        23.01        16.14 
TCGA-DK-A3IT TCGA-DK-AA6Q TCGA-E5-A2PC TCGA-FD-A3N6 TCGA-FD-A3SM TCGA-FD-A5BU 
       21.30        13.58        43.59        27.98        17.98        19.33 
TCGA-G2-A3IB TCGA-G2-AA3C TCGA-GU-AATQ TCGA-K4-A3WS TCGA-K4-A5RI TCGA-R3-A69X 
        7.23         6.94         7.00        25.02        11.70        14.24 
TCGA-UY-A9PE TCGA-XF-A9SY TCGA-XF-AAN3 TCGA-XF-AAN5 TCGA-YC-A9TC TCGA-ZF-AA4U 
        4.54        21.04        86.30        75.39         0.66         8.61 

$`NFE2L2 WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        91.63       103.50       105.70         8.35 
TCGA-4Z-AA7M TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7S 
       16.27        44.94        16.83        16.77        17.16        34.98 
TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 
       27.62        49.12         0.62        41.75        51.16        66.54 
TCGA-4Z-AA84 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BL-A13J 
       15.12        10.22        47.80        33.83        40.08         2.66 
TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O 
        6.74        12.39         6.58        19.04        32.84        12.16 
TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20V TCGA-BT-A20W 
       17.88        19.50         5.06        14.89         5.06         8.35 
TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PJ 
        8.25        17.16        16.18        20.48         4.67        12.82 
TCGA-BT-A3PK TCGA-BT-A42C TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 
        9.96        28.70        24.26        28.41         8.98         1.94 
TCGA-C4-A0F1 TCGA-C4-A0F7 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47S 
        2.93         2.04         0.46         0.43         0.69        10.95 
TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 
       12.66        12.46        12.10        12.62        12.26        13.12 
TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YO 
       12.00        12.10        11.87        13.08        12.92         4.90 
TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E 
        7.20         5.46         5.19        16.31         1.84        13.58 
TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB 
       21.86         2.14        66.41        18.41        19.00        16.70 
TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 
      130.88       112.44        17.62        15.62         1.81        10.59 
TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM 
        7.79       123.85        87.32         2.20        13.58         7.82 
TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW 
        8.22        17.72        50.27        23.21         9.67        20.81 
TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW 
       10.55       140.81        48.00        17.98        64.18        41.56 
TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L 
       76.60        67.36        15.68        41.06        30.67        38.24 
TCGA-DK-AA6P TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA6X 
       15.02       166.03        12.36        10.49         8.65         7.53 
TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A4TZ TCGA-E5-A4U1 
       13.64        43.50        12.03        10.62        15.35        38.83 
TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 
       24.66         0.10         0.49         2.24        16.70        17.39 
TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF 
        0.56         0.66        14.56        13.97        12.99        14.33 
TCGA-E7-A7DU TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A97P 
        0.92         1.22        13.68        14.07        12.95        14.37 
TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 
        8.09        32.02        16.77         8.94        33.04         4.01 
TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SN 
       12.62        22.52        60.66        24.30        23.41        29.16 
TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N 
        5.52        25.74        46.78        19.79        12.85        22.98 
TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS 
       27.35        14.96        20.91         3.62        26.73        53.88 
TCGA-FD-A5BT TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 
       11.01         5.36         5.69         8.25        27.45        18.08 
TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA 
       58.92         2.70         7.10         6.28        13.35        62.86 
TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TG 
       18.81         6.15        12.69        12.36         2.27         3.06 
TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE 
        4.31         9.67        10.85        31.07         7.13        10.65 
TCGA-FJ-A3ZF TCGA-FJ-A871 TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EC TCGA-G2-A2EF 
       17.23         8.94         3.25         6.48        22.88        61.94 
TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IE 
       30.61        15.95        26.93        35.24        33.01        20.12 
TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 
       17.62        66.02        64.44        19.46        21.40         2.24 
TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS 
       15.81         4.50        15.91        14.07        17.75        24.92 
TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS 
        8.94        13.91         7.73         2.10         3.12        20.98 
TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 
        2.20         7.36        10.92        11.31        11.31         7.63 
TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATO TCGA-GU-AATP 
       27.09        20.05         5.62         4.73        10.65        32.98 
TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH 
       14.27        21.34        19.10        19.82        20.28         8.48 
TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO 
       10.59        27.35         8.58        19.07        22.72         1.51 
TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WU 
       19.40        38.60         3.06         9.01         8.22         3.45 
TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RH TCGA-K4-A5RJ 
       21.24         2.76         9.14        27.68         9.07         1.74 
TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO TCGA-LC-A66R TCGA-LT-A5Z6 
        1.81        15.42         6.38        11.80        15.32        15.58 
TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-S5-A6DX TCGA-S5-AA26 TCGA-SY-A9G0 
       13.48        12.23        16.67         1.84         3.75        12.43 
TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78N TCGA-UY-A78O 
       31.56        17.62        37.05        22.68        86.83        76.01 
TCGA-UY-A8OB TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PF TCGA-XF-A8HH 
       65.75        35.24        29.56        17.82         1.64         1.87 
TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SL 
       17.88        48.62        64.80        79.66         3.22        66.41 
TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 
       12.76        11.90        23.64        28.24        26.27        18.90 
TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAME 
        2.24        16.27        66.64         2.10        13.74        92.98 
TCGA-XF-AAMF TCGA-XF-AAMG TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ 
       10.82       110.60        11.31        54.90         7.63        71.57 
TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAMZ 
       91.73         2.96         8.32         6.77        98.99        44.32 
TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN4 TCGA-XF-AAN7 TCGA-XF-AAN8 
       56.48        30.94        61.45        27.06        18.81         3.88 
TCGA-YC-A8S6 TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R2 
        9.63        11.97        13.64        18.64         7.36        21.11 
TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RC 
       24.13        30.28        27.19        21.86        28.41        74.56 
TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-A9RM 
       13.41         3.48        52.73        52.60        82.49        47.84 
TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4V TCGA-ZF-AA4W 
       20.22         2.89        34.06        19.69        59.38        60.16 
TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA56 
       63.02        38.73        35.41        57.90        19.40         8.52 
TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-ZF-AA5P 
       47.15        19.17         5.52        10.13 

  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
            0.66             0.10 
  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
           86.30           166.03 
  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
           15.55            15.65 
[1] "0.7 - 86.3 (15.6)"  "0.1 - 166.0 (15.6)"
[1] "hr=" "1.3"
D20V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  NFE2L2 MUTATED         0        3        12        9
  NFE2L2 WILD-TYPE       4      114       110      119
D20V3, multiclass
           clus
vv          NFE2L2 MUTATED NFE2L2 WILD-TYPE
  STAGE I                0                4
  STAGE II               3              114
  STAGE III             12              110
  STAGE IV               9              119
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1+T2  T3  T4
  NFE2L2 MUTATED          4  17   1
  NFE2L2 WILD-TYPE      110 162  51
D20V4, multiclass
          clus
vv         NFE2L2 MUTATED NFE2L2 WILD-TYPE
  T0+T1+T2              4              110
  T3                   17              162
  T4                    1               51
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  NFE2L2 MUTATED    13   4   4   0
  NFE2L2 WILD-TYPE 200  37  71   8
D20V5, multiclass
    clus
vv   NFE2L2 MUTATED NFE2L2 WILD-TYPE
  N0             13              200
  N1              4               37
  N2              4               71
  N3              0                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"
D20V6, binary
                  cls
clus                 0   1
  NFE2L2 MUTATED     9   2
  NFE2L2 WILD-TYPE 173   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NFE2L2 MUTATED      9    2
  NFE2L2 WILD-TYPE  173    8
   clus
vv  NFE2L2 MUTATED NFE2L2 WILD-TYPE
  0              9              173
  1              2                8
[1] 2 2
[1] FALSE
D20V7, binary
                  cls
clus                 0   1
  NFE2L2 MUTATED    11  13
  NFE2L2 WILD-TYPE  85 267
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NFE2L2 MUTATED     11   13
  NFE2L2 WILD-TYPE   85  267
        clus
vv       NFE2L2 MUTATED NFE2L2 WILD-TYPE
  FEMALE             11               85
  MALE               13              267
[1] 2 2
[1] FALSE
D20V8, continuous
D20V9, continuous
D20V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  NFE2L2 MUTATED       0                         3    20
  NFE2L2 WILD-TYPE    38                        18   281
D20V11, multiclass
                           clus
vv                          NFE2L2 MUTATED NFE2L2 WILD-TYPE
  ASIAN                                  0               38
  BLACK OR AFRICAN AMERICAN              3               18
  WHITE                                 20              281
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V12, binary
                  cls
clus                 0   1
  NFE2L2 MUTATED     0  23
  NFE2L2 WILD-TYPE   8 315
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NFE2L2 MUTATED      0   23
  NFE2L2 WILD-TYPE    8  315
                        clus
vv                       NFE2L2 MUTATED NFE2L2 WILD-TYPE
  HISPANIC OR LATINO                  0                8
  NOT HISPANIC OR LATINO             23              315
[1] 2 2
[1] FALSE

Clustering(21) Variable = RHOA MUTATION ANALYSIS
D21V1, survival
                sevent
clus2              0   1
  RHOA MUTATED     8   9
  RHOA WILD-TYPE 211 142
  RHOA MUTATED RHOA WILD-TYPE 
            17            353 
  RHOA MUTATED RHOA WILD-TYPE 
             9            142 
$`RHOA MUTATED`
TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-BT-A2LD TCGA-DK-A2I1 TCGA-DK-AA6U TCGA-FD-A3SO 
       49.12         0.62        20.48        10.59        10.49         5.52 
TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A6TI TCGA-G2-A2EK TCGA-GU-A767 
        2.70         7.10         6.28         9.67        15.95         4.73 
TCGA-H4-A2HQ TCGA-UY-A78O TCGA-UY-A8OB TCGA-ZF-A9RM TCGA-ZF-AA5N 
       19.40        76.01        65.75        47.84         5.52 

$`RHOA WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        91.63       103.50       105.70         8.35 
TCGA-4Z-AA7M TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7S 
       16.27        44.94        16.83        16.77        17.16        34.98 
TCGA-4Z-AA7W TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA84 TCGA-4Z-AA86 
       27.62        41.75        51.16        66.54        15.12        10.22 
TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM 
       47.80        33.83        40.08         7.33         2.66         6.74 
TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O 
       12.39         6.58        13.15        19.04        32.84        12.16 
TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20V 
       17.88        19.50         5.06        14.89        14.96         5.06 
TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A3PJ 
        8.35         8.25        17.16        16.18         4.67        12.82 
TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ 
        9.96        17.56        28.70        24.26        28.41         8.98 
TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-C4-A0F6 TCGA-C4-A0F7 TCGA-CF-A1HR TCGA-CF-A1HS 
        1.94         2.93        23.01         2.04         0.46         0.43 
TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X 
        0.69        10.95        12.66        12.46        12.10        12.62 
TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A9FF TCGA-CF-A9FM 
       12.26        13.12        12.00        12.10        11.87        13.08 
TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL 
       12.92         4.90         7.20         5.46         5.19        16.31 
TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 
        1.84        13.58        21.86         2.14        66.41        18.41 
TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF 
       19.00        16.70       130.88       112.44        16.14        17.62 
TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK 
       15.62         1.81         7.79       123.85        87.32         2.20 
TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT 
       13.58         7.82         8.22        17.72        50.27        21.30 
TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 
       23.21         9.67        20.81        10.55       140.81        48.00 
TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 
       17.98        64.18        41.56        76.60        67.36        15.68 
TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6S 
       41.06        30.67        38.24        15.02        13.58       166.03 
TCGA-DK-AA6T TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA76 
       12.36         8.65         7.53        13.64        43.50        12.03 
TCGA-DK-AA77 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 
       10.62        43.59        15.35        38.83        24.66         0.10 
TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF 
        0.49         2.24        16.70        17.39         0.56         0.66 
TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7DV 
       14.56        13.97        12.99        14.33         0.92         1.22 
TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B3 
       13.68        14.07        12.95        14.37         8.09        32.02 
TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 
       16.77         8.94        33.04         4.01        12.62        22.52 
TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN 
       27.98        60.66        24.30        23.41        17.98        29.16 
TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P 
       25.74        46.78        19.79        12.85        22.98        27.35 
TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT 
       14.96        20.91         3.62        26.73        53.88        11.01 
TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 
       19.33         5.36         5.69         8.25        27.45        18.08 
TCGA-FD-A5C1 TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD 
       58.92        13.35        62.86        18.81         6.15        12.69 
TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TK TCGA-FJ-A3Z7 
       12.36         2.27         3.06         4.31        10.85        31.07 
TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FJ-A871 TCGA-FT-A3EE TCGA-FT-A61P 
        7.13        10.65        17.23         8.94         3.25         6.48 
TCGA-G2-A2EC TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES 
       22.88        61.94        30.61        26.93        35.24        33.01 
TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3D 
        7.23        20.12        17.62        66.02         6.94        64.44 
TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC 
       19.46        21.40         2.24        15.81         4.50        15.91 
TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 
       14.07        17.75        24.92         8.94        13.91         7.73 
TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42P 
        2.10         3.12        20.98         2.20         7.36        10.92 
TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 
       11.31        11.31         7.63        27.09        20.05         5.62 
TCGA-GU-AATO TCGA-GU-AATP TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX 
       10.65        32.98         7.00        14.27        21.34        19.10 
TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E 
       19.82        20.28         8.48        10.59        27.35         8.58 
TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND 
       19.07        22.72         1.51        38.60         3.06         9.01 
TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC 
        8.22        25.02         3.45        21.24         2.76         9.14 
TCGA-K4-A54R TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB 
       27.68         9.07        11.70         1.74         1.81        15.42 
TCGA-K4-A83P TCGA-K4-AAQO TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI 
        6.38        11.80        15.32        15.58        13.48        12.23 
TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 TCGA-SY-A9G0 TCGA-SY-A9G5 
       16.67        14.24         1.84         3.75        12.43        31.56 
TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78N TCGA-UY-A9PA TCGA-UY-A9PB 
       17.62        37.05        22.68        86.83        35.24        29.56 
TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG 
       17.82         4.54         1.64         1.87        17.88        48.62 
TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SL TCGA-XF-A9SV TCGA-XF-A9SW 
       64.80        79.66         3.22        66.41        12.76        11.90 
TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 
       23.64        21.04        28.24        26.27        18.90         2.24 
TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMF 
       16.27        66.64         2.10        13.74        92.98        10.82 
TCGA-XF-AAMG TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR 
      110.60        11.31        54.90         7.63        71.57        91.73 
TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN0 
        2.96         8.32         6.77        98.99        44.32        56.48 
TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN7 
       30.94        61.45        86.30        27.06        75.39        18.81 
TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R0 
        3.88         9.63         0.66        11.97        13.64        18.64 
TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R7 
        7.36        21.11        24.13        30.28        27.19        21.86 
TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RG 
       28.41        74.56        13.41         3.48        52.73        52.60 
TCGA-ZF-A9RL TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4U 
       82.49        20.22         2.89        34.06        19.69         8.61 
TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA53 
       59.38        60.16        63.02        38.73        35.41        57.90 
TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5P 
       19.40         8.52        47.15        19.17        10.13 

  RHOA MUTATED RHOA WILD-TYPE 
          0.62           0.10 
  RHOA MUTATED RHOA WILD-TYPE 
         76.01         166.03 
  RHOA MUTATED RHOA WILD-TYPE 
         10.49          15.81 
[1] "0.6 - 76.0 (10.5)"  "0.1 - 166.0 (15.8)"
[1] "hr=" "1.5"
D21V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  RHOA MUTATED         1        7         1        8
  RHOA WILD-TYPE       3      110       121      120
D21V3, multiclass
           clus
vv          RHOA MUTATED RHOA WILD-TYPE
  STAGE I              1              3
  STAGE II             7            110
  STAGE III            1            121
  STAGE IV             8            120
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1+T2  T3  T4
  RHOA MUTATED          7   6   1
  RHOA WILD-TYPE      107 173  51
D21V4, multiclass
          clus
vv         RHOA MUTATED RHOA WILD-TYPE
  T0+T1+T2            7            107
  T3                  6            173
  T4                  1             51
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  RHOA MUTATED     9   4   2   0
  RHOA WILD-TYPE 204  37  73   8
D21V5, multiclass
    clus
vv   RHOA MUTATED RHOA WILD-TYPE
  N0            9            204
  N1            4             37
  N2            2             73
  N3            0              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"
D21V6, binary
                cls
clus               0   1
  RHOA MUTATED     6   2
  RHOA WILD-TYPE 176   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  RHOA MUTATED      6    2
  RHOA WILD-TYPE  176    8
   clus
vv  RHOA MUTATED RHOA WILD-TYPE
  0            6            176
  1            2              8
[1] 2 2
[1] FALSE
D21V7, binary
                cls
clus               0   1
  RHOA MUTATED     5  12
  RHOA WILD-TYPE  91 268
[1] "tbl2"
                cls
clus             [,1] [,2]
  RHOA MUTATED      5   12
  RHOA WILD-TYPE   91  268
        clus
vv       RHOA MUTATED RHOA WILD-TYPE
  FEMALE            5             91
  MALE             12            268
[1] 2 2
[1] FALSE
D21V8, continuous
[1] "Remove cluster labels:" "RHOA MUTATED"          
clus
  RHOA MUTATED RHOA WILD-TYPE 
             2            118 
    TCGA-2F-A9KO     TCGA-2F-A9KP     TCGA-2F-A9KQ     TCGA-2F-A9KR 
"RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" 
    TCGA-2F-A9KT     TCGA-2F-A9KW     TCGA-CF-A1HS     TCGA-CF-A27C 
"RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" 
    TCGA-CF-A3MF     TCGA-CF-A3MG     TCGA-CF-A3MH     TCGA-CF-A3MI 
"RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" 
    TCGA-CF-A47S     TCGA-CF-A47T     TCGA-CF-A47V     TCGA-CF-A47W 
"RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" 
    TCGA-CF-A47X     TCGA-CF-A47Y     TCGA-CF-A5U8     TCGA-CF-A5UA 
"RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" 
    TCGA-CF-A7I0     TCGA-DK-A2HX     TCGA-DK-A3IN     TCGA-DK-A3IV 
"RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" 
    TCGA-DK-A3WX     TCGA-DK-A3X2     TCGA-DK-A6B2     TCGA-DK-A6B5 
"RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" 
    TCGA-DK-A6B6     TCGA-DK-AA6P     TCGA-DK-AA6S     TCGA-DK-AA6W 
"RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" 
    TCGA-DK-AA76     TCGA-E5-A2PC     TCGA-E5-A4TZ     TCGA-E5-A4U1 
"RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" 
    TCGA-E7-A519     TCGA-E7-A541     TCGA-E7-A7DU     TCGA-E7-A7DV 
"RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" 
    TCGA-FT-A61P     TCGA-G2-A2EC     TCGA-G2-A2EF     TCGA-G2-A2EJ 
"RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" 
    TCGA-G2-A2EL     TCGA-G2-A2EO     TCGA-G2-A2ES     TCGA-G2-A3IB 
"RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" 
    TCGA-G2-A3IE     TCGA-G2-A3VY     TCGA-GC-A3BM     TCGA-GC-A3I6 
"RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" 
    TCGA-GC-A3OO     TCGA-GC-A3RC     TCGA-GC-A3RD     TCGA-GC-A3YS 
"RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" 
    TCGA-GC-A6I1     TCGA-GC-A6I3     TCGA-GD-A3OS     TCGA-GD-A6C6 
"RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" 
    TCGA-GV-A3JV     TCGA-GV-A3JW     TCGA-GV-A3JX     TCGA-GV-A3JZ 
"RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" 
    TCGA-GV-A3QF     TCGA-GV-A3QH     TCGA-GV-A3QI     TCGA-GV-A3QK 
"RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" 
    TCGA-GV-A40E     TCGA-GV-A40G     TCGA-GV-A6ZA     TCGA-SY-A9G0 
"RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" 
    TCGA-SY-A9G5     TCGA-UY-A78L     TCGA-UY-A78M     TCGA-UY-A78N 
"RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" 
    TCGA-XF-A8HH     TCGA-XF-A8HI     TCGA-XF-A9SG     TCGA-XF-A9SH 
"RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" 
    TCGA-XF-A9SI     TCGA-XF-A9SJ     TCGA-XF-A9SL     TCGA-XF-A9SV 
"RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" 
    TCGA-XF-A9SW     TCGA-XF-A9SX     TCGA-XF-A9SY     TCGA-XF-A9SZ 
"RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" 
    TCGA-XF-A9T0     TCGA-XF-A9T2     TCGA-XF-A9T3     TCGA-XF-A9T4 
"RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" 
    TCGA-XF-A9T5     TCGA-XF-A9T6     TCGA-XF-A9T8     TCGA-XF-AAME 
"RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" 
    TCGA-XF-AAMF     TCGA-XF-AAMG     TCGA-XF-AAMH     TCGA-XF-AAMJ 
"RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" 
    TCGA-XF-AAML     TCGA-XF-AAMQ     TCGA-XF-AAMR     TCGA-XF-AAMT 
"RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" 
    TCGA-XF-AAMW     TCGA-XF-AAMX     TCGA-XF-AAMY     TCGA-XF-AAMZ 
"RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" 
    TCGA-XF-AAN0     TCGA-XF-AAN1     TCGA-XF-AAN2     TCGA-XF-AAN3 
"RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" 
    TCGA-XF-AAN4     TCGA-XF-AAN5     TCGA-XF-AAN7     TCGA-XF-AAN8 
"RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" 
    TCGA-YF-AA3L     TCGA-YF-AA3M 
"RHOA WILD-TYPE" "RHOA WILD-TYPE" 
D21V9, continuous
D21V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RHOA MUTATED       1                         1    15
  RHOA WILD-TYPE    37                        20   286
D21V11, multiclass
                           clus
vv                          RHOA MUTATED RHOA WILD-TYPE
  ASIAN                                1             37
  BLACK OR AFRICAN AMERICAN            1             20
  WHITE                               15            286
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V12, binary
                cls
clus               0   1
  RHOA MUTATED     1  14
  RHOA WILD-TYPE   7 324
[1] "tbl2"
                cls
clus             [,1] [,2]
  RHOA MUTATED      1   14
  RHOA WILD-TYPE    7  324
                        clus
vv                       RHOA MUTATED RHOA WILD-TYPE
  HISPANIC OR LATINO                1              7
  NOT HISPANIC OR LATINO           14            324
[1] 2 2
[1] FALSE

Clustering(22) Variable = PTEN MUTATION ANALYSIS
D22V1, survival
                sevent
clus2              0   1
  PTEN MUTATED     8   5
  PTEN WILD-TYPE 211 146
  PTEN MUTATED PTEN WILD-TYPE 
            13            357 
  PTEN MUTATED PTEN WILD-TYPE 
             5            146 
$`PTEN MUTATED`
TCGA-BL-A5ZZ TCGA-DK-A2I6 TCGA-DK-A3IN TCGA-DK-A3WW TCGA-FJ-A871 TCGA-G2-A2EL 
       12.39        87.32         8.22        20.81         8.94        26.93 
TCGA-G2-A3VY TCGA-G2-AA3D TCGA-GV-A40E TCGA-LT-A5Z6 TCGA-UY-A78L TCGA-UY-A9PE 
       17.62        64.44         8.58        15.58        37.05         4.54 
TCGA-XF-AAMF 
       10.82 

$`PTEN WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        91.63       103.50       105.70         8.35 
TCGA-4Z-AA7M TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7S 
       16.27        44.94        16.83        16.77        17.16        34.98 
TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 
       27.62        49.12         0.62        41.75        51.16        66.54 
TCGA-4Z-AA84 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BL-A13I 
       15.12        10.22        47.80        33.83        40.08         7.33 
TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N 
        2.66         6.74         6.58        13.15        19.04        32.84 
TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U 
       12.16        17.88        19.50         5.06        14.89        14.96 
TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A2LD 
        5.06         8.35         8.25        17.16        16.18        20.48 
TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E 
        4.67        12.82         9.96        17.56        28.70        24.26 
TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-C4-A0F6 TCGA-C4-A0F7 
       28.41         8.98         1.94         2.93        23.01         2.04 
TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V 
        0.46         0.43         0.69        10.95        12.66        12.46 
TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 
       12.10        12.62        12.26        13.12        12.00        12.10 
TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ 
       11.87        13.08        12.92         4.90         7.20         5.46 
TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 
        5.19        16.31         1.84        13.58        21.86         2.14 
TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD 
       66.41        18.41        19.00        16.70       130.88       112.44 
TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 
       16.14        17.62        15.62         1.81        10.59         7.79 
TCGA-DK-A2I4 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IQ TCGA-DK-A3IS 
      123.85         2.20        13.58         7.82        17.72        50.27 
TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 
       21.30        23.21         9.67        10.55       140.81        48.00 
TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 
       17.98        64.18        41.56        76.60        67.36        15.68 
TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6S 
       41.06        30.67        38.24        15.02        13.58       166.03 
TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA74 
       12.36        10.49         8.65         7.53        13.64        43.50 
TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 
       12.03        10.62        43.59        15.35        38.83        24.66 
TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KE 
        0.10         0.49         2.24        16.70        17.39         0.56 
TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DU 
        0.66        14.56        13.97        12.99        14.33         0.92 
TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A97P TCGA-E7-A97Q 
        1.22        13.68        14.07        12.95        14.37         8.09 
TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 
       32.02        16.77         8.94        33.04         4.01        12.62 
TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM 
       22.52        27.98        60.66        24.30        23.41        17.98 
TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS 
       29.16         5.52        25.74        46.78        19.79        12.85 
TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BR 
       22.98        27.35        14.96        20.91         3.62        26.73 
TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY 
       53.88        11.01        19.33         5.36         5.69         8.25 
TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P 
       27.45        18.08        58.92         2.70         7.10         6.28 
TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE 
       13.35        62.86        18.81         6.15        12.69        12.36 
TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z7 
        2.27         3.06         4.31         9.67        10.85        31.07 
TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EC 
        7.13        10.65        17.23         3.25         6.48        22.88 
TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB 
       61.94        30.61        15.95        35.24        33.01         7.23 
TCGA-G2-A3IE TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 
       20.12        66.02         6.94        19.46        21.40         2.24 
TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS 
       15.81         4.50        15.91        14.07        17.75        24.92 
TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS 
        8.94        13.91         7.73         2.10         3.12        20.98 
TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 
        2.20         7.36        10.92        11.31        11.31         7.63 
TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATO TCGA-GU-AATP 
       27.09        20.05         5.62         4.73        10.65        32.98 
TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF 
        7.00        14.27        21.34        19.10        19.82        20.28 
TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO 
        8.48        10.59        27.35        19.07        22.72         1.51 
TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS 
       19.40        38.60         3.06         9.01         8.22        25.02 
TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RH 
        3.45        21.24         2.76         9.14        27.68         9.07 
TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO 
       11.70         1.74         1.81        15.42         6.38        11.80 
TCGA-LC-A66R TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX 
       15.32        13.48        12.23        16.67        14.24         1.84 
TCGA-S5-AA26 TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78M TCGA-UY-A78N 
        3.75        12.43        31.56        17.62        22.68        86.83 
TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PF 
       76.01        65.75        35.24        29.56        17.82         1.64 
TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SJ 
        1.87        17.88        48.62        64.80        79.66         3.22 
TCGA-XF-A9SL TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ 
       66.41        12.76        11.90        23.64        21.04        28.24 
TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 
       26.27        18.90         2.24        16.27        66.64         2.10 
TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMG TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML 
       13.74        92.98       110.60        11.31        54.90         7.63 
TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAMY 
       71.57        91.73         2.96         8.32         6.77        98.99 
TCGA-XF-AAMZ TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN4 
       44.32        56.48        30.94        61.45        86.30        27.06 
TCGA-XF-AAN5 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L 
       75.39        18.81         3.88         9.63         0.66        11.97 
TCGA-YF-AA3M TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R4 
       13.64        18.64         7.36        21.11        24.13        30.28 
TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RE 
       27.19        21.86        28.41        74.56        13.41         3.48 
TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N 
       52.73        52.60        82.49        47.84        20.22         2.89 
TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA4X 
       34.06        19.69         8.61        59.38        60.16        63.02 
TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 
       38.73        35.41        57.90        19.40         8.52        47.15 
TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-ZF-AA5P 
       19.17         5.52        10.13 

  PTEN MUTATED PTEN WILD-TYPE 
          4.54           0.10 
  PTEN MUTATED PTEN WILD-TYPE 
         87.32         166.03 
  PTEN MUTATED PTEN WILD-TYPE 
         15.58          15.68 
[1] "4.5 - 87.3 (15.6)"  "0.1 - 166.0 (15.7)"
[1] "hr=" "1.1"
D22V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  PTEN MUTATED         0        4         4        5
  PTEN WILD-TYPE       4      113       118      123
D22V3, multiclass
           clus
vv          PTEN MUTATED PTEN WILD-TYPE
  STAGE I              0              4
  STAGE II             4            113
  STAGE III            4            118
  STAGE IV             5            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"
                vv
clus             T0+T1+T2  T3  T4
  PTEN MUTATED          2   3   3
  PTEN WILD-TYPE      112 176  49
D22V4, multiclass
          clus
vv         PTEN MUTATED PTEN WILD-TYPE
  T0+T1+T2            2            112
  T3                  3            176
  T4                  3             49
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  PTEN MUTATED     4   2   3   0
  PTEN WILD-TYPE 209  39  72   8
D22V5, multiclass
    clus
vv   PTEN MUTATED PTEN WILD-TYPE
  N0            4            209
  N1            2             39
  N2            3             72
  N3            0              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"
D22V6, binary
                cls
clus               0   1
  PTEN MUTATED     5   0
  PTEN WILD-TYPE 177  10
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTEN MUTATED      5    0
  PTEN WILD-TYPE  177   10
   clus
vv  PTEN MUTATED PTEN WILD-TYPE
  0            5            177
  1            0             10
[1] 2 2
[1] FALSE
D22V7, binary
                cls
clus               0   1
  PTEN MUTATED     1  12
  PTEN WILD-TYPE  95 268
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTEN MUTATED      1   12
  PTEN WILD-TYPE   95  268
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  FEMALE            1             95
  MALE             12            268
[1] 2 2
[1] FALSE
D22V8, continuous
D22V9, continuous
D22V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PTEN MUTATED       1                         0    12
  PTEN WILD-TYPE    37                        21   289
D22V11, multiclass
                           clus
vv                          PTEN MUTATED PTEN WILD-TYPE
  ASIAN                                1             37
  BLACK OR AFRICAN AMERICAN            0             21
  WHITE                               12            289
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V12, binary
                cls
clus               0   1
  PTEN MUTATED     0  13
  PTEN WILD-TYPE   8 325
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTEN MUTATED      0   13
  PTEN WILD-TYPE    8  325
                        clus
vv                       PTEN MUTATED PTEN WILD-TYPE
  HISPANIC OR LATINO                0              8
  NOT HISPANIC OR LATINO           13            325
[1] 2 2
[1] FALSE

Clustering(23) Variable = C3ORF70 MUTATION ANALYSIS
D23V1, survival
                   sevent
clus2                 0   1
  C3ORF70 MUTATED    12   5
  C3ORF70 WILD-TYPE 207 146
  C3ORF70 MUTATED C3ORF70 WILD-TYPE 
               17               353 
  C3ORF70 MUTATED C3ORF70 WILD-TYPE 
                5               146 
$`C3ORF70 MUTATED`
TCGA-4Z-AA81 TCGA-BT-A0YX TCGA-DK-A1AD TCGA-DK-A2I4 TCGA-DK-A3IS TCGA-DK-A6AW 
       41.75        13.15       112.44       123.85        50.27        41.56 
TCGA-FD-A6TB TCGA-G2-A2EO TCGA-GU-A42Q TCGA-H4-A2HQ TCGA-K4-A5RJ TCGA-PQ-A6FI 
       18.81        35.24        11.31        19.40         1.74        12.23 
TCGA-UY-A9PF TCGA-XF-AAML TCGA-XF-AAN5 TCGA-ZF-A9R7 TCGA-ZF-A9RC 
        1.64         7.63        75.39        21.86        74.56 

$`C3ORF70 WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        91.63       103.50       105.70         8.35 
TCGA-4Z-AA7M TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7S 
       16.27        44.94        16.83        16.77        17.16        34.98 
TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA84 
       27.62        49.12         0.62        51.16        66.54        15.12 
TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J 
       10.22        47.80        33.83        40.08         7.33         2.66 
TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O 
        6.74        12.39         6.58        19.04        32.84        12.16 
TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20V 
       17.88        19.50         5.06        14.89        14.96         5.06 
TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH 
        8.35         8.25        17.16        16.18        20.48         4.67 
TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E TCGA-BT-A42F 
       12.82         9.96        17.56        28.70        24.26        28.41 
TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-C4-A0F6 TCGA-C4-A0F7 TCGA-CF-A1HR 
        8.98         1.94         2.93        23.01         2.04         0.46 
TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W 
        0.43         0.69        10.95        12.66        12.46        12.10 
TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A9FF 
       12.62        12.26        13.12        12.00        12.10        11.87 
TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3QU 
       13.08        12.92         4.90         7.20         5.46         5.19 
TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 
       16.31         1.84        13.58        21.86         2.14        66.41 
TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AE TCGA-DK-A1AF 
       18.41        19.00        16.70       130.88        16.14        17.62 
TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I6 TCGA-DK-A3IK 
       15.62         1.81        10.59         7.79        87.32         2.20 
TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IT TCGA-DK-A3IU 
       13.58         7.82         8.22        17.72        21.30        23.21 
TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A3X2 
        9.67        20.81        10.55       140.81        48.00        17.98 
TCGA-DK-A6AV TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 
       64.18        76.60        67.36        15.68        41.06        30.67 
TCGA-DK-AA6L TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6U 
       38.24        15.02        13.58       166.03        12.36        10.49 
TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA76 TCGA-DK-AA77 
        8.65         7.53        13.64        43.50        12.03        10.62 
TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ 
       43.59        15.35        38.83        24.66         0.10         0.49 
TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 
        2.24        16.70        17.39         0.56         0.66        14.56 
TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7DV TCGA-E7-A7PW 
       13.97        12.99        14.33         0.92         1.22        13.68 
TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 
       14.07        12.95        14.37         8.09        32.02        16.77 
TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 
        8.94        33.04         4.01        12.62        22.52        27.98 
TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO 
       60.66        24.30        23.41        17.98        29.16         5.52 
TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P 
       25.74        46.78        19.79        12.85        22.98        27.35 
TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT 
       14.96        20.91         3.62        26.73        53.88        11.01 
TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 
       19.33         5.36         5.69         8.25        27.45        18.08 
TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA 
       58.92         2.70         7.10         6.28        13.35        62.86 
TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH 
        6.15        12.69        12.36         2.27         3.06         4.31 
TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF 
        9.67        10.85        31.07         7.13        10.65        17.23 
TCGA-FJ-A871 TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EC TCGA-G2-A2EF TCGA-G2-A2EJ 
        8.94         3.25         6.48        22.88        61.94        30.61 
TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY 
       15.95        26.93        33.01         7.23        20.12        17.62 
TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 
       66.02         6.94        64.44        19.46        21.40         2.24 
TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS 
       15.81         4.50        15.91        14.07        17.75        24.92 
TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS 
        8.94        13.91         7.73         2.10         3.12        20.98 
TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 
        2.20         7.36        10.92        11.31         7.63        27.09 
TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATO TCGA-GU-AATP TCGA-GU-AATQ 
       20.05         5.62         4.73        10.65        32.98         7.00 
TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH 
       14.27        21.34        19.10        19.82        20.28         8.48 
TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO 
       10.59        27.35         8.58        19.07        22.72         1.51 
TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU 
       38.60         3.06         9.01         8.22        25.02         3.45 
TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RH TCGA-K4-A5RI 
       21.24         2.76         9.14        27.68         9.07        11.70 
TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO TCGA-LC-A66R TCGA-LT-A5Z6 
        1.81        15.42         6.38        11.80        15.32        15.58 
TCGA-MV-A51V TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 TCGA-SY-A9G0 
       13.48        16.67        14.24         1.84         3.75        12.43 
TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78N TCGA-UY-A78O 
       31.56        17.62        37.05        22.68        86.83        76.01 
TCGA-UY-A8OB TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE TCGA-XF-A8HH 
       65.75        35.24        29.56        17.82         4.54         1.87 
TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SL 
       17.88        48.62        64.80        79.66         3.22        66.41 
TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T0 
       12.76        11.90        23.64        21.04        28.24        26.27 
TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 
       18.90         2.24        16.27        66.64         2.10        13.74 
TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMG TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAMQ 
       92.98        10.82       110.60        11.31        54.90        71.57 
TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAMZ 
       91.73         2.96         8.32         6.77        98.99        44.32 
TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN7 
       56.48        30.94        61.45        86.30        27.06        18.81 
TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R0 
        3.88         9.63         0.66        11.97        13.64        18.64 
TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R9 
        7.36        21.11        24.13        30.28        27.19        28.41 
TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-A9RM 
       13.41         3.48        52.73        52.60        82.49        47.84 
TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4U TCGA-ZF-AA4V 
       20.22         2.89        34.06        19.69         8.61        59.38 
TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA53 TCGA-ZF-AA54 
       60.16        63.02        38.73        35.41        57.90        19.40 
TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-ZF-AA5P 
        8.52        47.15        19.17         5.52        10.13 

  C3ORF70 MUTATED C3ORF70 WILD-TYPE 
             1.64              0.10 
  C3ORF70 MUTATED C3ORF70 WILD-TYPE 
           123.85            166.03 
  C3ORF70 MUTATED C3ORF70 WILD-TYPE 
            21.86             15.42 
[1] "1.6 - 123.8 (21.9)" "0.1 - 166.0 (15.4)"
[1] "hr=" "2"  
D23V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  C3ORF70 MUTATED         0        7         7        3
  C3ORF70 WILD-TYPE       4      110       115      125
D23V3, multiclass
           clus
vv          C3ORF70 MUTATED C3ORF70 WILD-TYPE
  STAGE I                 0                 4
  STAGE II                7               110
  STAGE III               7               115
  STAGE IV                3               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"
                   vv
clus                T0+T1+T2  T3  T4
  C3ORF70 MUTATED          6   9   0
  C3ORF70 WILD-TYPE      108 170  52
D23V4, multiclass
          clus
vv         C3ORF70 MUTATED C3ORF70 WILD-TYPE
  T0+T1+T2               6               108
  T3                     9               170
  T4                     0                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"
                   vv
clus                 N0  N1  N2  N3
  C3ORF70 MUTATED    13   0   2   0
  C3ORF70 WILD-TYPE 200  41  73   8
D23V5, multiclass
    clus
vv   C3ORF70 MUTATED C3ORF70 WILD-TYPE
  N0              13               200
  N1               0                41
  N2               2                73
  N3               0                 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"
D23V6, binary
                   cls
clus                  0   1
  C3ORF70 MUTATED     9   1
  C3ORF70 WILD-TYPE 173   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C3ORF70 MUTATED      9    1
  C3ORF70 WILD-TYPE  173    9
   clus
vv  C3ORF70 MUTATED C3ORF70 WILD-TYPE
  0               9               173
  1               1                 9
[1] 2 2
[1] FALSE
D23V7, binary
                   cls
clus                  0   1
  C3ORF70 MUTATED     4  13
  C3ORF70 WILD-TYPE  92 267
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C3ORF70 MUTATED      4   13
  C3ORF70 WILD-TYPE   92  267
        clus
vv       C3ORF70 MUTATED C3ORF70 WILD-TYPE
  FEMALE               4                92
  MALE                13               267
[1] 2 2
[1] FALSE
D23V8, continuous
D23V9, continuous
D23V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  C3ORF70 MUTATED       0                         1    16
  C3ORF70 WILD-TYPE    38                        20   285
D23V11, multiclass
                           clus
vv                          C3ORF70 MUTATED C3ORF70 WILD-TYPE
  ASIAN                                   0                38
  BLACK OR AFRICAN AMERICAN               1                20
  WHITE                                  16               285
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V12, binary
                   cls
clus                  0   1
  C3ORF70 MUTATED     0  15
  C3ORF70 WILD-TYPE   8 323
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C3ORF70 MUTATED      0   15
  C3ORF70 WILD-TYPE    8  323
                        clus
vv                       C3ORF70 MUTATED C3ORF70 WILD-TYPE
  HISPANIC OR LATINO                   0                 8
  NOT HISPANIC OR LATINO              15               323
[1] 2 2
[1] FALSE

Clustering(24) Variable = RBM10 MUTATION ANALYSIS
D24V1, survival
                 sevent
clus2               0   1
  RBM10 MUTATED    12   9
  RBM10 WILD-TYPE 207 142
  RBM10 MUTATED RBM10 WILD-TYPE 
             21             349 
  RBM10 MUTATED RBM10 WILD-TYPE 
              9             142 
$`RBM10 MUTATED`
TCGA-2F-A9KT TCGA-BL-A13J TCGA-BT-A20V TCGA-C4-A0F1 TCGA-CU-A72E TCGA-DK-A2HX 
      105.70         2.66         5.06         2.93        13.58         1.81 
TCGA-DK-A3IN TCGA-DK-A6AW TCGA-DK-AA76 TCGA-E5-A4TZ TCGA-E7-A5KE TCGA-FD-A3NA 
        8.22        41.56        12.03        15.35         0.56        60.66 
TCGA-FD-A62O TCGA-FD-A6TA TCGA-FD-A6TK TCGA-GU-A42P TCGA-HQ-A5NE TCGA-K4-A4AB 
        7.10        62.86        10.85        10.92         8.22         2.76 
TCGA-UY-A9PF TCGA-XF-A9SZ TCGA-ZF-AA53 
        1.64        28.24        57.90 

$`RBM10 WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KW TCGA-4Z-AA7M 
       22.29        11.97        91.63       103.50         8.35        16.27 
TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7W 
       44.94        16.83        16.77        17.16        34.98        27.62 
TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA84 
       49.12         0.62        41.75        51.16        66.54        15.12 
TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A3JM 
       10.22        47.80        33.83        40.08         7.33         6.74 
TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O 
       12.39         6.58        13.15        19.04        32.84        12.16 
TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20W 
       17.88        19.50         5.06        14.89        14.96         8.35 
TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PJ 
        8.25        17.16        16.18        20.48         4.67        12.82 
TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ 
        9.96        17.56        28.70        24.26        28.41         8.98 
TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-C4-A0F7 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C 
        1.94        23.01         2.04         0.46         0.43         0.69 
TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y 
       10.95        12.66        12.46        12.10        12.62        12.26 
TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A0YN 
       13.12        12.00        12.10        11.87        13.08        12.92 
TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 
        4.90         7.20         5.46         5.19        16.31         1.84 
TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB 
       21.86         2.14        66.41        18.41        19.00        16.70 
TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I1 
      130.88       112.44        16.14        17.62        15.62        10.59 
TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM 
        7.79       123.85        87.32         2.20        13.58         7.82 
TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW 
       17.72        50.27        21.30        23.21         9.67        20.81 
TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6B0 
       10.55       140.81        48.00        17.98        64.18        76.60 
TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6P 
       67.36        15.68        41.06        30.67        38.24        15.02 
TCGA-DK-AA6Q TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA6X 
       13.58       166.03        12.36        10.49         8.65         7.53 
TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA77 TCGA-E5-A2PC TCGA-E5-A4U1 TCGA-E7-A3X6 
       13.64        43.50        10.62        43.59        38.83        24.66 
TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KF 
        0.10         0.49         2.24        16.70        17.39         0.66 
TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7DV 
       14.56        13.97        12.99        14.33         0.92         1.22 
TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B3 
       13.68        14.07        12.95        14.37         8.09        32.02 
TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 
       16.77         8.94        33.04         4.01        12.62        22.52 
TCGA-FD-A3N6 TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO 
       27.98        24.30        23.41        17.98        29.16         5.52 
TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P 
       25.74        46.78        19.79        12.85        22.98        27.35 
TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT 
       14.96        20.91         3.62        26.73        53.88        11.01 
TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 
       19.33         5.36         5.69         8.25        27.45        18.08 
TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TB TCGA-FD-A6TC 
       58.92         2.70         6.28        13.35        18.81         6.15 
TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI 
       12.69        12.36         2.27         3.06         4.31         9.67 
TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FJ-A871 TCGA-FT-A3EE 
       31.07         7.13        10.65        17.23         8.94         3.25 
TCGA-FT-A61P TCGA-G2-A2EC TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL 
        6.48        22.88        61.94        30.61        15.95        26.93 
TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B 
       35.24        33.01         7.23        20.12        17.62        66.02 
TCGA-G2-AA3C TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO 
        6.94        64.44        19.46        21.40         2.24        15.81 
TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A6I1 
        4.50        15.91        14.07        17.75        24.92         8.94 
TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 
       13.91         7.73         2.10         3.12        20.98         2.20 
TCGA-GD-A76B TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A764 
        7.36        11.31        11.31         7.63        27.09        20.05 
TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATO TCGA-GU-AATP TCGA-GU-AATQ TCGA-GV-A3JV 
        5.62         4.73        10.65        32.98         7.00        14.27 
TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI 
       21.34        19.10        19.82        20.28         8.48        10.59 
TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-H4-A2HQ 
       27.35         8.58        19.07        22.72         1.51        19.40 
TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV 
       38.60         3.06         9.01        25.02         3.45        21.24 
TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ 
        9.14        27.68         9.07        11.70         1.74         1.81 
TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V 
       15.42         6.38        11.80        15.32        15.58        13.48 
TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 TCGA-SY-A9G0 
       12.23        16.67        14.24         1.84         3.75        12.43 
TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78N TCGA-UY-A78O 
       31.56        17.62        37.05        22.68        86.83        76.01 
TCGA-UY-A8OB TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE TCGA-XF-A8HH 
       65.75        35.24        29.56        17.82         4.54         1.87 
TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SL 
       17.88        48.62        64.80        79.66         3.22        66.41 
TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9T0 TCGA-XF-A9T2 
       12.76        11.90        23.64        21.04        26.27        18.90 
TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAME 
        2.24        16.27        66.64         2.10        13.74        92.98 
TCGA-XF-AAMF TCGA-XF-AAMG TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ 
       10.82       110.60        11.31        54.90         7.63        71.57 
TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAMZ 
       91.73         2.96         8.32         6.77        98.99        44.32 
TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN5 
       56.48        30.94        61.45        86.30        27.06        75.39 
TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-YF-AA3M 
       18.81         3.88         9.63         0.66        11.97        13.64 
TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R5 
       18.64         7.36        21.11        24.13        30.28        27.19 
TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RF 
       21.86        28.41        74.56        13.41         3.48        52.73 
TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4R 
       52.60        82.49        47.84        20.22         2.89        34.06 
TCGA-ZF-AA4T TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA51 
       19.69         8.61        59.38        60.16        63.02        38.73 
TCGA-ZF-AA52 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N 
       35.41        19.40         8.52        47.15        19.17         5.52 
TCGA-ZF-AA5P 
       10.13 

  RBM10 MUTATED RBM10 WILD-TYPE 
           0.56            0.10 
  RBM10 MUTATED RBM10 WILD-TYPE 
         105.70          166.03 
  RBM10 MUTATED RBM10 WILD-TYPE 
          10.85           16.14 
[1] "0.6 - 105.7 (10.8)" "0.1 - 166.0 (16.1)"
[1] "hr=" "1.3"
D24V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  RBM10 MUTATED         0        6         5       10
  RBM10 WILD-TYPE       4      111       117      118
D24V3, multiclass
           clus
vv          RBM10 MUTATED RBM10 WILD-TYPE
  STAGE I               0               4
  STAGE II              6             111
  STAGE III             5             117
  STAGE IV             10             118
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1+T2  T3  T4
  RBM10 MUTATED          5  10   5
  RBM10 WILD-TYPE      109 169  47
D24V4, multiclass
          clus
vv         RBM10 MUTATED RBM10 WILD-TYPE
  T0+T1+T2             5             109
  T3                  10             169
  T4                   5              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"
                 vv
clus               N0  N1  N2  N3
  RBM10 MUTATED    10   1   9   0
  RBM10 WILD-TYPE 203  40  66   8
D24V5, multiclass
    clus
vv   RBM10 MUTATED RBM10 WILD-TYPE
  N0            10             203
  N1             1              40
  N2             9              66
  N3             0               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"
D24V6, binary
                 cls
clus                0   1
  RBM10 MUTATED    13   0
  RBM10 WILD-TYPE 169  10
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBM10 MUTATED     13    0
  RBM10 WILD-TYPE  169   10
   clus
vv  RBM10 MUTATED RBM10 WILD-TYPE
  0            13             169
  1             0              10
[1] 2 2
[1] FALSE
D24V7, binary
                 cls
clus                0   1
  RBM10 MUTATED     4  17
  RBM10 WILD-TYPE  92 263
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBM10 MUTATED      4   17
  RBM10 WILD-TYPE   92  263
        clus
vv       RBM10 MUTATED RBM10 WILD-TYPE
  FEMALE             4              92
  MALE              17             263
[1] 2 2
[1] FALSE
D24V8, continuous
D24V9, continuous
D24V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RBM10 MUTATED       1                         1    17
  RBM10 WILD-TYPE    37                        20   284
D24V11, multiclass
                           clus
vv                          RBM10 MUTATED RBM10 WILD-TYPE
  ASIAN                                 1              37
  BLACK OR AFRICAN AMERICAN             1              20
  WHITE                                17             284
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V12, binary
                 cls
clus                0   1
  RBM10 MUTATED     0  19
  RBM10 WILD-TYPE   8 319
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBM10 MUTATED      0   19
  RBM10 WILD-TYPE    8  319
                        clus
vv                       RBM10 MUTATED RBM10 WILD-TYPE
  HISPANIC OR LATINO                 0               8
  NOT HISPANIC OR LATINO            19             319
[1] 2 2
[1] FALSE

Clustering(25) Variable = PSIP1 MUTATION ANALYSIS
D25V1, survival
                 sevent
clus2               0   1
  PSIP1 MUTATED    12   7
  PSIP1 WILD-TYPE 207 144
  PSIP1 MUTATED PSIP1 WILD-TYPE 
             19             351 
  PSIP1 MUTATED PSIP1 WILD-TYPE 
              7             144 
$`PSIP1 MUTATED`
TCGA-2F-A9KT TCGA-4Z-AA80 TCGA-BT-A2LB TCGA-CF-A27C TCGA-DK-A1AG TCGA-DK-A3IS 
      105.70         0.62        16.18         0.69        15.62        50.27 
TCGA-DK-A6AW TCGA-DK-AA6W TCGA-E5-A4U1 TCGA-E7-A5KF TCGA-FD-A3SO TCGA-FD-A3SS 
       41.56         8.65        38.83         0.66         5.52        12.85 
TCGA-FD-A5BR TCGA-FD-A6TC TCGA-G2-A3VY TCGA-MV-A51V TCGA-UY-A78M TCGA-XF-A9SV 
       26.73         6.15        17.62        13.48        22.68        12.76 
TCGA-XF-AAML 
        7.63 

$`PSIP1 WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KW TCGA-4Z-AA7M 
       22.29        11.97        91.63       103.50         8.35        16.27 
TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7W 
       44.94        16.83        16.77        17.16        34.98        27.62 
TCGA-4Z-AA7Y TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA84 TCGA-4Z-AA86 
       49.12        41.75        51.16        66.54        15.12        10.22 
TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM 
       47.80        33.83        40.08         7.33         2.66         6.74 
TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O 
       12.39         6.58        13.15        19.04        32.84        12.16 
TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20V 
       17.88        19.50         5.06        14.89        14.96         5.06 
TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PJ 
        8.35         8.25        17.16        20.48         4.67        12.82 
TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ 
        9.96        17.56        28.70        24.26        28.41         8.98 
TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-C4-A0F6 TCGA-C4-A0F7 TCGA-CF-A1HR TCGA-CF-A1HS 
        1.94         2.93        23.01         2.04         0.46         0.43 
TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y 
       10.95        12.66        12.46        12.10        12.62        12.26 
TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A0YN 
       13.12        12.00        12.10        11.87        13.08        12.92 
TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 
        4.90         7.20         5.46         5.19        16.31         1.84 
TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA 
       13.58        21.86         2.14        66.41        18.41        19.00 
TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A2HX 
       16.70       130.88       112.44        16.14        17.62         1.81 
TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL 
       10.59         7.79       123.85        87.32         2.20        13.58 
TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV 
        7.82         8.22        17.72        21.30        23.21         9.67 
TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV 
       20.81        10.55       140.81        48.00        17.98        64.18 
TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L 
       76.60        67.36        15.68        41.06        30.67        38.24 
TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6X 
       15.02        13.58       166.03        12.36        10.49         7.53 
TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A2PC TCGA-E5-A4TZ 
       13.64        43.50        12.03        10.62        43.59        15.35 
TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 
       24.66         0.10         0.49         2.24        16.70        17.39 
TCGA-E7-A5KE TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DU 
        0.56        14.56        13.97        12.99        14.33         0.92 
TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A97P TCGA-E7-A97Q 
        1.22        13.68        14.07        12.95        14.37         8.09 
TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 
       32.02        16.77         8.94        33.04         4.01        12.62 
TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM 
       22.52        27.98        60.66        24.30        23.41        17.98 
TCGA-FD-A3SN TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A43N TCGA-FD-A43P 
       29.16        25.74        46.78        19.79        22.98        27.35 
TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU 
       14.96        20.91         3.62        53.88        11.01        19.33 
TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 
        5.36         5.69         8.25        27.45        18.08        58.92 
TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB 
        2.70         7.10         6.28        13.35        62.86        18.81 
TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI 
       12.69        12.36         2.27         3.06         4.31         9.67 
TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FJ-A871 
       10.85        31.07         7.13        10.65        17.23         8.94 
TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EC TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK 
        3.25         6.48        22.88        61.94        30.61        15.95 
TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3B 
       26.93        35.24        33.01         7.23        20.12        66.02 
TCGA-G2-AA3C TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO 
        6.94        64.44        19.46        21.40         2.24        15.81 
TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A6I1 
        4.50        15.91        14.07        17.75        24.92         8.94 
TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 
       13.91         7.73         2.10         3.12        20.98         2.20 
TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 
        7.36        10.92        11.31        11.31         7.63        27.09 
TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATO TCGA-GU-AATP TCGA-GU-AATQ 
       20.05         5.62         4.73        10.65        32.98         7.00 
TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH 
       14.27        21.34        19.10        19.82        20.28         8.48 
TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO 
       10.59        27.35         8.58        19.07        22.72         1.51 
TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS 
       19.40        38.60         3.06         9.01         8.22        25.02 
TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RH 
        3.45        21.24         2.76         9.14        27.68         9.07 
TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO 
       11.70         1.74         1.81        15.42         6.38        11.80 
TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX 
       15.32        15.58        12.23        16.67        14.24         1.84 
TCGA-S5-AA26 TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78N 
        3.75        12.43        31.56        17.62        37.05        86.83 
TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE 
       76.01        65.75        35.24        29.56        17.82         4.54 
TCGA-UY-A9PF TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI 
        1.64         1.87        17.88        48.62        64.80        79.66 
TCGA-XF-A9SJ TCGA-XF-A9SL TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ 
        3.22        66.41        11.90        23.64        21.04        28.24 
TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 
       26.27        18.90         2.24        16.27        66.64         2.10 
TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMG TCGA-XF-AAMH TCGA-XF-AAMJ 
       13.74        92.98        10.82       110.60        11.31        54.90 
TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAMY 
       71.57        91.73         2.96         8.32         6.77        98.99 
TCGA-XF-AAMZ TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN4 
       44.32        56.48        30.94        61.45        86.30        27.06 
TCGA-XF-AAN5 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L 
       75.39        18.81         3.88         9.63         0.66        11.97 
TCGA-YF-AA3M TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R4 
       13.64        18.64         7.36        21.11        24.13        30.28 
TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RE 
       27.19        21.86        28.41        74.56        13.41         3.48 
TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N 
       52.73        52.60        82.49        47.84        20.22         2.89 
TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA4X 
       34.06        19.69         8.61        59.38        60.16        63.02 
TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 
       38.73        35.41        57.90        19.40         8.52        47.15 
TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-ZF-AA5P 
       19.17         5.52        10.13 

  PSIP1 MUTATED PSIP1 WILD-TYPE 
           0.62            0.10 
  PSIP1 MUTATED PSIP1 WILD-TYPE 
         105.70          166.03 
  PSIP1 MUTATED PSIP1 WILD-TYPE 
          13.48           15.81 
[1] "0.6 - 105.7 (13.5)" "0.1 - 166.0 (15.8)"
[1] "hr=" "1"  
D25V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  PSIP1 MUTATED         0       10         4        4
  PSIP1 WILD-TYPE       4      107       118      124
D25V3, multiclass
           clus
vv          PSIP1 MUTATED PSIP1 WILD-TYPE
  STAGE I               0               4
  STAGE II             10             107
  STAGE III             4             118
  STAGE IV              4             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"
                 vv
clus              T0+T1+T2  T3  T4
  PSIP1 MUTATED         10   5   3
  PSIP1 WILD-TYPE      104 174  49
D25V4, multiclass
          clus
vv         PSIP1 MUTATED PSIP1 WILD-TYPE
  T0+T1+T2            10             104
  T3                   5             174
  T4                   3              49
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  PSIP1 MUTATED    14   1   2   1
  PSIP1 WILD-TYPE 199  40  73   7
D25V5, multiclass
    clus
vv   PSIP1 MUTATED PSIP1 WILD-TYPE
  N0            14             199
  N1             1              40
  N2             2              73
  N3             1               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"
D25V6, binary
                 cls
clus                0   1
  PSIP1 MUTATED    11   1
  PSIP1 WILD-TYPE 171   9
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PSIP1 MUTATED     11    1
  PSIP1 WILD-TYPE  171    9
   clus
vv  PSIP1 MUTATED PSIP1 WILD-TYPE
  0            11             171
  1             1               9
[1] 2 2
[1] FALSE
D25V7, binary
                 cls
clus                0   1
  PSIP1 MUTATED     3  16
  PSIP1 WILD-TYPE  93 264
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PSIP1 MUTATED      3   16
  PSIP1 WILD-TYPE   93  264
        clus
vv       PSIP1 MUTATED PSIP1 WILD-TYPE
  FEMALE             3              93
  MALE              16             264
[1] 2 2
[1] FALSE
D25V8, continuous
D25V9, continuous
D25V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PSIP1 MUTATED       4                         0    14
  PSIP1 WILD-TYPE    34                        21   287
D25V11, multiclass
                           clus
vv                          PSIP1 MUTATED PSIP1 WILD-TYPE
  ASIAN                                 4              34
  BLACK OR AFRICAN AMERICAN             0              21
  WHITE                                14             287
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V12, binary
                 cls
clus                0   1
  PSIP1 MUTATED     0  18
  PSIP1 WILD-TYPE   8 320
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PSIP1 MUTATED      0   18
  PSIP1 WILD-TYPE    8  320
                        clus
vv                       PSIP1 MUTATED PSIP1 WILD-TYPE
  HISPANIC OR LATINO                 0               8
  NOT HISPANIC OR LATINO            18             320
[1] 2 2
[1] FALSE

Clustering(26) Variable = ASXL2 MUTATION ANALYSIS
D26V1, survival
                 sevent
clus2               0   1
  ASXL2 MUTATED    22  13
  ASXL2 WILD-TYPE 197 138
  ASXL2 MUTATED ASXL2 WILD-TYPE 
             35             335 
  ASXL2 MUTATED ASXL2 WILD-TYPE 
             13             138 
$`ASXL2 MUTATED`
TCGA-4Z-AA7W TCGA-BT-A0YX TCGA-BT-A20N TCGA-BT-A20T TCGA-CF-A1HR TCGA-CF-A9FF 
       27.62        13.15        32.84        14.89         0.46        11.87 
TCGA-CU-A5W6 TCGA-DK-A1AC TCGA-DK-A6AW TCGA-DK-A6B1 TCGA-E5-A4TZ TCGA-E7-A3X6 
        1.84       130.88        41.56        67.36        15.35        24.66 
TCGA-E7-A7DU TCGA-E7-A7XN TCGA-FD-A3SS TCGA-FD-A5BU TCGA-FD-A5C0 TCGA-FD-A62P 
        0.92        14.07        12.85        19.33        18.08         6.28 
TCGA-FD-A6TC TCGA-G2-AA3B TCGA-GD-A2C5 TCGA-GU-A764 TCGA-GV-A3JZ TCGA-S5-AA26 
        6.15        66.02         7.73        20.05        19.82         3.75 
TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A9PE TCGA-XF-A9T6 TCGA-XF-AAMX TCGA-XF-AAN7 
       31.56        17.62         4.54         2.10         6.77        18.81 
TCGA-ZF-A9RC TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-AA54 TCGA-ZF-AA5N 
       74.56        52.60        82.49        19.40         5.52 

$`ASXL2 WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        91.63       103.50       105.70         8.35 
TCGA-4Z-AA7M TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7S 
       16.27        44.94        16.83        16.77        17.16        34.98 
TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA84 
       49.12         0.62        41.75        51.16        66.54        15.12 
TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J 
       10.22        47.80        33.83        40.08         7.33         2.66 
TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20P 
        6.74        12.39         6.58        19.04        12.16        17.88 
TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X 
       19.50         5.06        14.96         5.06         8.35         8.25 
TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK 
       17.16        16.18        20.48         4.67        12.82         9.96 
TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 
       17.56        28.70        24.26        28.41         8.98         1.94 
TCGA-C4-A0F1 TCGA-C4-A0F6 TCGA-C4-A0F7 TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47S 
        2.93        23.01         2.04         0.43         0.69        10.95 
TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 
       12.66        12.46        12.10        12.62        12.26        13.12 
TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR 
       12.00        12.10        13.08        12.92         4.90         7.20 
TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 
        5.46         5.19        16.31        13.58        21.86         2.14 
TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AD TCGA-DK-A1AE 
       66.41        18.41        19.00        16.70       112.44        16.14 
TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 
       17.62        15.62         1.81        10.59         7.79       123.85 
TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ 
       87.32         2.20        13.58         7.82         8.22        17.72 
TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX 
       50.27        21.30        23.21         9.67        20.81        10.55 
TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6B0 TCGA-DK-A6B2 
      140.81        48.00        17.98        64.18        76.60        15.68 
TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6S 
       41.06        30.67        38.24        15.02        13.58       166.03 
TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA74 
       12.36        10.49         8.65         7.53        13.64        43.50 
TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A2PC TCGA-E5-A4U1 TCGA-E7-A3Y1 TCGA-E7-A4IJ 
       12.03        10.62        43.59        38.83         0.10         0.49 
TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 
        2.24        16.70        17.39         0.56         0.66        14.56 
TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A85H 
       13.97        12.99        14.33         1.22        13.68        12.95 
TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 
       14.37         8.09        32.02        16.77         8.94        33.04 
TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ 
        4.01        12.62        22.52        27.98        60.66        24.30 
TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ 
       23.41        17.98        29.16         5.52        25.74        46.78 
TCGA-FD-A3SR TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X 
       19.79        22.98        27.35        14.96        20.91         3.62 
TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY 
       26.73        53.88        11.01         5.36         5.69         8.25 
TCGA-FD-A5BZ TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TA 
       27.45        58.92         2.70         7.10        13.35        62.86 
TCGA-FD-A6TB TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH 
       18.81        12.69        12.36         2.27         3.06         4.31 
TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF 
        9.67        10.85        31.07         7.13        10.65        17.23 
TCGA-FJ-A871 TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EC TCGA-G2-A2EF TCGA-G2-A2EJ 
        8.94         3.25         6.48        22.88        61.94        30.61 
TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE 
       15.95        26.93        35.24        33.01         7.23        20.12 
TCGA-G2-A3VY TCGA-G2-AA3C TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 
       17.62         6.94        64.44        19.46        21.40         2.24 
TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS 
       15.81         4.50        15.91        14.07        17.75        24.92 
TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 
        8.94        13.91         2.10         3.12        20.98         2.20 
TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 
        7.36        10.92        11.31        11.31         7.63        27.09 
TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATO TCGA-GU-AATP TCGA-GU-AATQ TCGA-GV-A3JV 
        5.62         4.73        10.65        32.98         7.00        14.27 
TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK 
       21.34        19.10        20.28         8.48        10.59        27.35 
TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE 
        8.58        19.07        22.72         1.51        19.40        38.60 
TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV 
        3.06         9.01         8.22        25.02         3.45        21.24 
TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ 
        2.76         9.14        27.68         9.07        11.70         1.74 
TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO TCGA-LC-A66R TCGA-LT-A5Z6 
        1.81        15.42         6.38        11.80        15.32        15.58 
TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX TCGA-SY-A9G0 
       13.48        12.23        16.67        14.24         1.84        12.43 
TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78N TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A9PA 
       37.05        22.68        86.83        76.01        65.75        35.24 
TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PF TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG 
       29.56        17.82         1.64         1.87        17.88        48.62 
TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SL TCGA-XF-A9SV TCGA-XF-A9SW 
       64.80        79.66         3.22        66.41        12.76        11.90 
TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 
       23.64        21.04        28.24        26.27        18.90         2.24 
TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMG 
       16.27        66.64        13.74        92.98        10.82       110.60 
TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMT 
       11.31        54.90         7.63        71.57        91.73         2.96 
TCGA-XF-AAMW TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN2 
        8.32        98.99        44.32        56.48        30.94        61.45 
TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YC-A9TC 
       86.30        27.06        75.39         3.88         9.63         0.66 
TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R3 
       11.97        13.64        18.64         7.36        21.11        24.13 
TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RD TCGA-ZF-A9RE 
       30.28        27.19        21.86        28.41        13.41         3.48 
TCGA-ZF-A9RF TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4R TCGA-ZF-AA4T 
       52.73        47.84        20.22         2.89        34.06        19.69 
TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 
        8.61        59.38        60.16        63.02        38.73        35.41 
TCGA-ZF-AA53 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5P 
       57.90         8.52        47.15        19.17        10.13 

  ASXL2 MUTATED ASXL2 WILD-TYPE 
           0.46            0.10 
  ASXL2 MUTATED ASXL2 WILD-TYPE 
         130.88          166.03 
  ASXL2 MUTATED ASXL2 WILD-TYPE 
          17.62           15.62 
[1] "0.5 - 130.9 (17.6)" "0.1 - 166.0 (15.6)"
[1] "hr=" "1.1"
D26V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  ASXL2 MUTATED         0       10        14       10
  ASXL2 WILD-TYPE       4      107       108      118
D26V3, multiclass
           clus
vv          ASXL2 MUTATED ASXL2 WILD-TYPE
  STAGE I               0               4
  STAGE II             10             107
  STAGE III            14             108
  STAGE IV             10             118
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1+T2  T3  T4
  ASXL2 MUTATED         11  16   6
  ASXL2 WILD-TYPE      103 163  46
D26V4, multiclass
          clus
vv         ASXL2 MUTATED ASXL2 WILD-TYPE
  T0+T1+T2            11             103
  T3                  16             163
  T4                   6              46
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  ASXL2 MUTATED    22   2   5   2
  ASXL2 WILD-TYPE 191  39  70   6
D26V5, multiclass
    clus
vv   ASXL2 MUTATED ASXL2 WILD-TYPE
  N0            22             191
  N1             2              39
  N2             5              70
  N3             2               6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V6, binary
                 cls
clus                0   1
  ASXL2 MUTATED    14   1
  ASXL2 WILD-TYPE 168   9
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ASXL2 MUTATED     14    1
  ASXL2 WILD-TYPE  168    9
   clus
vv  ASXL2 MUTATED ASXL2 WILD-TYPE
  0            14             168
  1             1               9
[1] 2 2
[1] FALSE
D26V7, binary
                 cls
clus                0   1
  ASXL2 MUTATED     9  26
  ASXL2 WILD-TYPE  87 254
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ASXL2 MUTATED      9   26
  ASXL2 WILD-TYPE   87  254
        clus
vv       ASXL2 MUTATED ASXL2 WILD-TYPE
  FEMALE             9              87
  MALE              26             254
[1] 2 2
[1] FALSE
D26V8, continuous
D26V9, continuous
D26V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ASXL2 MUTATED       3                         3    28
  ASXL2 WILD-TYPE    35                        18   273
D26V11, multiclass
                           clus
vv                          ASXL2 MUTATED ASXL2 WILD-TYPE
  ASIAN                                 3              35
  BLACK OR AFRICAN AMERICAN             3              18
  WHITE                                28             273
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V12, binary
                 cls
clus                0   1
  ASXL2 MUTATED     0  32
  ASXL2 WILD-TYPE   8 306
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ASXL2 MUTATED      0   32
  ASXL2 WILD-TYPE    8  306
                        clus
vv                       ASXL2 MUTATED ASXL2 WILD-TYPE
  HISPANIC OR LATINO                 0               8
  NOT HISPANIC OR LATINO            32             306
[1] 2 2
[1] FALSE

Clustering(27) Variable = FAT1 MUTATION ANALYSIS
D27V1, survival
                sevent
clus2              0   1
  FAT1 MUTATED    29  21
  FAT1 WILD-TYPE 190 130
  FAT1 MUTATED FAT1 WILD-TYPE 
            50            320 
  FAT1 MUTATED FAT1 WILD-TYPE 
            21            130 
$`FAT1 MUTATED`
TCGA-2F-A9KO TCGA-BL-A13I TCGA-BT-A20O TCGA-BT-A20U TCGA-BT-A2LB TCGA-BT-A3PK 
       22.29         7.33        12.16        14.96        16.18         9.96 
TCGA-BT-A42B TCGA-CF-A27C TCGA-CU-A3YL TCGA-DK-A1AG TCGA-DK-A3IQ TCGA-DK-A6AV 
       17.56         0.69        16.31        15.62        17.72        64.18 
TCGA-DK-A6B6 TCGA-DK-AA6Q TCGA-DK-AA6S TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A4IJ 
       30.67        13.58       166.03        15.35        38.83         0.49 
TCGA-FD-A3B4 TCGA-FD-A6TK TCGA-G2-A2EJ TCGA-G2-A2EO TCGA-G2-AA3B TCGA-GC-A3WC 
       16.77        10.85        30.61        35.24        66.02        17.75 
TCGA-GC-A6I1 TCGA-GU-A762 TCGA-GU-AATP TCGA-GV-A3QI TCGA-GV-A6ZA TCGA-HQ-A2OF 
        8.94         7.63        32.98        10.59        22.72         3.06 
TCGA-K4-A3WS TCGA-K4-A54R TCGA-S5-AA26 TCGA-XF-A9SG TCGA-XF-A9SX TCGA-XF-A9T8 
       25.02        27.68         3.75        48.62        23.64        13.74 
TCGA-XF-AAME TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMT TCGA-XF-AAN5 TCGA-YC-A9TC 
       92.98         7.63        71.57         2.96        75.39         0.66 
TCGA-YF-AA3L TCGA-ZF-A9RC TCGA-ZF-A9RL TCGA-ZF-A9RN TCGA-ZF-AA4T TCGA-ZF-AA4W 
       11.97        74.56        82.49        20.22        19.69        60.16 
TCGA-ZF-AA53 TCGA-ZF-AA5N 
       57.90         5.52 

$`FAT1 WILD-TYPE`
TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW TCGA-4Z-AA7M 
       11.97        91.63       103.50       105.70         8.35        16.27 
TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7W 
       44.94        16.83        16.77        17.16        34.98        27.62 
TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA84 
       49.12         0.62        41.75        51.16        66.54        15.12 
TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BL-A13J TCGA-BL-A3JM 
       10.22        47.80        33.83        40.08         2.66         6.74 
TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20P 
       12.39         6.58        13.15        19.04        32.84        17.88 
TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X 
       19.50         5.06        14.89         5.06         8.35         8.25 
TCGA-BT-A2LA TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A42C TCGA-BT-A42E 
       17.16        20.48         4.67        12.82        28.70        24.26 
TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-C4-A0F6 TCGA-C4-A0F7 
       28.41         8.98         1.94         2.93        23.01         2.04 
TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W 
        0.46         0.43        10.95        12.66        12.46        12.10 
TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A9FF 
       12.62        12.26        13.12        12.00        12.10        11.87 
TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3QU 
       13.08        12.92         4.90         7.20         5.46         5.19 
TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 
        1.84        13.58        21.86         2.14        66.41        18.41 
TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF 
       19.00        16.70       130.88       112.44        16.14        17.62 
TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK 
        1.81        10.59         7.79       123.85        87.32         2.20 
TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU 
       13.58         7.82         8.22        50.27        21.30        23.21 
TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A3X2 
        9.67        20.81        10.55       140.81        48.00        17.98 
TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-AA6L 
       41.56        76.60        67.36        15.68        41.06        38.24 
TCGA-DK-AA6P TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA71 
       15.02        12.36        10.49         8.65         7.53        13.64 
TCGA-DK-AA74 TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A2PC TCGA-E7-A3X6 TCGA-E7-A3Y1 
       43.50        12.03        10.62        43.59        24.66         0.10 
TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 
        2.24        16.70        17.39         0.56         0.66        14.56 
TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7DV TCGA-E7-A7PW 
       13.97        12.99        14.33         0.92         1.22        13.68 
TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B5 
       14.07        12.95        14.37         8.09        32.02         8.94 
TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA 
       33.04         4.01        12.62        22.52        27.98        60.66 
TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP 
       24.30        23.41        17.98        29.16         5.52        25.74 
TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S 
       46.78        19.79        12.85        22.98        27.35        14.96 
TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU 
       20.91         3.62        26.73        53.88        11.01        19.33 
TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 
        5.36         5.69         8.25        27.45        18.08        58.92 
TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB 
        2.70         7.10         6.28        13.35        62.86        18.81 
TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH 
        6.15        12.69        12.36         2.27         3.06         4.31 
TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FJ-A871 
        9.67        31.07         7.13        10.65        17.23         8.94 
TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EC TCGA-G2-A2EF TCGA-G2-A2EK TCGA-G2-A2EL 
        3.25         6.48        22.88        61.94        15.95        26.93 
TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3C TCGA-G2-AA3D 
       33.01         7.23        20.12        17.62         6.94        64.44 
TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC 
       19.46        21.40         2.24        15.81         4.50        15.91 
TCGA-GC-A3RD TCGA-GC-A3YS TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ 
       14.07        24.92        13.91         7.73         2.10         3.12 
TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R 
       20.98         2.20         7.36        10.92        11.31        11.31 
TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATO TCGA-GU-AATQ 
       27.09        20.05         5.62         4.73        10.65         7.00 
TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH 
       14.27        21.34        19.10        19.82        20.28         8.48 
TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE 
       27.35         8.58        19.07         1.51        19.40        38.60 
TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC 
        9.01         8.22         3.45        21.24         2.76         9.14 
TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P 
        9.07        11.70         1.74         1.81        15.42         6.38 
TCGA-K4-AAQO TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN 
       11.80        15.32        15.58        13.48        12.23        16.67 
TCGA-R3-A69X TCGA-S5-A6DX TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L 
       14.24         1.84        12.43        31.56        17.62        37.05 
TCGA-UY-A78M TCGA-UY-A78N TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A9PA TCGA-UY-A9PB 
       22.68        86.83        76.01        65.75        35.24        29.56 
TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SH 
       17.82         4.54         1.64         1.87        17.88        64.80 
TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SL TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SY 
       79.66         3.22        66.41        12.76        11.90        21.04 
TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T5 
       28.24        26.27        18.90         2.24        16.27        66.64 
TCGA-XF-A9T6 TCGA-XF-AAMF TCGA-XF-AAMG TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAMR 
        2.10        10.82       110.60        11.31        54.90        91.73 
TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN0 TCGA-XF-AAN1 
        8.32         6.77        98.99        44.32        56.48        30.94 
TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 
       61.45        86.30        27.06        18.81         3.88         9.63 
TCGA-YF-AA3M TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R4 
       13.64        18.64         7.36        21.11        24.13        30.28 
TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RF 
       27.19        21.86        28.41        13.41         3.48        52.73 
TCGA-ZF-A9RG TCGA-ZF-A9RM TCGA-ZF-AA4N TCGA-ZF-AA4R TCGA-ZF-AA4U TCGA-ZF-AA4V 
       52.60        47.84         2.89        34.06         8.61        59.38 
TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 
       63.02        38.73        35.41        19.40         8.52        47.15 
TCGA-ZF-AA5H TCGA-ZF-AA5P 
       19.17        10.13 

  FAT1 MUTATED FAT1 WILD-TYPE 
          0.49           0.10 
  FAT1 MUTATED FAT1 WILD-TYPE 
        166.03         140.81 
  FAT1 MUTATED FAT1 WILD-TYPE 
         17.64          15.07 
[1] "0.5 - 166.0 (17.6)" "0.1 - 140.8 (15.1)"
[1] "hr=" "1.1"
D27V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  FAT1 MUTATED         0       17        21       11
  FAT1 WILD-TYPE       4      100       101      117
D27V3, multiclass
           clus
vv          FAT1 MUTATED FAT1 WILD-TYPE
  STAGE I              0              4
  STAGE II            17            100
  STAGE III           21            101
  STAGE IV            11            117
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1+T2  T3  T4
  FAT1 MUTATED         16  25   5
  FAT1 WILD-TYPE       98 154  47
D27V4, multiclass
          clus
vv         FAT1 MUTATED FAT1 WILD-TYPE
  T0+T1+T2           16             98
  T3                 25            154
  T4                  5             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"
                vv
clus              N0  N1  N2  N3
  FAT1 MUTATED    34   3   6   0
  FAT1 WILD-TYPE 179  38  69   8
D27V5, multiclass
    clus
vv   FAT1 MUTATED FAT1 WILD-TYPE
  N0           34            179
  N1            3             38
  N2            6             69
  N3            0              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"
D27V6, binary
                cls
clus               0   1
  FAT1 MUTATED    19   2
  FAT1 WILD-TYPE 163   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  FAT1 MUTATED     19    2
  FAT1 WILD-TYPE  163    8
   clus
vv  FAT1 MUTATED FAT1 WILD-TYPE
  0           19            163
  1            2              8
[1] 2 2
[1] FALSE
D27V7, binary
                cls
clus               0   1
  FAT1 MUTATED    19  31
  FAT1 WILD-TYPE  77 249
[1] "tbl2"
                cls
clus             [,1] [,2]
  FAT1 MUTATED     19   31
  FAT1 WILD-TYPE   77  249
        clus
vv       FAT1 MUTATED FAT1 WILD-TYPE
  FEMALE           19             77
  MALE             31            249
[1] 2 2
[1] FALSE
D27V8, continuous
D27V9, continuous
D27V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  FAT1 MUTATED       3                         2    41
  FAT1 WILD-TYPE    35                        19   260
D27V11, multiclass
                           clus
vv                          FAT1 MUTATED FAT1 WILD-TYPE
  ASIAN                                3             35
  BLACK OR AFRICAN AMERICAN            2             19
  WHITE                               41            260
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V12, binary
                cls
clus               0   1
  FAT1 MUTATED     2  47
  FAT1 WILD-TYPE   6 291
[1] "tbl2"
                cls
clus             [,1] [,2]
  FAT1 MUTATED      2   47
  FAT1 WILD-TYPE    6  291
                        clus
vv                       FAT1 MUTATED FAT1 WILD-TYPE
  HISPANIC OR LATINO                2              6
  NOT HISPANIC OR LATINO           47            291
[1] 2 2
[1] FALSE

Clustering(28) Variable = SPTAN1 MUTATION ANALYSIS
D28V1, survival
                  sevent
clus2                0   1
  SPTAN1 MUTATED    29  14
  SPTAN1 WILD-TYPE 190 137
  SPTAN1 MUTATED SPTAN1 WILD-TYPE 
              43              327 
  SPTAN1 MUTATED SPTAN1 WILD-TYPE 
              14              137 
$`SPTAN1 MUTATED`
TCGA-2F-A9KQ TCGA-4Z-AA7O TCGA-4Z-AA7W TCGA-4Z-AA87 TCGA-BT-A0YX TCGA-BT-A20R 
       91.63        16.83        27.62        47.80        13.15         5.06 
TCGA-BT-A42C TCGA-BT-A42E TCGA-BT-A42F TCGA-CF-A47S TCGA-CF-A47V TCGA-CF-A7I0 
       28.70        24.26        28.41        10.95        12.46        12.10 
TCGA-CF-A9FF TCGA-DK-A1A6 TCGA-DK-A1AA TCGA-DK-A2I1 TCGA-DK-A3WY TCGA-DK-A6B5 
       11.87        66.41        19.00        10.59       140.81        41.06 
TCGA-E7-A3X6 TCGA-FD-A3SN TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A5BZ TCGA-FD-A6TB 
       24.66        29.16        46.78        19.79        27.45        18.81 
TCGA-FD-A6TI TCGA-FD-A6TK TCGA-G2-A2EC TCGA-G2-A2EO TCGA-G2-A3IE TCGA-G2-A3VY 
        9.67        10.85        22.88        35.24        20.12        17.62 
TCGA-GC-A3BM TCGA-GU-A766 TCGA-GV-A3JX TCGA-GV-A6ZA TCGA-MV-A51V TCGA-UY-A78K 
       21.40         5.62        19.10        22.72        13.48        17.62 
TCGA-XF-A9SV TCGA-XF-A9T8 TCGA-XF-AAMG TCGA-XF-AAMY TCGA-XF-AAN0 TCGA-XF-AAN1 
       12.76        13.74       110.60        98.99        56.48        30.94 
TCGA-ZF-A9RL 
       82.49 

$`SPTAN1 WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW TCGA-4Z-AA7M 
       22.29        11.97       103.50       105.70         8.35        16.27 
TCGA-4Z-AA7N TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7Y TCGA-4Z-AA80 
       44.94        16.77        17.16        34.98        49.12         0.62 
TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA84 TCGA-4Z-AA86 TCGA-4Z-AA89 
       41.75        51.16        66.54        15.12        10.22        33.83 
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 
       40.08         7.33         2.66         6.74        12.39         6.58 
TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20T 
       19.04        32.84        12.16        17.88        19.50        14.89 
TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB 
       14.96         5.06         8.35         8.25        17.16        16.18 
TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B TCGA-C4-A0EZ 
       20.48         4.67        12.82         9.96        17.56         8.98 
TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-C4-A0F6 TCGA-C4-A0F7 TCGA-CF-A1HR TCGA-CF-A1HS 
        1.94         2.93        23.01         2.04         0.46         0.43 
TCGA-CF-A27C TCGA-CF-A47T TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 
        0.69        12.66        12.10        12.62        12.26        13.12 
TCGA-CF-A5UA TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ 
       12.00        13.08        12.92         4.90         7.20         5.46 
TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 
        5.19        16.31         1.84        13.58        21.86         2.14 
TCGA-DK-A1A7 TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF 
       18.41        16.70       130.88       112.44        16.14        17.62 
TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK 
       15.62         1.81         7.79       123.85        87.32         2.20 
TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT 
       13.58         7.82         8.22        17.72        50.27        21.30 
TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3X1 TCGA-DK-A3X2 
       23.21         9.67        20.81        10.55        48.00        17.98 
TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B6 
       64.18        41.56        76.60        67.36        15.68        30.67 
TCGA-DK-AA6L TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6U 
       38.24        15.02        13.58       166.03        12.36        10.49 
TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA76 TCGA-DK-AA77 
        8.65         7.53        13.64        43.50        12.03        10.62 
TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ 
       43.59        15.35        38.83         0.10         0.49         2.24 
TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 
       16.70        17.39         0.56         0.66        14.56        13.97 
TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A7XN 
       12.99        14.33         0.92         1.22        13.68        14.07 
TCGA-E7-A85H TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 
       12.95        14.37         8.09        32.02        16.77         8.94 
TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA 
       33.04         4.01        12.62        22.52        27.98        60.66 
TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SS 
       24.30        23.41        17.98         5.52        25.74        12.85 
TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BR 
       22.98        27.35        14.96        20.91         3.62        26.73 
TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY 
       53.88        11.01        19.33         5.36         5.69         8.25 
TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S 
       18.08        58.92         2.70         7.10         6.28        13.35 
TCGA-FD-A6TA TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TG 
       62.86         6.15        12.69        12.36         2.27         3.06 
TCGA-FD-A6TH TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FJ-A871 
        4.31        31.07         7.13        10.65        17.23         8.94 
TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL 
        3.25         6.48        61.94        30.61        15.95        26.93 
TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3D TCGA-G2-AA3F 
       33.01         7.23        66.02         6.94        64.44        19.46 
TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC 
        2.24        15.81         4.50        15.91        14.07        17.75 
TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ 
       24.92         8.94        13.91         7.73         2.10         3.12 
TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R 
       20.98         2.20         7.36        10.92        11.31        11.31 
TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A767 TCGA-GU-AATO TCGA-GU-AATP 
        7.63        27.09        20.05         4.73        10.65        32.98 
TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH 
        7.00        14.27        21.34        19.82        20.28         8.48 
TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-H4-A2HO TCGA-H4-A2HQ 
       10.59        27.35         8.58        19.07         1.51        19.40 
TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU 
       38.60         3.06         9.01         8.22        25.02         3.45 
TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RH TCGA-K4-A5RI 
       21.24         2.76         9.14        27.68         9.07        11.70 
TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO TCGA-LC-A66R 
        1.74         1.81        15.42         6.38        11.80        15.32 
TCGA-LT-A5Z6 TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 
       15.58        12.23        16.67        14.24         1.84         3.75 
TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78N TCGA-UY-A78O 
       12.43        31.56        37.05        22.68        86.83        76.01 
TCGA-UY-A8OB TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF 
       65.75        35.24        29.56        17.82         4.54         1.64 
TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SJ 
        1.87        17.88        48.62        64.80        79.66         3.22 
TCGA-XF-A9SL TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T0 
       66.41        11.90        23.64        21.04        28.24        26.27 
TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-AAME 
       18.90         2.24        16.27        66.64         2.10        92.98 
TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR 
       10.82        11.31        54.90         7.63        71.57        91.73 
TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAMZ TCGA-XF-AAN2 TCGA-XF-AAN3 
        2.96         8.32         6.77        44.32        61.45        86.30 
TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YC-A9TC 
       27.06        75.39        18.81         3.88         9.63         0.66 
TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R3 
       11.97        13.64        18.64         7.36        21.11        24.13 
TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RD 
       30.28        27.19        21.86        28.41        74.56        13.41 
TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N 
        3.48        52.73        52.60        47.84        20.22         2.89 
TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA4X 
       34.06        19.69         8.61        59.38        60.16        63.02 
TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 
       38.73        35.41        57.90        19.40         8.52        47.15 
TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-ZF-AA5P 
       19.17         5.52        10.13 

  SPTAN1 MUTATED SPTAN1 WILD-TYPE 
            5.06             0.10 
  SPTAN1 MUTATED SPTAN1 WILD-TYPE 
          140.81           166.03 
  SPTAN1 MUTATED SPTAN1 WILD-TYPE 
           21.40            14.96 
[1] "5.1 - 140.8 (21.4)" "0.1 - 166.0 (15.0)"
[1] "hr=" "1.8"
D28V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  SPTAN1 MUTATED         0       17        16       11
  SPTAN1 WILD-TYPE       4      100       106      117
D28V3, multiclass
           clus
vv          SPTAN1 MUTATED SPTAN1 WILD-TYPE
  STAGE I                0                4
  STAGE II              17              100
  STAGE III             16              106
  STAGE IV              11              117
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1+T2  T3  T4
  SPTAN1 MUTATED         13  16   9
  SPTAN1 WILD-TYPE      101 163  43
D28V4, multiclass
          clus
vv         SPTAN1 MUTATED SPTAN1 WILD-TYPE
  T0+T1+T2             13              101
  T3                   16              163
  T4                    9               43
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  SPTAN1 MUTATED    29   5   6   0
  SPTAN1 WILD-TYPE 184  36  69   8
D28V5, multiclass
    clus
vv   SPTAN1 MUTATED SPTAN1 WILD-TYPE
  N0             29              184
  N1              5               36
  N2              6               69
  N3              0                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"
D28V6, binary
                  cls
clus                 0   1
  SPTAN1 MUTATED    25   1
  SPTAN1 WILD-TYPE 157   9
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SPTAN1 MUTATED     25    1
  SPTAN1 WILD-TYPE  157    9
   clus
vv  SPTAN1 MUTATED SPTAN1 WILD-TYPE
  0             25              157
  1              1                9
[1] 2 2
[1] FALSE
D28V7, binary
                  cls
clus                 0   1
  SPTAN1 MUTATED     7  37
  SPTAN1 WILD-TYPE  89 243
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SPTAN1 MUTATED      7   37
  SPTAN1 WILD-TYPE   89  243
        clus
vv       SPTAN1 MUTATED SPTAN1 WILD-TYPE
  FEMALE              7               89
  MALE               37              243
[1] 2 2
[1] FALSE
D28V8, continuous
D28V9, continuous
D28V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SPTAN1 MUTATED       6                         3    34
  SPTAN1 WILD-TYPE    32                        18   267
D28V11, multiclass
                           clus
vv                          SPTAN1 MUTATED SPTAN1 WILD-TYPE
  ASIAN                                  6               32
  BLACK OR AFRICAN AMERICAN              3               18
  WHITE                                 34              267
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V12, binary
                  cls
clus                 0   1
  SPTAN1 MUTATED     2  38
  SPTAN1 WILD-TYPE   6 300
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SPTAN1 MUTATED      2   38
  SPTAN1 WILD-TYPE    6  300
                        clus
vv                       SPTAN1 MUTATED SPTAN1 WILD-TYPE
  HISPANIC OR LATINO                  2                6
  NOT HISPANIC OR LATINO             38              300
[1] 2 2
[1] FALSE

Clustering(29) Variable = ZBTB7B MUTATION ANALYSIS
D29V1, survival
                  sevent
clus2                0   1
  ZBTB7B MUTATED     7   3
  ZBTB7B WILD-TYPE 212 148
  ZBTB7B MUTATED ZBTB7B WILD-TYPE 
              10              360 
  ZBTB7B MUTATED ZBTB7B WILD-TYPE 
               3              148 
$`ZBTB7B MUTATED`
TCGA-4Z-AA89 TCGA-DK-A2I4 TCGA-FD-A3B7 TCGA-GD-A3OP TCGA-GD-A76B TCGA-GV-A40E 
       33.83       123.85         4.01         2.10         7.36         8.58 
TCGA-S5-AA26 TCGA-UY-A9PF TCGA-XF-AAN5 TCGA-ZF-AA51 
        3.75         1.64        75.39        38.73 

$`ZBTB7B WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        91.63       103.50       105.70         8.35 
TCGA-4Z-AA7M TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7S 
       16.27        44.94        16.83        16.77        17.16        34.98 
TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 
       27.62        49.12         0.62        41.75        51.16        66.54 
TCGA-4Z-AA84 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J 
       15.12        10.22        47.80        40.08         7.33         2.66 
TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N 
        6.74        12.39         6.58        13.15        19.04        32.84 
TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U 
       12.16        17.88        19.50         5.06        14.89        14.96 
TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A2LD 
        5.06         8.35         8.25        17.16        16.18        20.48 
TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E 
        4.67        12.82         9.96        17.56        28.70        24.26 
TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-C4-A0F6 TCGA-C4-A0F7 
       28.41         8.98         1.94         2.93        23.01         2.04 
TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V 
        0.46         0.43         0.69        10.95        12.66        12.46 
TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 
       12.10        12.62        12.26        13.12        12.00        12.10 
TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ 
       11.87        13.08        12.92         4.90         7.20         5.46 
TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 
        5.19        16.31         1.84        13.58        21.86         2.14 
TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD 
       66.41        18.41        19.00        16.70       130.88       112.44 
TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 
       16.14        17.62        15.62         1.81        10.59         7.79 
TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ 
       87.32         2.20        13.58         7.82         8.22        17.72 
TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX 
       50.27        21.30        23.21         9.67        20.81        10.55 
TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 
      140.81        48.00        17.98        64.18        41.56        76.60 
TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6P 
       67.36        15.68        41.06        30.67        38.24        15.02 
TCGA-DK-AA6Q TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA6X 
       13.58       166.03        12.36        10.49         8.65         7.53 
TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A2PC TCGA-E5-A4TZ 
       13.64        43.50        12.03        10.62        43.59        15.35 
TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 
       38.83        24.66         0.10         0.49         2.24        16.70 
TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME 
       17.39         0.56         0.66        14.56        13.97        12.99 
TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H 
       14.33         0.92         1.22        13.68        14.07        12.95 
TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 
       14.37         8.09        32.02        16.77         8.94        33.04 
TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL 
       12.62        22.52        27.98        60.66        24.30        23.41 
TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR 
       17.98        29.16         5.52        25.74        46.78        19.79 
TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X 
       12.85        22.98        27.35        14.96        20.91         3.62 
TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX 
       26.73        53.88        11.01        19.33         5.36         5.69 
TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O 
        8.25        27.45        18.08        58.92         2.70         7.10 
TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD 
        6.28        13.35        62.86        18.81         6.15        12.69 
TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FD-A6TK 
       12.36         2.27         3.06         4.31         9.67        10.85 
TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FJ-A871 TCGA-FT-A3EE 
       31.07         7.13        10.65        17.23         8.94         3.25 
TCGA-FT-A61P TCGA-G2-A2EC TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL 
        6.48        22.88        61.94        30.61        15.95        26.93 
TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B 
       35.24        33.01         7.23        20.12        17.62        66.02 
TCGA-G2-AA3C TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO 
        6.94        64.44        19.46        21.40         2.24        15.81 
TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A6I1 
        4.50        15.91        14.07        17.75        24.92         8.94 
TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42P 
       13.91         7.73         3.12        20.98         2.20        10.92 
TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 
       11.31        11.31         7.63        27.09        20.05         5.62 
TCGA-GU-A767 TCGA-GU-AATO TCGA-GU-AATP TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW 
        4.73        10.65        32.98         7.00        14.27        21.34 
TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK 
       19.10        19.82        20.28         8.48        10.59        27.35 
TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF 
       19.07        22.72         1.51        19.40        38.60         3.06 
TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB 
        9.01         8.22        25.02         3.45        21.24         2.76 
TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ 
        9.14        27.68         9.07        11.70         1.74         1.81 
TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V 
       15.42         6.38        11.80        15.32        15.58        13.48 
TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX TCGA-SY-A9G0 TCGA-SY-A9G5 
       12.23        16.67        14.24         1.84        12.43        31.56 
TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78N TCGA-UY-A78O TCGA-UY-A8OB 
       17.62        37.05        22.68        86.83        76.01        65.75 
TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE TCGA-XF-A8HH TCGA-XF-A8HI 
       35.24        29.56        17.82         4.54         1.87        17.88 
TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SL TCGA-XF-A9SV 
       48.62        64.80        79.66         3.22        66.41        12.76 
TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 
       11.90        23.64        21.04        28.24        26.27        18.90 
TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAME 
        2.24        16.27        66.64         2.10        13.74        92.98 
TCGA-XF-AAMF TCGA-XF-AAMG TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ 
       10.82       110.60        11.31        54.90         7.63        71.57 
TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAMZ 
       91.73         2.96         8.32         6.77        98.99        44.32 
TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN7 
       56.48        30.94        61.45        86.30        27.06        18.81 
TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R0 
        3.88         9.63         0.66        11.97        13.64        18.64 
TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R7 
        7.36        21.11        24.13        30.28        27.19        21.86 
TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RG 
       28.41        74.56        13.41         3.48        52.73        52.60 
TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4R TCGA-ZF-AA4T 
       82.49        47.84        20.22         2.89        34.06        19.69 
TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA52 TCGA-ZF-AA53 
        8.61        59.38        60.16        63.02        35.41        57.90 
TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-ZF-AA5P 
       19.40         8.52        47.15        19.17         5.52        10.13 

  ZBTB7B MUTATED ZBTB7B WILD-TYPE 
            1.64             0.10 
  ZBTB7B MUTATED ZBTB7B WILD-TYPE 
          123.85           166.03 
  ZBTB7B MUTATED ZBTB7B WILD-TYPE 
           7.970           15.745 
[1] "1.6 - 123.8 (8.0)"  "0.1 - 166.0 (15.7)"
[1] "hr=" "1.4"
D29V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  ZBTB7B MUTATED         0        3         4        3
  ZBTB7B WILD-TYPE       4      114       118      125
D29V3, multiclass
           clus
vv          ZBTB7B MUTATED ZBTB7B WILD-TYPE
  STAGE I                0                4
  STAGE II               3              114
  STAGE III              4              118
  STAGE IV               3              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"
                  vv
clus               T0+T1+T2  T3  T4
  ZBTB7B MUTATED          2   5   2
  ZBTB7B WILD-TYPE      112 174  50
D29V4, multiclass
          clus
vv         ZBTB7B MUTATED ZBTB7B WILD-TYPE
  T0+T1+T2              2              112
  T3                    5              174
  T4                    2               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"
                  vv
clus                N0  N1  N2  N3
  ZBTB7B MUTATED     6   0   2   0
  ZBTB7B WILD-TYPE 207  41  73   8
D29V5, multiclass
    clus
vv   ZBTB7B MUTATED ZBTB7B WILD-TYPE
  N0              6              207
  N1              0               41
  N2              2               73
  N3              0                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"
D29V6, binary
                  cls
clus                 0   1
  ZBTB7B MUTATED     3   0
  ZBTB7B WILD-TYPE 179  10
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZBTB7B MUTATED      3    0
  ZBTB7B WILD-TYPE  179   10
   clus
vv  ZBTB7B MUTATED ZBTB7B WILD-TYPE
  0              3              179
  1              0               10
[1] 2 2
[1] FALSE
D29V7, binary
                  cls
clus                 0   1
  ZBTB7B MUTATED     4   6
  ZBTB7B WILD-TYPE  92 274
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZBTB7B MUTATED      4    6
  ZBTB7B WILD-TYPE   92  274
        clus
vv       ZBTB7B MUTATED ZBTB7B WILD-TYPE
  FEMALE              4               92
  MALE                6              274
[1] 2 2
[1] FALSE
D29V8, continuous
[1] "Remove cluster labels:" "ZBTB7B MUTATED"        
clus
  ZBTB7B MUTATED ZBTB7B WILD-TYPE 
               2              118 
      TCGA-2F-A9KO       TCGA-2F-A9KP       TCGA-2F-A9KQ       TCGA-2F-A9KR 
"ZBTB7B WILD-TYPE" "ZBTB7B WILD-TYPE" "ZBTB7B WILD-TYPE" "ZBTB7B WILD-TYPE" 
      TCGA-2F-A9KT       TCGA-2F-A9KW       TCGA-CF-A1HS       TCGA-CF-A27C 
"ZBTB7B WILD-TYPE" "ZBTB7B WILD-TYPE" "ZBTB7B WILD-TYPE" "ZBTB7B WILD-TYPE" 
      TCGA-CF-A3MF       TCGA-CF-A3MG       TCGA-CF-A3MH       TCGA-CF-A3MI 
"ZBTB7B WILD-TYPE" "ZBTB7B WILD-TYPE" "ZBTB7B WILD-TYPE" "ZBTB7B WILD-TYPE" 
      TCGA-CF-A47S       TCGA-CF-A47T       TCGA-CF-A47V       TCGA-CF-A47W 
"ZBTB7B WILD-TYPE" "ZBTB7B WILD-TYPE" "ZBTB7B WILD-TYPE" "ZBTB7B WILD-TYPE" 
      TCGA-CF-A47X       TCGA-CF-A47Y       TCGA-CF-A5U8       TCGA-CF-A5UA 
"ZBTB7B WILD-TYPE" "ZBTB7B WILD-TYPE" "ZBTB7B WILD-TYPE" "ZBTB7B WILD-TYPE" 
      TCGA-CF-A7I0       TCGA-DK-A2HX       TCGA-DK-A3IN       TCGA-DK-A3IV 
"ZBTB7B WILD-TYPE" "ZBTB7B WILD-TYPE" "ZBTB7B WILD-TYPE" "ZBTB7B WILD-TYPE" 
      TCGA-DK-A3WX       TCGA-DK-A3X2       TCGA-DK-A6B2       TCGA-DK-A6B5 
"ZBTB7B WILD-TYPE" "ZBTB7B WILD-TYPE" "ZBTB7B WILD-TYPE" "ZBTB7B WILD-TYPE" 
      TCGA-DK-A6B6       TCGA-DK-AA6P       TCGA-DK-AA6S       TCGA-DK-AA6U 
"ZBTB7B WILD-TYPE" "ZBTB7B WILD-TYPE" "ZBTB7B WILD-TYPE" "ZBTB7B WILD-TYPE" 
      TCGA-DK-AA6W       TCGA-DK-AA76       TCGA-E5-A2PC       TCGA-E5-A4TZ 
"ZBTB7B WILD-TYPE" "ZBTB7B WILD-TYPE" "ZBTB7B WILD-TYPE" "ZBTB7B WILD-TYPE" 
      TCGA-E5-A4U1       TCGA-E7-A519       TCGA-E7-A541       TCGA-E7-A7DU 
"ZBTB7B WILD-TYPE" "ZBTB7B WILD-TYPE" "ZBTB7B WILD-TYPE" "ZBTB7B WILD-TYPE" 
      TCGA-E7-A7DV       TCGA-FT-A61P       TCGA-G2-A2EC       TCGA-G2-A2EF 
"ZBTB7B WILD-TYPE" "ZBTB7B WILD-TYPE" "ZBTB7B WILD-TYPE" "ZBTB7B WILD-TYPE" 
      TCGA-G2-A2EJ       TCGA-G2-A2EK       TCGA-G2-A2EL       TCGA-G2-A2EO 
"ZBTB7B WILD-TYPE" "ZBTB7B WILD-TYPE" "ZBTB7B WILD-TYPE" "ZBTB7B WILD-TYPE" 
      TCGA-G2-A2ES       TCGA-G2-A3IB       TCGA-G2-A3IE       TCGA-G2-A3VY 
"ZBTB7B WILD-TYPE" "ZBTB7B WILD-TYPE" "ZBTB7B WILD-TYPE" "ZBTB7B WILD-TYPE" 
      TCGA-GC-A3BM       TCGA-GC-A3I6       TCGA-GC-A3OO       TCGA-GC-A3RC 
"ZBTB7B WILD-TYPE" "ZBTB7B WILD-TYPE" "ZBTB7B WILD-TYPE" "ZBTB7B WILD-TYPE" 
      TCGA-GC-A3RD       TCGA-GC-A3YS       TCGA-GC-A6I1       TCGA-GC-A6I3 
"ZBTB7B WILD-TYPE" "ZBTB7B WILD-TYPE" "ZBTB7B WILD-TYPE" "ZBTB7B WILD-TYPE" 
      TCGA-GD-A3OS       TCGA-GD-A6C6       TCGA-GV-A3JV       TCGA-GV-A3JW 
"ZBTB7B WILD-TYPE" "ZBTB7B WILD-TYPE" "ZBTB7B WILD-TYPE" "ZBTB7B WILD-TYPE" 
      TCGA-GV-A3JX       TCGA-GV-A3JZ       TCGA-GV-A3QF       TCGA-GV-A3QH 
"ZBTB7B WILD-TYPE" "ZBTB7B WILD-TYPE" "ZBTB7B WILD-TYPE" "ZBTB7B WILD-TYPE" 
      TCGA-GV-A3QI       TCGA-GV-A3QK       TCGA-GV-A40G       TCGA-GV-A6ZA 
"ZBTB7B WILD-TYPE" "ZBTB7B WILD-TYPE" "ZBTB7B WILD-TYPE" "ZBTB7B WILD-TYPE" 
      TCGA-SY-A9G0       TCGA-SY-A9G5       TCGA-UY-A78L       TCGA-UY-A78M 
"ZBTB7B WILD-TYPE" "ZBTB7B WILD-TYPE" "ZBTB7B WILD-TYPE" "ZBTB7B WILD-TYPE" 
      TCGA-UY-A78N       TCGA-XF-A8HH       TCGA-XF-A8HI       TCGA-XF-A9SG 
"ZBTB7B WILD-TYPE" "ZBTB7B WILD-TYPE" "ZBTB7B WILD-TYPE" "ZBTB7B WILD-TYPE" 
      TCGA-XF-A9SH       TCGA-XF-A9SI       TCGA-XF-A9SJ       TCGA-XF-A9SL 
"ZBTB7B WILD-TYPE" "ZBTB7B WILD-TYPE" "ZBTB7B WILD-TYPE" "ZBTB7B WILD-TYPE" 
      TCGA-XF-A9SV       TCGA-XF-A9SW       TCGA-XF-A9SX       TCGA-XF-A9SY 
"ZBTB7B WILD-TYPE" "ZBTB7B WILD-TYPE" "ZBTB7B WILD-TYPE" "ZBTB7B WILD-TYPE" 
      TCGA-XF-A9SZ       TCGA-XF-A9T0       TCGA-XF-A9T2       TCGA-XF-A9T3 
"ZBTB7B WILD-TYPE" "ZBTB7B WILD-TYPE" "ZBTB7B WILD-TYPE" "ZBTB7B WILD-TYPE" 
      TCGA-XF-A9T4       TCGA-XF-A9T5       TCGA-XF-A9T6       TCGA-XF-A9T8 
"ZBTB7B WILD-TYPE" "ZBTB7B WILD-TYPE" "ZBTB7B WILD-TYPE" "ZBTB7B WILD-TYPE" 
      TCGA-XF-AAME       TCGA-XF-AAMF       TCGA-XF-AAMG       TCGA-XF-AAMH 
"ZBTB7B WILD-TYPE" "ZBTB7B WILD-TYPE" "ZBTB7B WILD-TYPE" "ZBTB7B WILD-TYPE" 
      TCGA-XF-AAMJ       TCGA-XF-AAML       TCGA-XF-AAMQ       TCGA-XF-AAMR 
"ZBTB7B WILD-TYPE" "ZBTB7B WILD-TYPE" "ZBTB7B WILD-TYPE" "ZBTB7B WILD-TYPE" 
      TCGA-XF-AAMT       TCGA-XF-AAMW       TCGA-XF-AAMX       TCGA-XF-AAMY 
"ZBTB7B WILD-TYPE" "ZBTB7B WILD-TYPE" "ZBTB7B WILD-TYPE" "ZBTB7B WILD-TYPE" 
      TCGA-XF-AAMZ       TCGA-XF-AAN0       TCGA-XF-AAN1       TCGA-XF-AAN2 
"ZBTB7B WILD-TYPE" "ZBTB7B WILD-TYPE" "ZBTB7B WILD-TYPE" "ZBTB7B WILD-TYPE" 
      TCGA-XF-AAN3       TCGA-XF-AAN4       TCGA-XF-AAN7       TCGA-XF-AAN8 
"ZBTB7B WILD-TYPE" "ZBTB7B WILD-TYPE" "ZBTB7B WILD-TYPE" "ZBTB7B WILD-TYPE" 
      TCGA-YF-AA3L       TCGA-YF-AA3M 
"ZBTB7B WILD-TYPE" "ZBTB7B WILD-TYPE" 
D29V9, continuous
D29V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ZBTB7B MUTATED       0                         2     8
  ZBTB7B WILD-TYPE    38                        19   293
D29V11, multiclass
                           clus
vv                          ZBTB7B MUTATED ZBTB7B WILD-TYPE
  ASIAN                                  0               38
  BLACK OR AFRICAN AMERICAN              2               19
  WHITE                                  8              293
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V12, binary
                  cls
clus                 0   1
  ZBTB7B MUTATED     0   9
  ZBTB7B WILD-TYPE   8 329
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZBTB7B MUTATED      0    9
  ZBTB7B WILD-TYPE    8  329
                        clus
vv                       ZBTB7B MUTATED ZBTB7B WILD-TYPE
  HISPANIC OR LATINO                  0                8
  NOT HISPANIC OR LATINO              9              329
[1] 2 2
[1] FALSE

Clustering(30) Variable = CUL1 MUTATION ANALYSIS
D30V1, survival
                sevent
clus2              0   1
  CUL1 MUTATED    10   8
  CUL1 WILD-TYPE 209 143
  CUL1 MUTATED CUL1 WILD-TYPE 
            18            352 
  CUL1 MUTATED CUL1 WILD-TYPE 
             8            143 
$`CUL1 MUTATED`
TCGA-BT-A0S7 TCGA-C4-A0F1 TCGA-CU-A0YO TCGA-CU-A3YL TCGA-DK-A1A3 TCGA-DK-A3WW 
        6.58         2.93         4.90        16.31        21.86        20.81 
TCGA-E7-A7XN TCGA-FD-A6TD TCGA-FD-A6TH TCGA-G2-A2EC TCGA-G2-A3VY TCGA-GV-A3JX 
       14.07        12.69         4.31        22.88        17.62        19.10 
TCGA-K4-A5RI TCGA-UY-A9PE TCGA-XF-A9SX TCGA-YF-AA3M TCGA-ZF-A9R4 TCGA-ZF-A9RL 
       11.70         4.54        23.64        13.64        30.28        82.49 

$`CUL1 WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        91.63       103.50       105.70         8.35 
TCGA-4Z-AA7M TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7S 
       16.27        44.94        16.83        16.77        17.16        34.98 
TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 
       27.62        49.12         0.62        41.75        51.16        66.54 
TCGA-4Z-AA84 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BL-A13I 
       15.12        10.22        47.80        33.83        40.08         7.33 
TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N 
        2.66         6.74        12.39        13.15        19.04        32.84 
TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U 
       12.16        17.88        19.50         5.06        14.89        14.96 
TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A2LD 
        5.06         8.35         8.25        17.16        16.18        20.48 
TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E 
        4.67        12.82         9.96        17.56        28.70        24.26 
TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-C4-A0F7 TCGA-CF-A1HR 
       28.41         8.98         1.94        23.01         2.04         0.46 
TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W 
        0.43         0.69        10.95        12.66        12.46        12.10 
TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A9FF 
       12.62        12.26        13.12        12.00        12.10        11.87 
TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A5W6 
       13.08        12.92         7.20         5.46         5.19         1.84 
TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB 
       13.58         2.14        66.41        18.41        19.00        16.70 
TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX 
      130.88       112.44        16.14        17.62        15.62         1.81 
TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL 
       10.59         7.79       123.85        87.32         2.20        13.58 
TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU 
        7.82         8.22        17.72        50.27        21.30        23.21 
TCGA-DK-A3IV TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV 
        9.67        10.55       140.81        48.00        17.98        64.18 
TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 
       41.56        76.60        67.36        15.68        41.06        30.67 
TCGA-DK-AA6L TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6U 
       38.24        15.02        13.58       166.03        12.36        10.49 
TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA76 TCGA-DK-AA77 
        8.65         7.53        13.64        43.50        12.03        10.62 
TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ 
       43.59        15.35        38.83        24.66         0.10         0.49 
TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 
        2.24        16.70        17.39         0.56         0.66        14.56 
TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7DV TCGA-E7-A7PW 
       13.97        12.99        14.33         0.92         1.22        13.68 
TCGA-E7-A85H TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 
       12.95        14.37         8.09        32.02        16.77         8.94 
TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA 
       33.04         4.01        12.62        22.52        27.98        60.66 
TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP 
       24.30        23.41        17.98        29.16         5.52        25.74 
TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S 
       46.78        19.79        12.85        22.98        27.35        14.96 
TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU 
       20.91         3.62        26.73        53.88        11.01        19.33 
TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 
        5.36         5.69         8.25        27.45        18.08        58.92 
TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB 
        2.70         7.10         6.28        13.35        62.86        18.81 
TCGA-FD-A6TC TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TI TCGA-FD-A6TK 
        6.15        12.36         2.27         3.06         9.67        10.85 
TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FJ-A871 TCGA-FT-A3EE 
       31.07         7.13        10.65        17.23         8.94         3.25 
TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO 
        6.48        61.94        30.61        15.95        26.93        35.24 
TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3D 
       33.01         7.23        20.12        66.02         6.94        64.44 
TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC 
       19.46        21.40         2.24        15.81         4.50        15.91 
TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 
       14.07        17.75        24.92         8.94        13.91         7.73 
TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42P 
        2.10         3.12        20.98         2.20         7.36        10.92 
TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 
       11.31        11.31         7.63        27.09        20.05         5.62 
TCGA-GU-A767 TCGA-GU-AATO TCGA-GU-AATP TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW 
        4.73        10.65        32.98         7.00        14.27        21.34 
TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E 
       19.82        20.28         8.48        10.59        27.35         8.58 
TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF 
       19.07        22.72         1.51        19.40        38.60         3.06 
TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB 
        9.01         8.22        25.02         3.45        21.24         2.76 
TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RH TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB 
        9.14        27.68         9.07         1.74         1.81        15.42 
TCGA-K4-A83P TCGA-K4-AAQO TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI 
        6.38        11.80        15.32        15.58        13.48        12.23 
TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 TCGA-SY-A9G0 TCGA-SY-A9G5 
       16.67        14.24         1.84         3.75        12.43        31.56 
TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78N TCGA-UY-A78O TCGA-UY-A8OB 
       17.62        37.05        22.68        86.83        76.01        65.75 
TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PF TCGA-XF-A8HH TCGA-XF-A8HI 
       35.24        29.56        17.82         1.64         1.87        17.88 
TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SL TCGA-XF-A9SV 
       48.62        64.80        79.66         3.22        66.41        12.76 
TCGA-XF-A9SW TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 
       11.90        21.04        28.24        26.27        18.90         2.24 
TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMF 
       16.27        66.64         2.10        13.74        92.98        10.82 
TCGA-XF-AAMG TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR 
      110.60        11.31        54.90         7.63        71.57        91.73 
TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN0 
        2.96         8.32         6.77        98.99        44.32        56.48 
TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN7 
       30.94        61.45        86.30        27.06        75.39        18.81 
TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R0 TCGA-ZF-A9R1 
        3.88         9.63         0.66        11.97        18.64         7.36 
TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RC 
       21.11        24.13        27.19        21.86        28.41        74.56 
TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RM TCGA-ZF-A9RN 
       13.41         3.48        52.73        52.60        47.84        20.22 
TCGA-ZF-AA4N TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W 
        2.89        34.06        19.69         8.61        59.38        60.16 
TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA56 
       63.02        38.73        35.41        57.90        19.40         8.52 
TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-ZF-AA5P 
       47.15        19.17         5.52        10.13 

  CUL1 MUTATED CUL1 WILD-TYPE 
          2.93           0.10 
  CUL1 MUTATED CUL1 WILD-TYPE 
         82.49         166.03 
  CUL1 MUTATED CUL1 WILD-TYPE 
         15.19          15.65 
[1] "2.9 - 82.5 (15.2)"  "0.1 - 166.0 (15.6)"
[1] "hr=" "1.3"
D30V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  CUL1 MUTATED         0        5         8        5
  CUL1 WILD-TYPE       4      112       114      123
D30V3, multiclass
           clus
vv          CUL1 MUTATED CUL1 WILD-TYPE
  STAGE I              0              4
  STAGE II             5            112
  STAGE III            8            114
  STAGE IV             5            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"
                vv
clus             T0+T1+T2  T3  T4
  CUL1 MUTATED          3  10   2
  CUL1 WILD-TYPE      111 169  50
D30V4, multiclass
          clus
vv         CUL1 MUTATED CUL1 WILD-TYPE
  T0+T1+T2            3            111
  T3                 10            169
  T4                  2             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"
                vv
clus              N0  N1  N2  N3
  CUL1 MUTATED     9   0   5   0
  CUL1 WILD-TYPE 204  41  70   8
D30V5, multiclass
    clus
vv   CUL1 MUTATED CUL1 WILD-TYPE
  N0            9            204
  N1            0             41
  N2            5             70
  N3            0              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"
D30V6, binary
                cls
clus               0   1
  CUL1 MUTATED     7   0
  CUL1 WILD-TYPE 175  10
[1] "tbl2"
                cls
clus             [,1] [,2]
  CUL1 MUTATED      7    0
  CUL1 WILD-TYPE  175   10
   clus
vv  CUL1 MUTATED CUL1 WILD-TYPE
  0            7            175
  1            0             10
[1] 2 2
[1] FALSE
D30V7, binary
                cls
clus               0   1
  CUL1 MUTATED     3  15
  CUL1 WILD-TYPE  93 265
[1] "tbl2"
                cls
clus             [,1] [,2]
  CUL1 MUTATED      3   15
  CUL1 WILD-TYPE   93  265
        clus
vv       CUL1 MUTATED CUL1 WILD-TYPE
  FEMALE            3             93
  MALE             15            265
[1] 2 2
[1] FALSE
D30V8, continuous
D30V9, continuous
D30V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CUL1 MUTATED       2                         1    13
  CUL1 WILD-TYPE    36                        20   288
D30V11, multiclass
                           clus
vv                          CUL1 MUTATED CUL1 WILD-TYPE
  ASIAN                                2             36
  BLACK OR AFRICAN AMERICAN            1             20
  WHITE                               13            288
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V12, binary
                cls
clus               0   1
  CUL1 MUTATED     1  16
  CUL1 WILD-TYPE   7 322
[1] "tbl2"
                cls
clus             [,1] [,2]
  CUL1 MUTATED      1   16
  CUL1 WILD-TYPE    7  322
                        clus
vv                       CUL1 MUTATED CUL1 WILD-TYPE
  HISPANIC OR LATINO                1              7
  NOT HISPANIC OR LATINO           16            322
[1] 2 2
[1] FALSE

Clustering(31) Variable = KLF5 MUTATION ANALYSIS
D31V1, survival
                sevent
clus2              0   1
  KLF5 MUTATED    15   7
  KLF5 WILD-TYPE 204 144
  KLF5 MUTATED KLF5 WILD-TYPE 
            22            348 
  KLF5 MUTATED KLF5 WILD-TYPE 
             7            144 
$`KLF5 MUTATED`
TCGA-4Z-AA87 TCGA-BL-A3JM TCGA-BT-A0YX TCGA-BT-A42C TCGA-C4-A0F6 TCGA-DK-A3IU 
       47.80         6.74        13.15        28.70        23.01        23.21 
TCGA-DK-A3X1 TCGA-DK-A6B0 TCGA-DK-AA71 TCGA-E7-A3Y1 TCGA-FD-A3SS TCGA-FJ-A3Z9 
       48.00        76.60        13.64         0.10        12.85         7.13 
TCGA-GC-A3WC TCGA-GD-A76B TCGA-GV-A3QK TCGA-K4-A83P TCGA-S5-A6DX TCGA-SY-A9G5 
       17.75         7.36        27.35         6.38         1.84        31.56 
TCGA-XF-A9SY TCGA-XF-A9T3 TCGA-XF-AAMH TCGA-ZF-A9R9 
       21.04         2.24        11.31        28.41 

$`KLF5 WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        91.63       103.50       105.70         8.35 
TCGA-4Z-AA7M TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7S 
       16.27        44.94        16.83        16.77        17.16        34.98 
TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 
       27.62        49.12         0.62        41.75        51.16        66.54 
TCGA-4Z-AA84 TCGA-4Z-AA86 TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J 
       15.12        10.22        33.83        40.08         7.33         2.66 
TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P 
       12.39         6.58        19.04        32.84        12.16        17.88 
TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20W 
       19.50         5.06        14.89        14.96         5.06         8.35 
TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PJ 
        8.25        17.16        16.18        20.48         4.67        12.82 
TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 
        9.96        17.56        24.26        28.41         8.98         1.94 
TCGA-C4-A0F1 TCGA-C4-A0F7 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47S 
        2.93         2.04         0.46         0.43         0.69        10.95 
TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 
       12.66        12.46        12.10        12.62        12.26        13.12 
TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YO 
       12.00        12.10        11.87        13.08        12.92         4.90 
TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E 
        7.20         5.46         5.19        16.31         1.84        13.58 
TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB 
       21.86         2.14        66.41        18.41        19.00        16.70 
TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX 
      130.88       112.44        16.14        17.62        15.62         1.81 
TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL 
       10.59         7.79       123.85        87.32         2.20        13.58 
TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IV 
        7.82         8.22        17.72        50.27        21.30         9.67 
TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW 
       20.81        10.55       140.81        17.98        64.18        41.56 
TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6P 
       67.36        15.68        41.06        30.67        38.24        15.02 
TCGA-DK-AA6Q TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA6X 
       13.58       166.03        12.36        10.49         8.65         7.53 
TCGA-DK-AA74 TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E5-A4U1 
       43.50        12.03        10.62        43.59        15.35        38.83 
TCGA-E7-A3X6 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KE 
       24.66         0.49         2.24        16.70        17.39         0.56 
TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DU 
        0.66        14.56        13.97        12.99        14.33         0.92 
TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A97P TCGA-E7-A97Q 
        1.22        13.68        14.07        12.95        14.37         8.09 
TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 
       32.02        16.77         8.94        33.04         4.01        12.62 
TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM 
       22.52        27.98        60.66        24.30        23.41        17.98 
TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A43N 
       29.16         5.52        25.74        46.78        19.79        22.98 
TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS 
       27.35        14.96        20.91         3.62        26.73        53.88 
TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ 
       11.01        19.33         5.36         5.69         8.25        27.45 
TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S 
       18.08        58.92         2.70         7.10         6.28        13.35 
TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF 
       62.86        18.81         6.15        12.69        12.36         2.27 
TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3ZE 
        3.06         4.31         9.67        10.85        31.07        10.65 
TCGA-FJ-A3ZF TCGA-FJ-A871 TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EC TCGA-G2-A2EF 
       17.23         8.94         3.25         6.48        22.88        61.94 
TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB 
       30.61        15.95        26.93        35.24        33.01         7.23 
TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3D TCGA-G2-AA3F 
       20.12        17.62        66.02         6.94        64.44        19.46 
TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD 
       21.40         2.24        15.81         4.50        15.91        14.07 
TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ 
       24.92         8.94        13.91         7.73         2.10         3.12 
TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 
       20.98         2.20        10.92        11.31        11.31         7.63 
TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATO TCGA-GU-AATP 
       27.09        20.05         5.62         4.73        10.65        32.98 
TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF 
        7.00        14.27        21.34        19.10        19.82        20.28 
TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO 
        8.48        10.59         8.58        19.07        22.72         1.51 
TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS 
       19.40        38.60         3.06         9.01         8.22        25.02 
TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RH 
        3.45        21.24         2.76         9.14        27.68         9.07 
TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-AAQO TCGA-LC-A66R 
       11.70         1.74         1.81        15.42        11.80        15.32 
TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-AA26 
       15.58        13.48        12.23        16.67        14.24         3.75 
TCGA-SY-A9G0 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78N TCGA-UY-A78O 
       12.43        17.62        37.05        22.68        86.83        76.01 
TCGA-UY-A8OB TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF 
       65.75        35.24        29.56        17.82         4.54         1.64 
TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SJ 
        1.87        17.88        48.62        64.80        79.66         3.22 
TCGA-XF-A9SL TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SZ TCGA-XF-A9T0 
       66.41        12.76        11.90        23.64        28.24        26.27 
TCGA-XF-A9T2 TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAME 
       18.90        16.27        66.64         2.10        13.74        92.98 
TCGA-XF-AAMF TCGA-XF-AAMG TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR 
       10.82       110.60        54.90         7.63        71.57        91.73 
TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN0 
        2.96         8.32         6.77        98.99        44.32        56.48 
TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN7 
       30.94        61.45        86.30        27.06        75.39        18.81 
TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R0 
        3.88         9.63         0.66        11.97        13.64        18.64 
TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R7 
        7.36        21.11        24.13        30.28        27.19        21.86 
TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RL 
       74.56        13.41         3.48        52.73        52.60        82.49 
TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4U 
       47.84        20.22         2.89        34.06        19.69         8.61 
TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA53 
       59.38        60.16        63.02        38.73        35.41        57.90 
TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-ZF-AA5P 
       19.40         8.52        47.15        19.17         5.52        10.13 

  KLF5 MUTATED KLF5 WILD-TYPE 
          0.10           0.43 
  KLF5 MUTATED KLF5 WILD-TYPE 
         76.60         166.03 
  KLF5 MUTATED KLF5 WILD-TYPE 
        15.695         15.650 
[1] "0.1 - 76.6 (15.7)"  "0.4 - 166.0 (15.6)"
[1] "hr=" "1.2"
D31V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  KLF5 MUTATED         1        6         7        8
  KLF5 WILD-TYPE       3      111       115      120
D31V3, multiclass
           clus
vv          KLF5 MUTATED KLF5 WILD-TYPE
  STAGE I              1              3
  STAGE II             6            111
  STAGE III            7            115
  STAGE IV             8            120
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1+T2  T3  T4
  KLF5 MUTATED          5   9   6
  KLF5 WILD-TYPE      109 170  46
D31V4, multiclass
          clus
vv         KLF5 MUTATED KLF5 WILD-TYPE
  T0+T1+T2            5            109
  T3                  9            170
  T4                  6             46
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  KLF5 MUTATED    14   2   5   1
  KLF5 WILD-TYPE 199  39  70   7
D31V5, multiclass
    clus
vv   KLF5 MUTATED KLF5 WILD-TYPE
  N0           14            199
  N1            2             39
  N2            5             70
  N3            1              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"
D31V6, binary
                cls
clus               0   1
  KLF5 MUTATED    13   0
  KLF5 WILD-TYPE 169  10
[1] "tbl2"
                cls
clus             [,1] [,2]
  KLF5 MUTATED     13    0
  KLF5 WILD-TYPE  169   10
   clus
vv  KLF5 MUTATED KLF5 WILD-TYPE
  0           13            169
  1            0             10
[1] 2 2
[1] FALSE
D31V7, binary
                cls
clus               0   1
  KLF5 MUTATED     8  14
  KLF5 WILD-TYPE  88 266
[1] "tbl2"
                cls
clus             [,1] [,2]
  KLF5 MUTATED      8   14
  KLF5 WILD-TYPE   88  266
        clus
vv       KLF5 MUTATED KLF5 WILD-TYPE
  FEMALE            8             88
  MALE             14            266
[1] 2 2
[1] FALSE
D31V8, continuous
D31V9, continuous
D31V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  KLF5 MUTATED       0                         1    20
  KLF5 WILD-TYPE    38                        20   281
D31V11, multiclass
                           clus
vv                          KLF5 MUTATED KLF5 WILD-TYPE
  ASIAN                                0             38
  BLACK OR AFRICAN AMERICAN            1             20
  WHITE                               20            281
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V12, binary
                cls
clus               0   1
  KLF5 MUTATED     0  20
  KLF5 WILD-TYPE   8 318
[1] "tbl2"
                cls
clus             [,1] [,2]
  KLF5 MUTATED      0   20
  KLF5 WILD-TYPE    8  318
                        clus
vv                       KLF5 MUTATED KLF5 WILD-TYPE
  HISPANIC OR LATINO                0              8
  NOT HISPANIC OR LATINO           20            318
[1] 2 2
[1] FALSE

Clustering(32) Variable = RXRA MUTATION ANALYSIS
D32V1, survival
                sevent
clus2              0   1
  RXRA MUTATED    12  11
  RXRA WILD-TYPE 207 140
  RXRA MUTATED RXRA WILD-TYPE 
            23            347 
  RXRA MUTATED RXRA WILD-TYPE 
            11            140 
$`RXRA MUTATED`
TCGA-2F-A9KQ TCGA-4Z-AA80 TCGA-4Z-AA82 TCGA-BT-A3PH TCGA-CF-A47X TCGA-DK-A1AC 
       91.63         0.62        51.16         4.67        12.62       130.88 
TCGA-DK-A1AF TCGA-DK-A3IL TCGA-DK-A3IQ TCGA-DK-AA76 TCGA-E5-A4TZ TCGA-E7-A541 
       17.62        13.58        17.72        12.03        15.35        17.39 
TCGA-FD-A3B5 TCGA-FD-A3SN TCGA-FD-A5BX TCGA-FJ-A3ZF TCGA-G2-A2EF TCGA-GV-A3QH 
        8.94        29.16         5.69        17.23        61.94         8.48 
TCGA-GV-A40G TCGA-H4-A2HQ TCGA-UY-A9PF TCGA-XF-AAMH TCGA-ZF-AA53 
       19.07        19.40         1.64        11.31        57.90 

$`RXRA WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW TCGA-4Z-AA7M 
       22.29        11.97       103.50       105.70         8.35        16.27 
TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7W 
       44.94        16.83        16.77        17.16        34.98        27.62 
TCGA-4Z-AA7Y TCGA-4Z-AA81 TCGA-4Z-AA83 TCGA-4Z-AA84 TCGA-4Z-AA86 TCGA-4Z-AA87 
       49.12        41.75        66.54        15.12        10.22        47.80 
TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ 
       33.83        40.08         7.33         2.66         6.74        12.39 
TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P 
        6.58        13.15        19.04        32.84        12.16        17.88 
TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20W 
       19.50         5.06        14.89        14.96         5.06         8.35 
TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A3PK 
        8.25        17.16        16.18        20.48        12.82         9.96 
TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 
       17.56        28.70        24.26        28.41         8.98         1.94 
TCGA-C4-A0F1 TCGA-C4-A0F6 TCGA-C4-A0F7 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C 
        2.93        23.01         2.04         0.46         0.43         0.69 
TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47Y TCGA-CF-A5U8 
       10.95        12.66        12.46        12.10        12.26        13.12 
TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YO 
       12.00        12.10        11.87        13.08        12.92         4.90 
TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E 
        7.20         5.46         5.19        16.31         1.84        13.58 
TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB 
       21.86         2.14        66.41        18.41        19.00        16.70 
TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 
      112.44        16.14        15.62         1.81        10.59         7.79 
TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IS 
      123.85        87.32         2.20         7.82         8.22        50.27 
TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY 
       21.30        23.21         9.67        20.81        10.55       140.81 
TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 
       48.00        17.98        64.18        41.56        76.60        67.36 
TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6P TCGA-DK-AA6Q 
       15.68        41.06        30.67        38.24        15.02        13.58 
TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA71 
      166.03        12.36        10.49         8.65         7.53        13.64 
TCGA-DK-AA74 TCGA-DK-AA77 TCGA-E5-A2PC TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 
       43.50        10.62        43.59        38.83        24.66         0.10 
TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 
        0.49         2.24        16.70         0.56         0.66        14.56 
TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7DV TCGA-E7-A7PW 
       13.97        12.99        14.33         0.92         1.22        13.68 
TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 
       14.07        12.95        14.37         8.09        32.02        16.77 
TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA 
       33.04         4.01        12.62        22.52        27.98        60.66 
TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ 
       24.30        23.41        17.98         5.52        25.74        46.78 
TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U 
       19.79        12.85        22.98        27.35        14.96        20.91 
TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV 
        3.62        26.73        53.88        11.01        19.33         5.36 
TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O 
        8.25        27.45        18.08        58.92         2.70         7.10 
TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD 
        6.28        13.35        62.86        18.81         6.15        12.69 
TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FD-A6TK 
       12.36         2.27         3.06         4.31         9.67        10.85 
TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A871 TCGA-FT-A3EE TCGA-FT-A61P 
       31.07         7.13        10.65         8.94         3.25         6.48 
TCGA-G2-A2EC TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES 
       22.88        30.61        15.95        26.93        35.24        33.01 
TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3D 
        7.23        20.12        17.62        66.02         6.94        64.44 
TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC 
       19.46        21.40         2.24        15.81         4.50        15.91 
TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 
       14.07        17.75        24.92         8.94        13.91         7.73 
TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42P 
        2.10         3.12        20.98         2.20         7.36        10.92 
TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 
       11.31        11.31         7.63        27.09        20.05         5.62 
TCGA-GU-A767 TCGA-GU-AATO TCGA-GU-AATP TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW 
        4.73        10.65        32.98         7.00        14.27        21.34 
TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E 
       19.10        19.82        20.28        10.59        27.35         8.58 
TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE 
       22.72         1.51        38.60         3.06         9.01         8.22 
TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R 
       25.02         3.45        21.24         2.76         9.14        27.68 
TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P 
        9.07        11.70         1.74         1.81        15.42         6.38 
TCGA-K4-AAQO TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN 
       11.80        15.32        15.58        13.48        12.23        16.67 
TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78K 
       14.24         1.84         3.75        12.43        31.56        17.62 
TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78N TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A9PA 
       37.05        22.68        86.83        76.01        65.75        35.24 
TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG 
       29.56        17.82         4.54         1.87        17.88        48.62 
TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SL TCGA-XF-A9SV TCGA-XF-A9SW 
       64.80        79.66         3.22        66.41        12.76        11.90 
TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 
       23.64        21.04        28.24        26.27        18.90         2.24 
TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMF 
       16.27        66.64         2.10        13.74        92.98        10.82 
TCGA-XF-AAMG TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMT 
      110.60        54.90         7.63        71.57        91.73         2.96 
TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN0 TCGA-XF-AAN1 
        8.32         6.77        98.99        44.32        56.48        30.94 
TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN7 TCGA-XF-AAN8 
       61.45        86.30        27.06        75.39        18.81         3.88 
TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R0 TCGA-ZF-A9R1 
        9.63         0.66        11.97        13.64        18.64         7.36 
TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 
       21.11        24.13        30.28        27.19        21.86        28.41 
TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RL 
       74.56        13.41         3.48        52.73        52.60        82.49 
TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4U 
       47.84        20.22         2.89        34.06        19.69         8.61 
TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA54 
       59.38        60.16        63.02        38.73        35.41        19.40 
TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-ZF-AA5P 
        8.52        47.15        19.17         5.52        10.13 

  RXRA MUTATED RXRA WILD-TYPE 
          0.62           0.10 
  RXRA MUTATED RXRA WILD-TYPE 
        130.88         166.03 
  RXRA MUTATED RXRA WILD-TYPE 
         17.23          15.62 
[1] "0.6 - 130.9 (17.2)" "0.1 - 166.0 (15.6)"
[1] "hr=" "1.1"
D32V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  RXRA MUTATED         0        8         5       10
  RXRA WILD-TYPE       4      109       117      118
D32V3, multiclass
           clus
vv          RXRA MUTATED RXRA WILD-TYPE
  STAGE I              0              4
  STAGE II             8            109
  STAGE III            5            117
  STAGE IV            10            118
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1+T2  T3  T4
  RXRA MUTATED          7  10   1
  RXRA WILD-TYPE      107 169  51
D32V4, multiclass
          clus
vv         RXRA MUTATED RXRA WILD-TYPE
  T0+T1+T2            7            107
  T3                 10            169
  T4                  1             51
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  RXRA MUTATED    11   4   5   0
  RXRA WILD-TYPE 202  37  70   8
D32V5, multiclass
    clus
vv   RXRA MUTATED RXRA WILD-TYPE
  N0           11            202
  N1            4             37
  N2            5             70
  N3            0              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"
D32V6, binary
                cls
clus               0   1
  RXRA MUTATED    12   1
  RXRA WILD-TYPE 170   9
[1] "tbl2"
                cls
clus             [,1] [,2]
  RXRA MUTATED     12    1
  RXRA WILD-TYPE  170    9
   clus
vv  RXRA MUTATED RXRA WILD-TYPE
  0           12            170
  1            1              9
[1] 2 2
[1] FALSE
D32V7, binary
                cls
clus               0   1
  RXRA MUTATED     4  19
  RXRA WILD-TYPE  92 261
[1] "tbl2"
                cls
clus             [,1] [,2]
  RXRA MUTATED      4   19
  RXRA WILD-TYPE   92  261
        clus
vv       RXRA MUTATED RXRA WILD-TYPE
  FEMALE            4             92
  MALE             19            261
[1] 2 2
[1] FALSE
D32V8, continuous
D32V9, continuous
D32V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RXRA MUTATED       1                         3    19
  RXRA WILD-TYPE    37                        18   282
D32V11, multiclass
                           clus
vv                          RXRA MUTATED RXRA WILD-TYPE
  ASIAN                                1             37
  BLACK OR AFRICAN AMERICAN            3             18
  WHITE                               19            282
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V12, binary
                cls
clus               0   1
  RXRA MUTATED     1  19
  RXRA WILD-TYPE   7 319
[1] "tbl2"
                cls
clus             [,1] [,2]
  RXRA MUTATED      1   19
  RXRA WILD-TYPE    7  319
                        clus
vv                       RXRA MUTATED RXRA WILD-TYPE
  HISPANIC OR LATINO                1              7
  NOT HISPANIC OR LATINO           19            319
[1] 2 2
[1] FALSE

Clustering(33) Variable = GNA13 MUTATION ANALYSIS
D33V1, survival
                 sevent
clus2               0   1
  GNA13 MUTATED     8   2
  GNA13 WILD-TYPE 211 149
  GNA13 MUTATED GNA13 WILD-TYPE 
             10             360 
  GNA13 MUTATED GNA13 WILD-TYPE 
              2             149 
$`GNA13 MUTATED`
TCGA-BT-A42C TCGA-DK-A1AD TCGA-DK-AA6L TCGA-FD-A3SN TCGA-FD-A6TB TCGA-G2-A2EO 
       28.70       112.44        38.24        29.16        18.81        35.24 
TCGA-K4-A3WS TCGA-K4-A54R TCGA-SY-A9G0 TCGA-XF-AAML 
       25.02        27.68        12.43         7.63 

$`GNA13 WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        91.63       103.50       105.70         8.35 
TCGA-4Z-AA7M TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7S 
       16.27        44.94        16.83        16.77        17.16        34.98 
TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 
       27.62        49.12         0.62        41.75        51.16        66.54 
TCGA-4Z-AA84 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BL-A13I 
       15.12        10.22        47.80        33.83        40.08         7.33 
TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J 
        2.66         6.74        12.39         6.58        13.15        19.04 
TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T 
       32.84        12.16        17.88        19.50         5.06        14.89 
TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB 
       14.96         5.06         8.35         8.25        17.16        16.18 
TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42E 
       20.48         4.67        12.82         9.96        17.56        24.26 
TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-C4-A0F6 TCGA-C4-A0F7 
       28.41         8.98         1.94         2.93        23.01         2.04 
TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V 
        0.46         0.43         0.69        10.95        12.66        12.46 
TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 
       12.10        12.62        12.26        13.12        12.00        12.10 
TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ 
       11.87        13.08        12.92         4.90         7.20         5.46 
TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 
        5.19        16.31         1.84        13.58        21.86         2.14 
TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AE 
       66.41        18.41        19.00        16.70       130.88        16.14 
TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 
       17.62        15.62         1.81        10.59         7.79       123.85 
TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ 
       87.32         2.20        13.58         7.82         8.22        17.72 
TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX 
       50.27        21.30        23.21         9.67        20.81        10.55 
TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 
      140.81        48.00        17.98        64.18        41.56        76.60 
TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6P TCGA-DK-AA6Q 
       67.36        15.68        41.06        30.67        15.02        13.58 
TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA71 
      166.03        12.36        10.49         8.65         7.53        13.64 
TCGA-DK-AA74 TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E5-A4U1 
       43.50        12.03        10.62        43.59        15.35        38.83 
TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 
       24.66         0.10         0.49         2.24        16.70        17.39 
TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF 
        0.56         0.66        14.56        13.97        12.99        14.33 
TCGA-E7-A7DU TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A97P 
        0.92         1.22        13.68        14.07        12.95        14.37 
TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 
        8.09        32.02        16.77         8.94        33.04         4.01 
TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL 
       12.62        22.52        27.98        60.66        24.30        23.41 
TCGA-FD-A3SM TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS 
       17.98         5.52        25.74        46.78        19.79        12.85 
TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BR 
       22.98        27.35        14.96        20.91         3.62        26.73 
TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY 
       53.88        11.01        19.33         5.36         5.69         8.25 
TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P 
       27.45        18.08        58.92         2.70         7.10         6.28 
TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF 
       13.35        62.86         6.15        12.69        12.36         2.27 
TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 
        3.06         4.31         9.67        10.85        31.07         7.13 
TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FJ-A871 TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EC 
       10.65        17.23         8.94         3.25         6.48        22.88 
TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2ES TCGA-G2-A3IB 
       61.94        30.61        15.95        26.93        33.01         7.23 
TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3D TCGA-G2-AA3F 
       20.12        17.62        66.02         6.94        64.44        19.46 
TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD 
       21.40         2.24        15.81         4.50        15.91        14.07 
TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP 
       17.75        24.92         8.94        13.91         7.73         2.10 
TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42Q 
        3.12        20.98         2.20         7.36        10.92        11.31 
TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 
       11.31         7.63        27.09        20.05         5.62         4.73 
TCGA-GU-AATO TCGA-GU-AATP TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX 
       10.65        32.98         7.00        14.27        21.34        19.10 
TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E 
       19.82        20.28         8.48        10.59        27.35         8.58 
TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF 
       19.07        22.72         1.51        19.40        38.60         3.06 
TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC 
        9.01         8.22         3.45        21.24         2.76         9.14 
TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P 
        9.07        11.70         1.74         1.81        15.42         6.38 
TCGA-K4-AAQO TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN 
       11.80        15.32        15.58        13.48        12.23        16.67 
TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L 
       14.24         1.84         3.75        31.56        17.62        37.05 
TCGA-UY-A78M TCGA-UY-A78N TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A9PA TCGA-UY-A9PB 
       22.68        86.83        76.01        65.75        35.24        29.56 
TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG 
       17.82         4.54         1.64         1.87        17.88        48.62 
TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SL TCGA-XF-A9SV TCGA-XF-A9SW 
       64.80        79.66         3.22        66.41        12.76        11.90 
TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 
       23.64        21.04        28.24        26.27        18.90         2.24 
TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMF 
       16.27        66.64         2.10        13.74        92.98        10.82 
TCGA-XF-AAMG TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMT 
      110.60        11.31        54.90        71.57        91.73         2.96 
TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN0 TCGA-XF-AAN1 
        8.32         6.77        98.99        44.32        56.48        30.94 
TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN7 TCGA-XF-AAN8 
       61.45        86.30        27.06        75.39        18.81         3.88 
TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R0 TCGA-ZF-A9R1 
        9.63         0.66        11.97        13.64        18.64         7.36 
TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 
       21.11        24.13        30.28        27.19        21.86        28.41 
TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RL 
       74.56        13.41         3.48        52.73        52.60        82.49 
TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4U 
       47.84        20.22         2.89        34.06        19.69         8.61 
TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA53 
       59.38        60.16        63.02        38.73        35.41        57.90 
TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-ZF-AA5P 
       19.40         8.52        47.15        19.17         5.52        10.13 

  GNA13 MUTATED GNA13 WILD-TYPE 
           7.63            0.10 
  GNA13 MUTATED GNA13 WILD-TYPE 
         112.44          166.03 
  GNA13 MUTATED GNA13 WILD-TYPE 
         28.190          15.385 
[1] "7.6 - 112.4 (28.2)" "0.1 - 166.0 (15.4)"
[1] "hr=" "3"  
D33V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  GNA13 MUTATED         0        3         4        2
  GNA13 WILD-TYPE       4      114       118      126
D33V3, multiclass
           clus
vv          GNA13 MUTATED GNA13 WILD-TYPE
  STAGE I               0               4
  STAGE II              3             114
  STAGE III             4             118
  STAGE IV              2             126
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1+T2  T3  T4
  GNA13 MUTATED          2   6   1
  GNA13 WILD-TYPE      112 173  51
D33V4, multiclass
          clus
vv         GNA13 MUTATED GNA13 WILD-TYPE
  T0+T1+T2             2             112
  T3                   6             173
  T4                   1              51
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  GNA13 MUTATED     7   2   1   0
  GNA13 WILD-TYPE 206  39  74   8
D33V5, multiclass
    clus
vv   GNA13 MUTATED GNA13 WILD-TYPE
  N0             7             206
  N1             2              39
  N2             1              74
  N3             0               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"
D33V6, binary
                 cls
clus                0   1
  GNA13 MUTATED     4   0
  GNA13 WILD-TYPE 178  10
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GNA13 MUTATED      4    0
  GNA13 WILD-TYPE  178   10
   clus
vv  GNA13 MUTATED GNA13 WILD-TYPE
  0             4             178
  1             0              10
[1] 2 2
[1] FALSE
D33V7, binary
                 cls
clus                0   1
  GNA13 MUTATED     0  10
  GNA13 WILD-TYPE  96 270
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GNA13 MUTATED      0   10
  GNA13 WILD-TYPE   96  270
        clus
vv       GNA13 MUTATED GNA13 WILD-TYPE
  FEMALE             0              96
  MALE              10             270
[1] 2 2
[1] FALSE
D33V8, continuous
D33V9, continuous
D33V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  GNA13 MUTATED       0                         0    10
  GNA13 WILD-TYPE    38                        21   291
D33V11, multiclass
                           clus
vv                          GNA13 MUTATED GNA13 WILD-TYPE
  ASIAN                                 0              38
  BLACK OR AFRICAN AMERICAN             0              21
  WHITE                                10             291
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V12, binary
                 cls
clus                0   1
  GNA13 MUTATED     1   8
  GNA13 WILD-TYPE   7 330
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GNA13 MUTATED      1    8
  GNA13 WILD-TYPE    7  330
                        clus
vv                       GNA13 MUTATED GNA13 WILD-TYPE
  HISPANIC OR LATINO                 1               7
  NOT HISPANIC OR LATINO             8             330
[1] 2 2
[1] FALSE

Clustering(34) Variable = METTL3 MUTATION ANALYSIS
D34V1, survival
                  sevent
clus2                0   1
  METTL3 MUTATED    12   4
  METTL3 WILD-TYPE 207 147
  METTL3 MUTATED METTL3 WILD-TYPE 
              16              354 
  METTL3 MUTATED METTL3 WILD-TYPE 
               4              147 
$`METTL3 MUTATED`
TCGA-4Z-AA7S TCGA-DK-A1AC TCGA-DK-A6AW TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6S 
       34.98       130.88        41.56        41.06        30.67       166.03 
TCGA-DK-AA76 TCGA-E7-A85H TCGA-FD-A6TB TCGA-FD-A6TG TCGA-GD-A6C6 TCGA-K4-A83P 
       12.03        12.95        18.81         3.06         2.20         6.38 
TCGA-S5-AA26 TCGA-UY-A78M TCGA-XF-A9T0 TCGA-XF-AAN2 
        3.75        22.68        26.27        61.45 

$`METTL3 WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        91.63       103.50       105.70         8.35 
TCGA-4Z-AA7M TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7W 
       16.27        44.94        16.83        16.77        17.16        27.62 
TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA84 
       49.12         0.62        41.75        51.16        66.54        15.12 
TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J 
       10.22        47.80        33.83        40.08         7.33         2.66 
TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N 
        6.74        12.39         6.58        13.15        19.04        32.84 
TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U 
       12.16        17.88        19.50         5.06        14.89        14.96 
TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A2LD 
        5.06         8.35         8.25        17.16        16.18        20.48 
TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E 
        4.67        12.82         9.96        17.56        28.70        24.26 
TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-C4-A0F6 TCGA-C4-A0F7 
       28.41         8.98         1.94         2.93        23.01         2.04 
TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V 
        0.46         0.43         0.69        10.95        12.66        12.46 
TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 
       12.10        12.62        12.26        13.12        12.00        12.10 
TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ 
       11.87        13.08        12.92         4.90         7.20         5.46 
TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 
        5.19        16.31         1.84        13.58        21.86         2.14 
TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AD TCGA-DK-A1AE 
       66.41        18.41        19.00        16.70       112.44        16.14 
TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 
       17.62        15.62         1.81        10.59         7.79       123.85 
TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ 
       87.32         2.20        13.58         7.82         8.22        17.72 
TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX 
       50.27        21.30        23.21         9.67        20.81        10.55 
TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6B0 TCGA-DK-A6B1 
      140.81        48.00        17.98        64.18        76.60        67.36 
TCGA-DK-A6B2 TCGA-DK-AA6L TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-DK-AA6U 
       15.68        38.24        15.02        13.58        12.36        10.49 
TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA77 TCGA-E5-A2PC 
        8.65         7.53        13.64        43.50        10.62        43.59 
TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ 
       15.35        38.83        24.66         0.10         0.49         2.24 
TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 
       16.70        17.39         0.56         0.66        14.56        13.97 
TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A7XN 
       12.99        14.33         0.92         1.22        13.68        14.07 
TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 
       14.37         8.09        32.02        16.77         8.94        33.04 
TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ 
        4.01        12.62        22.52        27.98        60.66        24.30 
TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ 
       23.41        17.98        29.16         5.52        25.74        46.78 
TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U 
       19.79        12.85        22.98        27.35        14.96        20.91 
TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV 
        3.62        26.73        53.88        11.01        19.33         5.36 
TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N 
        5.69         8.25        27.45        18.08        58.92         2.70 
TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TC TCGA-FD-A6TD 
        7.10         6.28        13.35        62.86         6.15        12.69 
TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z7 
       12.36         2.27         4.31         9.67        10.85        31.07 
TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FJ-A871 TCGA-FT-A3EE TCGA-FT-A61P 
        7.13        10.65        17.23         8.94         3.25         6.48 
TCGA-G2-A2EC TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO 
       22.88        61.94        30.61        15.95        26.93        35.24 
TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3C 
       33.01         7.23        20.12        17.62        66.02         6.94 
TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB 
       64.44        19.46        21.40         2.24        15.81         4.50 
TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GC-A6I3 
       15.91        14.07        17.75        24.92         8.94        13.91 
TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A76B TCGA-GU-A42P 
        7.73         2.10         3.12        20.98         7.36        10.92 
TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 
       11.31        11.31         7.63        27.09        20.05         5.62 
TCGA-GU-A767 TCGA-GU-AATO TCGA-GU-AATP TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW 
        4.73        10.65        32.98         7.00        14.27        21.34 
TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK 
       19.10        19.82        20.28         8.48        10.59        27.35 
TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE 
        8.58        19.07        22.72         1.51        19.40        38.60 
TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV 
        3.06         9.01         8.22        25.02         3.45        21.24 
TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ 
        2.76         9.14        27.68         9.07        11.70         1.74 
TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-AAQO TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V 
        1.81        15.42        11.80        15.32        15.58        13.48 
TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX TCGA-SY-A9G0 TCGA-SY-A9G5 
       12.23        16.67        14.24         1.84        12.43        31.56 
TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78N TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A9PA 
       17.62        37.05        86.83        76.01        65.75        35.24 
TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HH TCGA-XF-A8HI 
       29.56        17.82         4.54         1.64         1.87        17.88 
TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SL TCGA-XF-A9SV 
       48.62        64.80        79.66         3.22        66.41        12.76 
TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T2 TCGA-XF-A9T3 
       11.90        23.64        21.04        28.24        18.90         2.24 
TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMF 
       16.27        66.64         2.10        13.74        92.98        10.82 
TCGA-XF-AAMG TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR 
      110.60        11.31        54.90         7.63        71.57        91.73 
TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN0 
        2.96         8.32         6.77        98.99        44.32        56.48 
TCGA-XF-AAN1 TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN7 TCGA-XF-AAN8 
       30.94        86.30        27.06        75.39        18.81         3.88 
TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R0 TCGA-ZF-A9R1 
        9.63         0.66        11.97        13.64        18.64         7.36 
TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 
       21.11        24.13        30.28        27.19        21.86        28.41 
TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RL 
       74.56        13.41         3.48        52.73        52.60        82.49 
TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4U 
       47.84        20.22         2.89        34.06        19.69         8.61 
TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA53 
       59.38        60.16        63.02        38.73        35.41        57.90 
TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-ZF-AA5P 
       19.40         8.52        47.15        19.17         5.52        10.13 

  METTL3 MUTATED METTL3 WILD-TYPE 
             2.2              0.1 
  METTL3 MUTATED METTL3 WILD-TYPE 
          166.03           140.81 
  METTL3 MUTATED METTL3 WILD-TYPE 
          24.475           15.500 
[1] "2.2 - 166.0 (24.5)" "0.1 - 140.8 (15.5)"
[1] "hr=" "2.2"
D34V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  METTL3 MUTATED         0        4         8        4
  METTL3 WILD-TYPE       4      113       114      124
D34V3, multiclass
           clus
vv          METTL3 MUTATED METTL3 WILD-TYPE
  STAGE I                0                4
  STAGE II               4              113
  STAGE III              8              114
  STAGE IV               4              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"
                  vv
clus               T0+T1+T2  T3  T4
  METTL3 MUTATED          3   8   3
  METTL3 WILD-TYPE      111 171  49
D34V4, multiclass
          clus
vv         METTL3 MUTATED METTL3 WILD-TYPE
  T0+T1+T2              3              111
  T3                    8              171
  T4                    3               49
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  METTL3 MUTATED    11   1   3   0
  METTL3 WILD-TYPE 202  40  72   8
D34V5, multiclass
    clus
vv   METTL3 MUTATED METTL3 WILD-TYPE
  N0             11              202
  N1              1               40
  N2              3               72
  N3              0                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"
D34V6, binary
                  cls
clus                 0   1
  METTL3 MUTATED     7   0
  METTL3 WILD-TYPE 175  10
[1] "tbl2"
                  cls
clus               [,1] [,2]
  METTL3 MUTATED      7    0
  METTL3 WILD-TYPE  175   10
   clus
vv  METTL3 MUTATED METTL3 WILD-TYPE
  0              7              175
  1              0               10
[1] 2 2
[1] FALSE
D34V7, binary
                  cls
clus                 0   1
  METTL3 MUTATED     2  14
  METTL3 WILD-TYPE  94 266
[1] "tbl2"
                  cls
clus               [,1] [,2]
  METTL3 MUTATED      2   14
  METTL3 WILD-TYPE   94  266
        clus
vv       METTL3 MUTATED METTL3 WILD-TYPE
  FEMALE              2               94
  MALE               14              266
[1] 2 2
[1] FALSE
D34V8, continuous
D34V9, continuous
D34V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  METTL3 MUTATED       2                         2    12
  METTL3 WILD-TYPE    36                        19   289
D34V11, multiclass
                           clus
vv                          METTL3 MUTATED METTL3 WILD-TYPE
  ASIAN                                  2               36
  BLACK OR AFRICAN AMERICAN              2               19
  WHITE                                 12              289
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V12, binary
                  cls
clus                 0   1
  METTL3 MUTATED     0  14
  METTL3 WILD-TYPE   8 324
[1] "tbl2"
                  cls
clus               [,1] [,2]
  METTL3 MUTATED      0   14
  METTL3 WILD-TYPE    8  324
                        clus
vv                       METTL3 MUTATED METTL3 WILD-TYPE
  HISPANIC OR LATINO                  0                8
  NOT HISPANIC OR LATINO             14              324
[1] 2 2
[1] FALSE

Clustering(35) Variable = ERBB3 MUTATION ANALYSIS
D35V1, survival
                 sevent
clus2               0   1
  ERBB3 MUTATED    24  16
  ERBB3 WILD-TYPE 195 135
  ERBB3 MUTATED ERBB3 WILD-TYPE 
             40             330 
  ERBB3 MUTATED ERBB3 WILD-TYPE 
             16             135 
$`ERBB3 MUTATED`
TCGA-2F-A9KW TCGA-4Z-AA7Q TCGA-4Z-AA81 TCGA-BT-A20R TCGA-DK-A1AA TCGA-DK-A1AG 
        8.35        16.77        41.75         5.06        19.00        15.62 
TCGA-DK-A3IL TCGA-DK-A3IN TCGA-DK-A6B1 TCGA-DK-A6B6 TCGA-DK-AA6P TCGA-DK-AA6S 
       13.58         8.22        67.36        30.67        15.02       166.03 
TCGA-DK-AA6X TCGA-E5-A4TZ TCGA-E7-A4IJ TCGA-E7-A541 TCGA-FD-A3B6 TCGA-FD-A3SJ 
        7.53        15.35         0.49        17.39        33.04        24.30 
TCGA-FD-A3SN TCGA-FD-A62O TCGA-FD-A6TB TCGA-FD-A6TG TCGA-FJ-A3ZF TCGA-G2-A2EF 
       29.16         7.10        18.81         3.06        17.23        61.94 
TCGA-G2-A2EO TCGA-G2-AA3B TCGA-GD-A3OQ TCGA-GU-A42R TCGA-HQ-A2OE TCGA-HQ-A5NE 
       35.24        66.02         3.12        11.31        38.60         8.22 
TCGA-K4-A6FZ TCGA-MV-A51V TCGA-XF-A8HH TCGA-XF-A9T8 TCGA-XF-AAMF TCGA-XF-AAML 
        1.81        13.48         1.87        13.74        10.82         7.63 
TCGA-YC-A8S6 TCGA-YF-AA3M TCGA-ZF-AA4U TCGA-ZF-AA53 
        9.63        13.64         8.61        57.90 

$`ERBB3 WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-4Z-AA7M 
       22.29        11.97        91.63       103.50       105.70        16.27 
TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7W TCGA-4Z-AA7Y 
       44.94        16.83        17.16        34.98        27.62        49.12 
TCGA-4Z-AA80 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA84 TCGA-4Z-AA86 TCGA-4Z-AA87 
        0.62        51.16        66.54        15.12        10.22        47.80 
TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ 
       33.83        40.08         7.33         2.66         6.74        12.39 
TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P 
        6.58        13.15        19.04        32.84        12.16        17.88 
TCGA-BT-A20Q TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X 
       19.50        14.89        14.96         5.06         8.35         8.25 
TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK 
       17.16        16.18        20.48         4.67        12.82         9.96 
TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 
       17.56        28.70        24.26        28.41         8.98         1.94 
TCGA-C4-A0F1 TCGA-C4-A0F6 TCGA-C4-A0F7 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C 
        2.93        23.01         2.04         0.46         0.43         0.69 
TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y 
       10.95        12.66        12.46        12.10        12.62        12.26 
TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A0YN 
       13.12        12.00        12.10        11.87        13.08        12.92 
TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 
        4.90         7.20         5.46         5.19        16.31         1.84 
TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AB 
       13.58        21.86         2.14        66.41        18.41        16.70 
TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A2HX TCGA-DK-A2I1 
      130.88       112.44        16.14        17.62         1.81        10.59 
TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IM TCGA-DK-A3IQ 
        7.79       123.85        87.32         2.20         7.82        17.72 
TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX 
       50.27        21.30        23.21         9.67        20.81        10.55 
TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 
      140.81        48.00        17.98        64.18        41.56        76.60 
TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-AA6L TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-DK-AA6U 
       15.68        41.06        38.24        13.58        12.36        10.49 
TCGA-DK-AA6W TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A2PC 
        8.65        13.64        43.50        12.03        10.62        43.59 
TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KE 
       38.83        24.66         0.10         2.24        16.70         0.56 
TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DU 
        0.66        14.56        13.97        12.99        14.33         0.92 
TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A97P TCGA-E7-A97Q 
        1.22        13.68        14.07        12.95        14.37         8.09 
TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 
       32.02        16.77         8.94         4.01        12.62        22.52 
TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SO TCGA-FD-A3SP 
       27.98        60.66        23.41        17.98         5.52        25.74 
TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S 
       46.78        19.79        12.85        22.98        27.35        14.96 
TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU 
       20.91         3.62        26.73        53.88        11.01        19.33 
TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 
        5.36         5.69         8.25        27.45        18.08        58.92 
TCGA-FD-A62N TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TC TCGA-FD-A6TD 
        2.70         6.28        13.35        62.86         6.15        12.69 
TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z7 
       12.36         2.27         4.31         9.67        10.85        31.07 
TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A871 TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EC 
        7.13        10.65         8.94         3.25         6.48        22.88 
TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE 
       30.61        15.95        26.93        33.01         7.23        20.12 
TCGA-G2-A3VY TCGA-G2-AA3C TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 
       17.62         6.94        64.44        19.46        21.40         2.24 
TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS 
       15.81         4.50        15.91        14.07        17.75        24.92 
TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OS TCGA-GD-A6C6 
        8.94        13.91         7.73         2.10        20.98         2.20 
TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A764 
        7.36        10.92        11.31         7.63        27.09        20.05 
TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATO TCGA-GU-AATP TCGA-GU-AATQ TCGA-GV-A3JV 
        5.62         4.73        10.65        32.98         7.00        14.27 
TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI 
       21.34        19.10        19.82        20.28         8.48        10.59 
TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-H4-A2HQ 
       27.35         8.58        19.07        22.72         1.51        19.40 
TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB 
        3.06         9.01        25.02         3.45        21.24         2.76 
TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6MB 
        9.14        27.68         9.07        11.70         1.74        15.42 
TCGA-K4-A83P TCGA-K4-AAQO TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-PQ-A6FI TCGA-PQ-A6FN 
        6.38        11.80        15.32        15.58        12.23        16.67 
TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78K 
       14.24         1.84         3.75        12.43        31.56        17.62 
TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78N TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A9PA 
       37.05        22.68        86.83        76.01        65.75        35.24 
TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HI TCGA-XF-A9SG 
       29.56        17.82         4.54         1.64        17.88        48.62 
TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SL TCGA-XF-A9SV TCGA-XF-A9SW 
       64.80        79.66         3.22        66.41        12.76        11.90 
TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 
       23.64        21.04        28.24        26.27        18.90         2.24 
TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-AAME TCGA-XF-AAMG TCGA-XF-AAMH 
       16.27        66.64         2.10        92.98       110.60        11.31 
TCGA-XF-AAMJ TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX 
       54.90        71.57        91.73         2.96         8.32         6.77 
TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 
       98.99        44.32        56.48        30.94        61.45        86.30 
TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A9TC TCGA-YF-AA3L 
       27.06        75.39        18.81         3.88         0.66        11.97 
TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R5 
       18.64         7.36        21.11        24.13        30.28        27.19 
TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RF 
       21.86        28.41        74.56        13.41         3.48        52.73 
TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4R 
       52.60        82.49        47.84        20.22         2.89        34.06 
TCGA-ZF-AA4T TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 
       19.69        59.38        60.16        63.02        38.73        35.41 
TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-ZF-AA5P 
       19.40         8.52        47.15        19.17         5.52        10.13 

  ERBB3 MUTATED ERBB3 WILD-TYPE 
           0.49            0.10 
  ERBB3 MUTATED ERBB3 WILD-TYPE 
         166.03          140.81 
  ERBB3 MUTATED ERBB3 WILD-TYPE 
          14.38           15.93 
[1] "0.5 - 166.0 (14.4)" "0.1 - 140.8 (15.9)"
[1] "hr=" "1"  
D35V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  ERBB3 MUTATED         0       14        15       10
  ERBB3 WILD-TYPE       4      103       107      118
D35V3, multiclass
           clus
vv          ERBB3 MUTATED ERBB3 WILD-TYPE
  STAGE I               0               4
  STAGE II             14             103
  STAGE III            15             107
  STAGE IV             10             118
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1+T2  T3  T4
  ERBB3 MUTATED         12  17   6
  ERBB3 WILD-TYPE      102 162  46
D35V4, multiclass
          clus
vv         ERBB3 MUTATED ERBB3 WILD-TYPE
  T0+T1+T2            12             102
  T3                  17             162
  T4                   6              46
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  ERBB3 MUTATED    23   2   9   0
  ERBB3 WILD-TYPE 190  39  66   8
D35V5, multiclass
    clus
vv   ERBB3 MUTATED ERBB3 WILD-TYPE
  N0            23             190
  N1             2              39
  N2             9              66
  N3             0               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"
D35V6, binary
                 cls
clus                0   1
  ERBB3 MUTATED    20   0
  ERBB3 WILD-TYPE 162  10
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERBB3 MUTATED     20    0
  ERBB3 WILD-TYPE  162   10
   clus
vv  ERBB3 MUTATED ERBB3 WILD-TYPE
  0            20             162
  1             0              10
[1] 2 2
[1] FALSE
D35V7, binary
                 cls
clus                0   1
  ERBB3 MUTATED     7  33
  ERBB3 WILD-TYPE  89 247
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERBB3 MUTATED      7   33
  ERBB3 WILD-TYPE   89  247
        clus
vv       ERBB3 MUTATED ERBB3 WILD-TYPE
  FEMALE             7              89
  MALE              33             247
[1] 2 2
[1] FALSE
D35V8, continuous
D35V9, continuous
D35V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ERBB3 MUTATED       1                         0    36
  ERBB3 WILD-TYPE    37                        21   265
D35V11, multiclass
                           clus
vv                          ERBB3 MUTATED ERBB3 WILD-TYPE
  ASIAN                                 1              37
  BLACK OR AFRICAN AMERICAN             0              21
  WHITE                                36             265
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V12, binary
                 cls
clus                0   1
  ERBB3 MUTATED     2  34
  ERBB3 WILD-TYPE   6 304
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERBB3 MUTATED      2   34
  ERBB3 WILD-TYPE    6  304
                        clus
vv                       ERBB3 MUTATED ERBB3 WILD-TYPE
  HISPANIC OR LATINO                 2               6
  NOT HISPANIC OR LATINO            34             304
[1] 2 2
[1] FALSE

Clustering(36) Variable = RUNX1 MUTATION ANALYSIS
D36V1, survival
                 sevent
clus2               0   1
  RUNX1 MUTATED     6   6
  RUNX1 WILD-TYPE 213 145
  RUNX1 MUTATED RUNX1 WILD-TYPE 
             12             358 
  RUNX1 MUTATED RUNX1 WILD-TYPE 
              6             145 
$`RUNX1 MUTATED`
TCGA-DK-A1AC TCGA-DK-AA6W TCGA-E7-A85H TCGA-FD-A3B3 TCGA-FD-A43P TCGA-GC-A3YS 
      130.88         8.65        12.95        32.02        27.35        24.92 
TCGA-UY-A78M TCGA-XF-A9T2 TCGA-XF-A9T8 TCGA-XF-AAN7 TCGA-ZF-A9RC TCGA-ZF-AA4N 
       22.68        18.90        13.74        18.81        74.56         2.89 

$`RUNX1 WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        91.63       103.50       105.70         8.35 
TCGA-4Z-AA7M TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7S 
       16.27        44.94        16.83        16.77        17.16        34.98 
TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 
       27.62        49.12         0.62        41.75        51.16        66.54 
TCGA-4Z-AA84 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BL-A13I 
       15.12        10.22        47.80        33.83        40.08         7.33 
TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J 
        2.66         6.74        12.39         6.58        13.15        19.04 
TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T 
       32.84        12.16        17.88        19.50         5.06        14.89 
TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB 
       14.96         5.06         8.35         8.25        17.16        16.18 
TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C 
       20.48         4.67        12.82         9.96        17.56        28.70 
TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-C4-A0F6 
       24.26        28.41         8.98         1.94         2.93        23.01 
TCGA-C4-A0F7 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T 
        2.04         0.46         0.43         0.69        10.95        12.66 
TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA 
       12.46        12.10        12.62        12.26        13.12        12.00 
TCGA-CF-A7I0 TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR 
       12.10        11.87        13.08        12.92         4.90         7.20 
TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 
        5.46         5.19        16.31         1.84        13.58        21.86 
TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AD 
        2.14        66.41        18.41        19.00        16.70       112.44 
TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 
       16.14        17.62        15.62         1.81        10.59         7.79 
TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN 
      123.85        87.32         2.20        13.58         7.82         8.22 
TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW 
       17.72        50.27        21.30        23.21         9.67        20.81 
TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW 
       10.55       140.81        48.00        17.98        64.18        41.56 
TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L 
       76.60        67.36        15.68        41.06        30.67        38.24 
TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6X 
       15.02        13.58       166.03        12.36        10.49         7.53 
TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A2PC TCGA-E5-A4TZ 
       13.64        43.50        12.03        10.62        43.59        15.35 
TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 
       38.83        24.66         0.10         0.49         2.24        16.70 
TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME 
       17.39         0.56         0.66        14.56        13.97        12.99 
TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A97P 
       14.33         0.92         1.22        13.68        14.07        14.37 
TCGA-E7-A97Q TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 
        8.09        16.77         8.94        33.04         4.01        12.62 
TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM 
       22.52        27.98        60.66        24.30        23.41        17.98 
TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS 
       29.16         5.52        25.74        46.78        19.79        12.85 
TCGA-FD-A43N TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS 
       22.98        14.96        20.91         3.62        26.73        53.88 
TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ 
       11.01        19.33         5.36         5.69         8.25        27.45 
TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S 
       18.08        58.92         2.70         7.10         6.28        13.35 
TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF 
       62.86        18.81         6.15        12.69        12.36         2.27 
TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 
        3.06         4.31         9.67        10.85        31.07         7.13 
TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FJ-A871 TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EC 
       10.65        17.23         8.94         3.25         6.48        22.88 
TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES 
       61.94        30.61        15.95        26.93        35.24        33.01 
TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3D 
        7.23        20.12        17.62        66.02         6.94        64.44 
TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC 
       19.46        21.40         2.24        15.81         4.50        15.91 
TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP 
       14.07        17.75         8.94        13.91         7.73         2.10 
TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42Q 
        3.12        20.98         2.20         7.36        10.92        11.31 
TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 
       11.31         7.63        27.09        20.05         5.62         4.73 
TCGA-GU-AATO TCGA-GU-AATP TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX 
       10.65        32.98         7.00        14.27        21.34        19.10 
TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E 
       19.82        20.28         8.48        10.59        27.35         8.58 
TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF 
       19.07        22.72         1.51        19.40        38.60         3.06 
TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB 
        9.01         8.22        25.02         3.45        21.24         2.76 
TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ 
        9.14        27.68         9.07        11.70         1.74         1.81 
TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V 
       15.42         6.38        11.80        15.32        15.58        13.48 
TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 TCGA-SY-A9G0 
       12.23        16.67        14.24         1.84         3.75        12.43 
TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78N TCGA-UY-A78O TCGA-UY-A8OB 
       31.56        17.62        37.05        86.83        76.01        65.75 
TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HH 
       35.24        29.56        17.82         4.54         1.64         1.87 
TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SL 
       17.88        48.62        64.80        79.66         3.22        66.41 
TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T0 
       12.76        11.90        23.64        21.04        28.24        26.27 
TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-AAME TCGA-XF-AAMF 
        2.24        16.27        66.64         2.10        92.98        10.82 
TCGA-XF-AAMG TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR 
      110.60        11.31        54.90         7.63        71.57        91.73 
TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN0 
        2.96         8.32         6.77        98.99        44.32        56.48 
TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN8 
       30.94        61.45        86.30        27.06        75.39         3.88 
TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R0 TCGA-ZF-A9R1 
        9.63         0.66        11.97        13.64        18.64         7.36 
TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 
       21.11        24.13        30.28        27.19        21.86        28.41 
TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-A9RM 
       13.41         3.48        52.73        52.60        82.49        47.84 
TCGA-ZF-A9RN TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W 
       20.22        34.06        19.69         8.61        59.38        60.16 
TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA56 
       63.02        38.73        35.41        57.90        19.40         8.52 
TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-ZF-AA5P 
       47.15        19.17         5.52        10.13 

  RUNX1 MUTATED RUNX1 WILD-TYPE 
           2.89            0.10 
  RUNX1 MUTATED RUNX1 WILD-TYPE 
         130.88          166.03 
  RUNX1 MUTATED RUNX1 WILD-TYPE 
          20.79           15.50 
[1] "2.9 - 130.9 (20.8)" "0.1 - 166.0 (15.5)"
[1] "hr=" "1"  
D36V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  RUNX1 MUTATED         0        3         6        3
  RUNX1 WILD-TYPE       4      114       116      125
D36V3, multiclass
           clus
vv          RUNX1 MUTATED RUNX1 WILD-TYPE
  STAGE I               0               4
  STAGE II              3             114
  STAGE III             6             116
  STAGE IV              3             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"
                 vv
clus              T0+T1+T2  T3  T4
  RUNX1 MUTATED          3   8   0
  RUNX1 WILD-TYPE      111 171  52
D36V4, multiclass
          clus
vv         RUNX1 MUTATED RUNX1 WILD-TYPE
  T0+T1+T2             3             111
  T3                   8             171
  T4                   0              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"
                 vv
clus               N0  N1  N2  N3
  RUNX1 MUTATED     8   2   1   0
  RUNX1 WILD-TYPE 205  39  74   8
D36V5, multiclass
    clus
vv   RUNX1 MUTATED RUNX1 WILD-TYPE
  N0             8             205
  N1             2              39
  N2             1              74
  N3             0               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"
D36V6, binary
                 cls
clus                0   1
  RUNX1 MUTATED     3   0
  RUNX1 WILD-TYPE 179  10
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RUNX1 MUTATED      3    0
  RUNX1 WILD-TYPE  179   10
   clus
vv  RUNX1 MUTATED RUNX1 WILD-TYPE
  0             3             179
  1             0              10
[1] 2 2
[1] FALSE
D36V7, binary
                 cls
clus                0   1
  RUNX1 MUTATED     2  10
  RUNX1 WILD-TYPE  94 270
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RUNX1 MUTATED      2   10
  RUNX1 WILD-TYPE   94  270
        clus
vv       RUNX1 MUTATED RUNX1 WILD-TYPE
  FEMALE             2              94
  MALE              10             270
[1] 2 2
[1] FALSE
D36V8, continuous
D36V9, continuous
D36V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RUNX1 MUTATED       2                         1     9
  RUNX1 WILD-TYPE    36                        20   292
D36V11, multiclass
                           clus
vv                          RUNX1 MUTATED RUNX1 WILD-TYPE
  ASIAN                                 2              36
  BLACK OR AFRICAN AMERICAN             1              20
  WHITE                                 9             292
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V12, binary
                 cls
clus                0   1
  RUNX1 MUTATED     0  11
  RUNX1 WILD-TYPE   8 327
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RUNX1 MUTATED      0   11
  RUNX1 WILD-TYPE    8  327
                        clus
vv                       RUNX1 MUTATED RUNX1 WILD-TYPE
  HISPANIC OR LATINO                 0               8
  NOT HISPANIC OR LATINO            11             327
[1] 2 2
[1] FALSE

Clustering(37) Variable = MBD1 MUTATION ANALYSIS
D37V1, survival
                sevent
clus2              0   1
  MBD1 MUTATED     7   4
  MBD1 WILD-TYPE 212 147
  MBD1 MUTATED MBD1 WILD-TYPE 
            11            359 
  MBD1 MUTATED MBD1 WILD-TYPE 
             4            147 
$`MBD1 MUTATED`
TCGA-BT-A3PJ TCGA-DK-A2I4 TCGA-DK-A3WX TCGA-DK-AA6U TCGA-E5-A4U1 TCGA-E7-A3Y1 
       12.82       123.85        10.55        10.49        38.83         0.10 
TCGA-FD-A3SR TCGA-G2-A2ES TCGA-K4-A54R TCGA-XF-A9T3 TCGA-XF-AAN2 
       19.79        33.01        27.68         2.24        61.45 

$`MBD1 WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        91.63       103.50       105.70         8.35 
TCGA-4Z-AA7M TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7S 
       16.27        44.94        16.83        16.77        17.16        34.98 
TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 
       27.62        49.12         0.62        41.75        51.16        66.54 
TCGA-4Z-AA84 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BL-A13I 
       15.12        10.22        47.80        33.83        40.08         7.33 
TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J 
        2.66         6.74        12.39         6.58        13.15        19.04 
TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T 
       32.84        12.16        17.88        19.50         5.06        14.89 
TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB 
       14.96         5.06         8.35         8.25        17.16        16.18 
TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E 
       20.48         4.67         9.96        17.56        28.70        24.26 
TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-C4-A0F6 TCGA-C4-A0F7 
       28.41         8.98         1.94         2.93        23.01         2.04 
TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V 
        0.46         0.43         0.69        10.95        12.66        12.46 
TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 
       12.10        12.62        12.26        13.12        12.00        12.10 
TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ 
       11.87        13.08        12.92         4.90         7.20         5.46 
TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 
        5.19        16.31         1.84        13.58        21.86         2.14 
TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD 
       66.41        18.41        19.00        16.70       130.88       112.44 
TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 
       16.14        17.62        15.62         1.81        10.59         7.79 
TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ 
       87.32         2.20        13.58         7.82         8.22        17.72 
TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WY 
       50.27        21.30        23.21         9.67        20.81       140.81 
TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 
       48.00        17.98        64.18        41.56        76.60        67.36 
TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6P TCGA-DK-AA6Q 
       15.68        41.06        30.67        38.24        15.02        13.58 
TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA74 
      166.03        12.36         8.65         7.53        13.64        43.50 
TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E7-A3X6 TCGA-E7-A4IJ 
       12.03        10.62        43.59        15.35        24.66         0.49 
TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 
        2.24        16.70        17.39         0.56         0.66        14.56 
TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7DV TCGA-E7-A7PW 
       13.97        12.99        14.33         0.92         1.22        13.68 
TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 
       14.07        12.95        14.37         8.09        32.02        16.77 
TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 
        8.94        33.04         4.01        12.62        22.52        27.98 
TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO 
       60.66        24.30        23.41        17.98        29.16         5.52 
TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S 
       25.74        46.78        12.85        22.98        27.35        14.96 
TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU 
       20.91         3.62        26.73        53.88        11.01        19.33 
TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 
        5.36         5.69         8.25        27.45        18.08        58.92 
TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB 
        2.70         7.10         6.28        13.35        62.86        18.81 
TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH 
        6.15        12.69        12.36         2.27         3.06         4.31 
TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF 
        9.67        10.85        31.07         7.13        10.65        17.23 
TCGA-FJ-A871 TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EC TCGA-G2-A2EF TCGA-G2-A2EJ 
        8.94         3.25         6.48        22.88        61.94        30.61 
TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY 
       15.95        26.93        35.24         7.23        20.12        17.62 
TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 
       66.02         6.94        64.44        19.46        21.40         2.24 
TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS 
       15.81         4.50        15.91        14.07        17.75        24.92 
TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS 
        8.94        13.91         7.73         2.10         3.12        20.98 
TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 
        2.20         7.36        10.92        11.31        11.31         7.63 
TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATO TCGA-GU-AATP 
       27.09        20.05         5.62         4.73        10.65        32.98 
TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF 
        7.00        14.27        21.34        19.10        19.82        20.28 
TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA 
        8.48        10.59        27.35         8.58        19.07        22.72 
TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE 
        1.51        19.40        38.60         3.06         9.01         8.22 
TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A5RH 
       25.02         3.45        21.24         2.76         9.14         9.07 
TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO 
       11.70         1.74         1.81        15.42         6.38        11.80 
TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X 
       15.32        15.58        13.48        12.23        16.67        14.24 
TCGA-S5-A6DX TCGA-S5-AA26 TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L 
        1.84         3.75        12.43        31.56        17.62        37.05 
TCGA-UY-A78M TCGA-UY-A78N TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A9PA TCGA-UY-A9PB 
       22.68        86.83        76.01        65.75        35.24        29.56 
TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG 
       17.82         4.54         1.64         1.87        17.88        48.62 
TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SL TCGA-XF-A9SV TCGA-XF-A9SW 
       64.80        79.66         3.22        66.41        12.76        11.90 
TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T4 
       23.64        21.04        28.24        26.27        18.90        16.27 
TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMG 
       66.64         2.10        13.74        92.98        10.82       110.60 
TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMT 
       11.31        54.90         7.63        71.57        91.73         2.96 
TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN0 TCGA-XF-AAN1 
        8.32         6.77        98.99        44.32        56.48        30.94 
TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 
       86.30        27.06        75.39        18.81         3.88         9.63 
TCGA-YC-A9TC TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R2 
        0.66        11.97        13.64        18.64         7.36        21.11 
TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RC 
       24.13        30.28        27.19        21.86        28.41        74.56 
TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-A9RM 
       13.41         3.48        52.73        52.60        82.49        47.84 
TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4U TCGA-ZF-AA4V 
       20.22         2.89        34.06        19.69         8.61        59.38 
TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA53 TCGA-ZF-AA54 
       60.16        63.02        38.73        35.41        57.90        19.40 
TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-ZF-AA5P 
        8.52        47.15        19.17         5.52        10.13 

  MBD1 MUTATED MBD1 WILD-TYPE 
          0.10           0.43 
  MBD1 MUTATED MBD1 WILD-TYPE 
        123.85         166.03 
  MBD1 MUTATED MBD1 WILD-TYPE 
         19.79          15.62 
[1] "0.1 - 123.8 (19.8)" "0.4 - 166.0 (15.6)"
[1] "hr=" "1.3"
D37V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  MBD1 MUTATED         1        5         3        2
  MBD1 WILD-TYPE       3      112       119      126
D37V3, multiclass
           clus
vv          MBD1 MUTATED MBD1 WILD-TYPE
  STAGE I              1              3
  STAGE II             5            112
  STAGE III            3            119
  STAGE IV             2            126
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1+T2  T3  T4
  MBD1 MUTATED          3   5   1
  MBD1 WILD-TYPE      111 174  51
D37V4, multiclass
          clus
vv         MBD1 MUTATED MBD1 WILD-TYPE
  T0+T1+T2            3            111
  T3                  5            174
  T4                  1             51
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  MBD1 MUTATED     8   0   2   1
  MBD1 WILD-TYPE 205  41  73   7
D37V5, multiclass
    clus
vv   MBD1 MUTATED MBD1 WILD-TYPE
  N0            8            205
  N1            0             41
  N2            2             73
  N3            1              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"
D37V6, binary
                cls
clus               0   1
  MBD1 MUTATED     7   0
  MBD1 WILD-TYPE 175  10
[1] "tbl2"
                cls
clus             [,1] [,2]
  MBD1 MUTATED      7    0
  MBD1 WILD-TYPE  175   10
   clus
vv  MBD1 MUTATED MBD1 WILD-TYPE
  0            7            175
  1            0             10
[1] 2 2
[1] FALSE
D37V7, binary
                cls
clus               0   1
  MBD1 MUTATED     2   9
  MBD1 WILD-TYPE  94 271
[1] "tbl2"
                cls
clus             [,1] [,2]
  MBD1 MUTATED      2    9
  MBD1 WILD-TYPE   94  271
        clus
vv       MBD1 MUTATED MBD1 WILD-TYPE
  FEMALE            2             94
  MALE              9            271
[1] 2 2
[1] FALSE
D37V8, continuous
D37V9, continuous
D37V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MBD1 MUTATED       0                         0    10
  MBD1 WILD-TYPE    38                        21   291
D37V11, multiclass
                           clus
vv                          MBD1 MUTATED MBD1 WILD-TYPE
  ASIAN                                0             38
  BLACK OR AFRICAN AMERICAN            0             21
  WHITE                               10            291
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V12, binary
                cls
clus               0   1
  MBD1 MUTATED     0  11
  MBD1 WILD-TYPE   8 327
[1] "tbl2"
                cls
clus             [,1] [,2]
  MBD1 MUTATED      0   11
  MBD1 WILD-TYPE    8  327
                        clus
vv                       MBD1 MUTATED MBD1 WILD-TYPE
  HISPANIC OR LATINO                0              8
  NOT HISPANIC OR LATINO           11            327
[1] 2 2
[1] FALSE

Clustering(38) Variable = FOXQ1 MUTATION ANALYSIS
D38V1, survival
                 sevent
clus2               0   1
  FOXQ1 MUTATED    10   4
  FOXQ1 WILD-TYPE 209 147
  FOXQ1 MUTATED FOXQ1 WILD-TYPE 
             14             356 
  FOXQ1 MUTATED FOXQ1 WILD-TYPE 
              4             147 
$`FOXQ1 MUTATED`
TCGA-4Z-AA80 TCGA-CF-A1HR TCGA-CU-A3YL TCGA-DK-A2I4 TCGA-DK-A3IM TCGA-DK-A3X1 
        0.62         0.46        16.31       123.85         7.82        48.00 
TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A6TA TCGA-G2-A2EF TCGA-G2-AA3C TCGA-GC-A3RB 
       14.37         8.09        62.86        61.94         6.94         4.50 
TCGA-XF-AAMQ TCGA-ZF-AA51 
       71.57        38.73 

$`FOXQ1 WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        91.63       103.50       105.70         8.35 
TCGA-4Z-AA7M TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7S 
       16.27        44.94        16.83        16.77        17.16        34.98 
TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA84 
       27.62        49.12        41.75        51.16        66.54        15.12 
TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J 
       10.22        47.80        33.83        40.08         7.33         2.66 
TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N 
        6.74        12.39         6.58        13.15        19.04        32.84 
TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U 
       12.16        17.88        19.50         5.06        14.89        14.96 
TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A2LD 
        5.06         8.35         8.25        17.16        16.18        20.48 
TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E 
        4.67        12.82         9.96        17.56        28.70        24.26 
TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-C4-A0F6 TCGA-C4-A0F7 
       28.41         8.98         1.94         2.93        23.01         2.04 
TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W 
        0.43         0.69        10.95        12.66        12.46        12.10 
TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A9FF 
       12.62        12.26        13.12        12.00        12.10        11.87 
TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3QU 
       13.08        12.92         4.90         7.20         5.46         5.19 
TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 
        1.84        13.58        21.86         2.14        66.41        18.41 
TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF 
       19.00        16.70       130.88       112.44        16.14        17.62 
TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I6 TCGA-DK-A3IK 
       15.62         1.81        10.59         7.79        87.32         2.20 
TCGA-DK-A3IL TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU 
       13.58         8.22        17.72        50.27        21.30        23.21 
TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X2 TCGA-DK-A6AV 
        9.67        20.81        10.55       140.81        17.98        64.18 
TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 
       41.56        76.60        67.36        15.68        41.06        30.67 
TCGA-DK-AA6L TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6U 
       38.24        15.02        13.58       166.03        12.36        10.49 
TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA76 TCGA-DK-AA77 
        8.65         7.53        13.64        43.50        12.03        10.62 
TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ 
       43.59        15.35        38.83        24.66         0.10         0.49 
TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 
        2.24        16.70        17.39         0.56         0.66        14.56 
TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7DV TCGA-E7-A7PW 
       13.97        12.99        14.33         0.92         1.22        13.68 
TCGA-E7-A7XN TCGA-E7-A85H TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 
       14.07        12.95        32.02        16.77         8.94        33.04 
TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ 
        4.01        12.62        22.52        27.98        60.66        24.30 
TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ 
       23.41        17.98        29.16         5.52        25.74        46.78 
TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U 
       19.79        12.85        22.98        27.35        14.96        20.91 
TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV 
        3.62        26.73        53.88        11.01        19.33         5.36 
TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N 
        5.69         8.25        27.45        18.08        58.92         2.70 
TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD 
        7.10         6.28        13.35        18.81         6.15        12.69 
TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FD-A6TK 
       12.36         2.27         3.06         4.31         9.67        10.85 
TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FJ-A871 TCGA-FT-A3EE 
       31.07         7.13        10.65        17.23         8.94         3.25 
TCGA-FT-A61P TCGA-G2-A2EC TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO 
        6.48        22.88        30.61        15.95        26.93        35.24 
TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3D 
       33.01         7.23        20.12        17.62        66.02        64.44 
TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RC TCGA-GC-A3RD 
       19.46        21.40         2.24        15.81        15.91        14.07 
TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP 
       17.75        24.92         8.94        13.91         7.73         2.10 
TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42Q 
        3.12        20.98         2.20         7.36        10.92        11.31 
TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 
       11.31         7.63        27.09        20.05         5.62         4.73 
TCGA-GU-AATO TCGA-GU-AATP TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX 
       10.65        32.98         7.00        14.27        21.34        19.10 
TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E 
       19.82        20.28         8.48        10.59        27.35         8.58 
TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF 
       19.07        22.72         1.51        19.40        38.60         3.06 
TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB 
        9.01         8.22        25.02         3.45        21.24         2.76 
TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ 
        9.14        27.68         9.07        11.70         1.74         1.81 
TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V 
       15.42         6.38        11.80        15.32        15.58        13.48 
TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 TCGA-SY-A9G0 
       12.23        16.67        14.24         1.84         3.75        12.43 
TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78N TCGA-UY-A78O 
       31.56        17.62        37.05        22.68        86.83        76.01 
TCGA-UY-A8OB TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF 
       65.75        35.24        29.56        17.82         4.54         1.64 
TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SJ 
        1.87        17.88        48.62        64.80        79.66         3.22 
TCGA-XF-A9SL TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ 
       66.41        12.76        11.90        23.64        21.04        28.24 
TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 
       26.27        18.90         2.24        16.27        66.64         2.10 
TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMG TCGA-XF-AAMH TCGA-XF-AAMJ 
       13.74        92.98        10.82       110.60        11.31        54.90 
TCGA-XF-AAML TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAMY 
        7.63        91.73         2.96         8.32         6.77        98.99 
TCGA-XF-AAMZ TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN4 
       44.32        56.48        30.94        61.45        86.30        27.06 
TCGA-XF-AAN5 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L 
       75.39        18.81         3.88         9.63         0.66        11.97 
TCGA-YF-AA3M TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R4 
       13.64        18.64         7.36        21.11        24.13        30.28 
TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RE 
       27.19        21.86        28.41        74.56        13.41         3.48 
TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N 
       52.73        52.60        82.49        47.84        20.22         2.89 
TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA4X 
       34.06        19.69         8.61        59.38        60.16        63.02 
TCGA-ZF-AA52 TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H 
       35.41        57.90        19.40         8.52        47.15        19.17 
TCGA-ZF-AA5N TCGA-ZF-AA5P 
        5.52        10.13 

  FOXQ1 MUTATED FOXQ1 WILD-TYPE 
           0.46            0.10 
  FOXQ1 MUTATED FOXQ1 WILD-TYPE 
         123.85          166.03 
  FOXQ1 MUTATED FOXQ1 WILD-TYPE 
          15.34           15.65 
[1] "0.5 - 123.8 (15.3)" "0.1 - 166.0 (15.6)"
[1] "hr=" "1.7"
D38V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  FOXQ1 MUTATED         0        5         5        3
  FOXQ1 WILD-TYPE       4      112       117      125
D38V3, multiclass
           clus
vv          FOXQ1 MUTATED FOXQ1 WILD-TYPE
  STAGE I               0               4
  STAGE II              5             112
  STAGE III             5             117
  STAGE IV              3             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"
                 vv
clus              T0+T1+T2  T3  T4
  FOXQ1 MUTATED          4   7   2
  FOXQ1 WILD-TYPE      110 172  50
D38V4, multiclass
          clus
vv         FOXQ1 MUTATED FOXQ1 WILD-TYPE
  T0+T1+T2             4             110
  T3                   7             172
  T4                   2              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"
                 vv
clus               N0  N1  N2  N3
  FOXQ1 MUTATED     9   1   1   1
  FOXQ1 WILD-TYPE 204  40  74   7
D38V5, multiclass
    clus
vv   FOXQ1 MUTATED FOXQ1 WILD-TYPE
  N0             9             204
  N1             1              40
  N2             1              74
  N3             1               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"
D38V6, binary
                 cls
clus                0   1
  FOXQ1 MUTATED    11   0
  FOXQ1 WILD-TYPE 171  10
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FOXQ1 MUTATED     11    0
  FOXQ1 WILD-TYPE  171   10
   clus
vv  FOXQ1 MUTATED FOXQ1 WILD-TYPE
  0            11             171
  1             0              10
[1] 2 2
[1] FALSE
D38V7, binary
                 cls
clus                0   1
  FOXQ1 MUTATED     4  10
  FOXQ1 WILD-TYPE  92 270
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FOXQ1 MUTATED      4   10
  FOXQ1 WILD-TYPE   92  270
        clus
vv       FOXQ1 MUTATED FOXQ1 WILD-TYPE
  FEMALE             4              92
  MALE              10             270
[1] 2 2
[1] FALSE
D38V8, continuous
[1] "Remove cluster labels:" "FOXQ1 MUTATED"         
clus
  FOXQ1 MUTATED FOXQ1 WILD-TYPE 
              2             118 
     TCGA-2F-A9KO      TCGA-2F-A9KP      TCGA-2F-A9KQ      TCGA-2F-A9KR 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-2F-A9KT      TCGA-2F-A9KW      TCGA-CF-A1HS      TCGA-CF-A27C 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-CF-A3MF      TCGA-CF-A3MG      TCGA-CF-A3MH      TCGA-CF-A3MI 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-CF-A47S      TCGA-CF-A47T      TCGA-CF-A47V      TCGA-CF-A47W 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-CF-A47X      TCGA-CF-A47Y      TCGA-CF-A5U8      TCGA-CF-A5UA 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-CF-A7I0      TCGA-DK-A2HX      TCGA-DK-A3IN      TCGA-DK-A3IV 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-DK-A3WX      TCGA-DK-A3X2      TCGA-DK-A6B2      TCGA-DK-A6B5 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-DK-A6B6      TCGA-DK-AA6P      TCGA-DK-AA6S      TCGA-DK-AA6U 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-DK-AA6W      TCGA-DK-AA76      TCGA-E5-A2PC      TCGA-E5-A4TZ 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-E5-A4U1      TCGA-E7-A519      TCGA-E7-A541      TCGA-E7-A7DU 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-E7-A7DV      TCGA-FT-A61P      TCGA-G2-A2EC      TCGA-G2-A2EJ 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-G2-A2EK      TCGA-G2-A2EL      TCGA-G2-A2EO      TCGA-G2-A2ES 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-G2-A3IB      TCGA-G2-A3IE      TCGA-G2-A3VY      TCGA-GC-A3BM 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-GC-A3I6      TCGA-GC-A3OO      TCGA-GC-A3RC      TCGA-GC-A3RD 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-GC-A3YS      TCGA-GC-A6I1      TCGA-GC-A6I3      TCGA-GD-A3OS 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-GD-A6C6      TCGA-GV-A3JV      TCGA-GV-A3JW      TCGA-GV-A3JX 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-GV-A3JZ      TCGA-GV-A3QF      TCGA-GV-A3QH      TCGA-GV-A3QI 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-GV-A3QK      TCGA-GV-A40E      TCGA-GV-A40G      TCGA-GV-A6ZA 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-SY-A9G0      TCGA-SY-A9G5      TCGA-UY-A78L      TCGA-UY-A78M 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-UY-A78N      TCGA-XF-A8HH      TCGA-XF-A8HI      TCGA-XF-A9SG 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-XF-A9SH      TCGA-XF-A9SI      TCGA-XF-A9SJ      TCGA-XF-A9SL 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-XF-A9SV      TCGA-XF-A9SW      TCGA-XF-A9SX      TCGA-XF-A9SY 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-XF-A9SZ      TCGA-XF-A9T0      TCGA-XF-A9T2      TCGA-XF-A9T3 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-XF-A9T4      TCGA-XF-A9T5      TCGA-XF-A9T6      TCGA-XF-A9T8 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-XF-AAME      TCGA-XF-AAMF      TCGA-XF-AAMG      TCGA-XF-AAMH 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-XF-AAMJ      TCGA-XF-AAML      TCGA-XF-AAMR      TCGA-XF-AAMT 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-XF-AAMW      TCGA-XF-AAMX      TCGA-XF-AAMY      TCGA-XF-AAMZ 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-XF-AAN0      TCGA-XF-AAN1      TCGA-XF-AAN2      TCGA-XF-AAN3 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-XF-AAN4      TCGA-XF-AAN5      TCGA-XF-AAN7      TCGA-XF-AAN8 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-YF-AA3L      TCGA-YF-AA3M 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
D38V9, continuous
D38V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  FOXQ1 MUTATED       2                         0    12
  FOXQ1 WILD-TYPE    36                        21   289
D38V11, multiclass
                           clus
vv                          FOXQ1 MUTATED FOXQ1 WILD-TYPE
  ASIAN                                 2              36
  BLACK OR AFRICAN AMERICAN             0              21
  WHITE                                12             289
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V12, binary
                 cls
clus                0   1
  FOXQ1 MUTATED     0  13
  FOXQ1 WILD-TYPE   8 325
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FOXQ1 MUTATED      0   13
  FOXQ1 WILD-TYPE    8  325
                        clus
vv                       FOXQ1 MUTATED FOXQ1 WILD-TYPE
  HISPANIC OR LATINO                 0               8
  NOT HISPANIC OR LATINO            13             325
[1] 2 2
[1] FALSE

Clustering(39) Variable = RPTN MUTATION ANALYSIS
D39V1, survival
                sevent
clus2              0   1
  RPTN MUTATED     8   7
  RPTN WILD-TYPE 211 144
  RPTN MUTATED RPTN WILD-TYPE 
            15            355 
  RPTN MUTATED RPTN WILD-TYPE 
             7            144 
$`RPTN MUTATED`
TCGA-4Z-AA86 TCGA-BT-A3PK TCGA-CU-A3YL TCGA-DK-A3IT TCGA-DK-A3WW TCGA-DK-AA6X 
       10.22         9.96        16.31        21.30        20.81         7.53 
TCGA-E7-A97Q TCGA-G2-A3IE TCGA-G2-AA3B TCGA-K4-A5RH TCGA-MV-A51V TCGA-XF-AAMY 
        8.09        20.12        66.02         9.07        13.48        98.99 
TCGA-XF-AAN2 TCGA-ZF-A9RE TCGA-ZF-AA52 
       61.45         3.48        35.41 

$`RPTN WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        91.63       103.50       105.70         8.35 
TCGA-4Z-AA7M TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7S 
       16.27        44.94        16.83        16.77        17.16        34.98 
TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 
       27.62        49.12         0.62        41.75        51.16        66.54 
TCGA-4Z-AA84 TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J 
       15.12        47.80        33.83        40.08         7.33         2.66 
TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N 
        6.74        12.39         6.58        13.15        19.04        32.84 
TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U 
       12.16        17.88        19.50         5.06        14.89        14.96 
TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A2LD 
        5.06         8.35         8.25        17.16        16.18        20.48 
TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E TCGA-BT-A42F 
        4.67        12.82        17.56        28.70        24.26        28.41 
TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-C4-A0F6 TCGA-C4-A0F7 TCGA-CF-A1HR 
        8.98         1.94         2.93        23.01         2.04         0.46 
TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W 
        0.43         0.69        10.95        12.66        12.46        12.10 
TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A9FF 
       12.62        12.26        13.12        12.00        12.10        11.87 
TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3QU 
       13.08        12.92         4.90         7.20         5.46         5.19 
TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 
        1.84        13.58        21.86         2.14        66.41        18.41 
TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF 
       19.00        16.70       130.88       112.44        16.14        17.62 
TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A2I6 
       15.62         1.81        10.59         7.79       123.85        87.32 
TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS 
        2.20        13.58         7.82         8.22        17.72        50.27 
TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A3X2 
       23.21         9.67        10.55       140.81        48.00        17.98 
TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 
       64.18        41.56        76.60        67.36        15.68        41.06 
TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6S TCGA-DK-AA6T 
       30.67        38.24        15.02        13.58       166.03        12.36 
TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA76 TCGA-DK-AA77 
       10.49         8.65        13.64        43.50        12.03        10.62 
TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ 
       43.59        15.35        38.83        24.66         0.10         0.49 
TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 
        2.24        16.70        17.39         0.56         0.66        14.56 
TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7DV TCGA-E7-A7PW 
       13.97        12.99        14.33         0.92         1.22        13.68 
TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A97P TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 
       14.07        12.95        14.37        32.02        16.77         8.94 
TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA 
       33.04         4.01        12.62        22.52        27.98        60.66 
TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP 
       24.30        23.41        17.98        29.16         5.52        25.74 
TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S 
       46.78        19.79        12.85        22.98        27.35        14.96 
TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU 
       20.91         3.62        26.73        53.88        11.01        19.33 
TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 
        5.36         5.69         8.25        27.45        18.08        58.92 
TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB 
        2.70         7.10         6.28        13.35        62.86        18.81 
TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH 
        6.15        12.69        12.36         2.27         3.06         4.31 
TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF 
        9.67        10.85        31.07         7.13        10.65        17.23 
TCGA-FJ-A871 TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EC TCGA-G2-A2EF TCGA-G2-A2EJ 
        8.94         3.25         6.48        22.88        61.94        30.61 
TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3VY 
       15.95        26.93        35.24        33.01         7.23        17.62 
TCGA-G2-AA3C TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO 
        6.94        64.44        19.46        21.40         2.24        15.81 
TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A6I1 
        4.50        15.91        14.07        17.75        24.92         8.94 
TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 
       13.91         7.73         2.10         3.12        20.98         2.20 
TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 
        7.36        10.92        11.31        11.31         7.63        27.09 
TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATO TCGA-GU-AATP TCGA-GU-AATQ 
       20.05         5.62         4.73        10.65        32.98         7.00 
TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH 
       14.27        21.34        19.10        19.82        20.28         8.48 
TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO 
       10.59        27.35         8.58        19.07        22.72         1.51 
TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS 
       19.40        38.60         3.06         9.01         8.22        25.02 
TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RI 
        3.45        21.24         2.76         9.14        27.68        11.70 
TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO TCGA-LC-A66R 
        1.74         1.81        15.42         6.38        11.80        15.32 
TCGA-LT-A5Z6 TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 
       15.58        12.23        16.67        14.24         1.84         3.75 
TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78N 
       12.43        31.56        17.62        37.05        22.68        86.83 
TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE 
       76.01        65.75        35.24        29.56        17.82         4.54 
TCGA-UY-A9PF TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI 
        1.64         1.87        17.88        48.62        64.80        79.66 
TCGA-XF-A9SJ TCGA-XF-A9SL TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY 
        3.22        66.41        12.76        11.90        23.64        21.04 
TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T5 
       28.24        26.27        18.90         2.24        16.27        66.64 
TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMG TCGA-XF-AAMH 
        2.10        13.74        92.98        10.82       110.60        11.31 
TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMW 
       54.90         7.63        71.57        91.73         2.96         8.32 
TCGA-XF-AAMX TCGA-XF-AAMZ TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN3 TCGA-XF-AAN4 
        6.77        44.32        56.48        30.94        86.30        27.06 
TCGA-XF-AAN5 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L 
       75.39        18.81         3.88         9.63         0.66        11.97 
TCGA-YF-AA3M TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R4 
       13.64        18.64         7.36        21.11        24.13        30.28 
TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RF 
       27.19        21.86        28.41        74.56        13.41        52.73 
TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4R 
       52.60        82.49        47.84        20.22         2.89        34.06 
TCGA-ZF-AA4T TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA51 
       19.69         8.61        59.38        60.16        63.02        38.73 
TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N 
       57.90        19.40         8.52        47.15        19.17         5.52 
TCGA-ZF-AA5P 
       10.13 

  RPTN MUTATED RPTN WILD-TYPE 
          3.48           0.10 
  RPTN MUTATED RPTN WILD-TYPE 
         98.99         166.03 
  RPTN MUTATED RPTN WILD-TYPE 
         16.31          15.62 
[1] "3.5 - 99.0 (16.3)"  "0.1 - 166.0 (15.6)"
[1] "hr=" "1"  
D39V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  RPTN MUTATED         0        6         7        2
  RPTN WILD-TYPE       4      111       115      126
D39V3, multiclass
           clus
vv          RPTN MUTATED RPTN WILD-TYPE
  STAGE I              0              4
  STAGE II             6            111
  STAGE III            7            115
  STAGE IV             2            126
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1+T2  T3  T4
  RPTN MUTATED          3   7   2
  RPTN WILD-TYPE      111 172  50
D39V4, multiclass
          clus
vv         RPTN MUTATED RPTN WILD-TYPE
  T0+T1+T2            3            111
  T3                  7            172
  T4                  2             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"
                vv
clus              N0  N1  N2  N3
  RPTN MUTATED    10   1   0   1
  RPTN WILD-TYPE 203  40  75   7
D39V5, multiclass
    clus
vv   RPTN MUTATED RPTN WILD-TYPE
  N0           10            203
  N1            1             40
  N2            0             75
  N3            1              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"
D39V6, binary
                cls
clus               0   1
  RPTN MUTATED     7   0
  RPTN WILD-TYPE 175  10
[1] "tbl2"
                cls
clus             [,1] [,2]
  RPTN MUTATED      7    0
  RPTN WILD-TYPE  175   10
   clus
vv  RPTN MUTATED RPTN WILD-TYPE
  0            7            175
  1            0             10
[1] 2 2
[1] FALSE
D39V7, binary
                cls
clus               0   1
  RPTN MUTATED     3  12
  RPTN WILD-TYPE  93 268
[1] "tbl2"
                cls
clus             [,1] [,2]
  RPTN MUTATED      3   12
  RPTN WILD-TYPE   93  268
        clus
vv       RPTN MUTATED RPTN WILD-TYPE
  FEMALE            3             93
  MALE             12            268
[1] 2 2
[1] FALSE
D39V8, continuous
D39V9, continuous
D39V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RPTN MUTATED       0                         1    14
  RPTN WILD-TYPE    38                        20   287
D39V11, multiclass
                           clus
vv                          RPTN MUTATED RPTN WILD-TYPE
  ASIAN                                0             38
  BLACK OR AFRICAN AMERICAN            1             20
  WHITE                               14            287
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V12, binary
                cls
clus               0   1
  RPTN MUTATED     0  14
  RPTN WILD-TYPE   8 324
[1] "tbl2"
                cls
clus             [,1] [,2]
  RPTN MUTATED      0   14
  RPTN WILD-TYPE    8  324
                        clus
vv                       RPTN MUTATED RPTN WILD-TYPE
  HISPANIC OR LATINO                0              8
  NOT HISPANIC OR LATINO           14            324
[1] 2 2
[1] FALSE

Clustering(40) Variable = SF1 MUTATION ANALYSIS
D40V1, survival
               sevent
clus2             0   1
  SF1 MUTATED     7   2
  SF1 WILD-TYPE 212 149
  SF1 MUTATED SF1 WILD-TYPE 
            9           361 
  SF1 MUTATED SF1 WILD-TYPE 
            2           149 
$`SF1 MUTATED`
TCGA-4Z-AA82 TCGA-CF-A47W TCGA-DK-A1AC TCGA-DK-A3IK TCGA-E7-A7DV TCGA-G2-AA3D 
       51.16        12.10       130.88         2.20         1.22        64.44 
TCGA-GC-A3YS TCGA-XF-AAN7 TCGA-ZF-A9RM 
       24.92        18.81        47.84 

$`SF1 WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        91.63       103.50       105.70         8.35 
TCGA-4Z-AA7M TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7S 
       16.27        44.94        16.83        16.77        17.16        34.98 
TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA83 TCGA-4Z-AA84 
       27.62        49.12         0.62        41.75        66.54        15.12 
TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J 
       10.22        47.80        33.83        40.08         7.33         2.66 
TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N 
        6.74        12.39         6.58        13.15        19.04        32.84 
TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U 
       12.16        17.88        19.50         5.06        14.89        14.96 
TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A2LD 
        5.06         8.35         8.25        17.16        16.18        20.48 
TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E 
        4.67        12.82         9.96        17.56        28.70        24.26 
TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-C4-A0F6 TCGA-C4-A0F7 
       28.41         8.98         1.94         2.93        23.01         2.04 
TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V 
        0.46         0.43         0.69        10.95        12.66        12.46 
TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A9FF 
       12.62        12.26        13.12        12.00        12.10        11.87 
TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3QU 
       13.08        12.92         4.90         7.20         5.46         5.19 
TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 
       16.31         1.84        13.58        21.86         2.14        66.41 
TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF 
       18.41        19.00        16.70       112.44        16.14        17.62 
TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A2I6 
       15.62         1.81        10.59         7.79       123.85        87.32 
TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT 
       13.58         7.82         8.22        17.72        50.27        21.30 
TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 
       23.21         9.67        20.81        10.55       140.81        48.00 
TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 
       17.98        64.18        41.56        76.60        67.36        15.68 
TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6S 
       41.06        30.67        38.24        15.02        13.58       166.03 
TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA74 
       12.36        10.49         8.65         7.53        13.64        43.50 
TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 
       12.03        10.62        43.59        15.35        38.83        24.66 
TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KE 
        0.10         0.49         2.24        16.70        17.39         0.56 
TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DU 
        0.66        14.56        13.97        12.99        14.33         0.92 
TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B3 
       13.68        14.07        12.95        14.37         8.09        32.02 
TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 
       16.77         8.94        33.04         4.01        12.62        22.52 
TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN 
       27.98        60.66        24.30        23.41        17.98        29.16 
TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N 
        5.52        25.74        46.78        19.79        12.85        22.98 
TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS 
       27.35        14.96        20.91         3.62        26.73        53.88 
TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ 
       11.01        19.33         5.36         5.69         8.25        27.45 
TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S 
       18.08        58.92         2.70         7.10         6.28        13.35 
TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF 
       62.86        18.81         6.15        12.69        12.36         2.27 
TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 
        3.06         4.31         9.67        10.85        31.07         7.13 
TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FJ-A871 TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EC 
       10.65        17.23         8.94         3.25         6.48        22.88 
TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES 
       61.94        30.61        15.95        26.93        35.24        33.01 
TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3F 
        7.23        20.12        17.62        66.02         6.94        19.46 
TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD 
       21.40         2.24        15.81         4.50        15.91        14.07 
TCGA-GC-A3WC TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ 
       17.75         8.94        13.91         7.73         2.10         3.12 
TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R 
       20.98         2.20         7.36        10.92        11.31        11.31 
TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATO 
        7.63        27.09        20.05         5.62         4.73        10.65 
TCGA-GU-AATP TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ 
       32.98         7.00        14.27        21.34        19.10        19.82 
TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G 
       20.28         8.48        10.59        27.35         8.58        19.07 
TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND 
       22.72         1.51        19.40        38.60         3.06         9.01 
TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC 
        8.22        25.02         3.45        21.24         2.76         9.14 
TCGA-K4-A54R TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB 
       27.68         9.07        11.70         1.74         1.81        15.42 
TCGA-K4-A83P TCGA-K4-AAQO TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI 
        6.38        11.80        15.32        15.58        13.48        12.23 
TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 TCGA-SY-A9G0 TCGA-SY-A9G5 
       16.67        14.24         1.84         3.75        12.43        31.56 
TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78N TCGA-UY-A78O TCGA-UY-A8OB 
       17.62        37.05        22.68        86.83        76.01        65.75 
TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HH 
       35.24        29.56        17.82         4.54         1.64         1.87 
TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SL 
       17.88        48.62        64.80        79.66         3.22        66.41 
TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T0 
       12.76        11.90        23.64        21.04        28.24        26.27 
TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 
       18.90         2.24        16.27        66.64         2.10        13.74 
TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMG TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML 
       92.98        10.82       110.60        11.31        54.90         7.63 
TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAMY 
       71.57        91.73         2.96         8.32         6.77        98.99 
TCGA-XF-AAMZ TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN4 
       44.32        56.48        30.94        61.45        86.30        27.06 
TCGA-XF-AAN5 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-YF-AA3M 
       75.39         3.88         9.63         0.66        11.97        13.64 
TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R5 
       18.64         7.36        21.11        24.13        30.28        27.19 
TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RF 
       21.86        28.41        74.56        13.41         3.48        52.73 
TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4R TCGA-ZF-AA4T 
       52.60        82.49        20.22         2.89        34.06        19.69 
TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 
        8.61        59.38        60.16        63.02        38.73        35.41 
TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N 
       57.90        19.40         8.52        47.15        19.17         5.52 
TCGA-ZF-AA5P 
       10.13 

  SF1 MUTATED SF1 WILD-TYPE 
         1.22          0.10 
  SF1 MUTATED SF1 WILD-TYPE 
       130.88        166.03 
  SF1 MUTATED SF1 WILD-TYPE 
        24.92         15.58 
[1] "1.2 - 130.9 (24.9)" "0.1 - 166.0 (15.6)"
[1] "hr=" "2.6"
D40V2, continuous
               vv
clus            STAGE I STAGE II STAGE III STAGE IV
  SF1 MUTATED         0        2         1        6
  SF1 WILD-TYPE       4      115       121      122
D40V3, multiclass
           clus
vv          SF1 MUTATED SF1 WILD-TYPE
  STAGE I             0             4
  STAGE II            2           115
  STAGE III           1           121
  STAGE IV            6           122
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            T0+T1+T2  T3  T4
  SF1 MUTATED          3   5   1
  SF1 WILD-TYPE      111 174  51
D40V4, multiclass
          clus
vv         SF1 MUTATED SF1 WILD-TYPE
  T0+T1+T2           3           111
  T3                 5           174
  T4                 1            51
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             N0  N1  N2  N3
  SF1 MUTATED     3   3   2   1
  SF1 WILD-TYPE 210  38  73   7
D40V5, multiclass
    clus
vv   SF1 MUTATED SF1 WILD-TYPE
  N0           3           210
  N1           3            38
  N2           2            73
  N3           1             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"
D40V6, binary
               cls
clus              0   1
  SF1 MUTATED     5   0
  SF1 WILD-TYPE 177  10
[1] "tbl2"
               cls
clus            [,1] [,2]
  SF1 MUTATED      5    0
  SF1 WILD-TYPE  177   10
   clus
vv  SF1 MUTATED SF1 WILD-TYPE
  0           5           177
  1           0            10
[1] 2 2
[1] FALSE
D40V7, binary
               cls
clus              0   1
  SF1 MUTATED     0   9
  SF1 WILD-TYPE  96 271
[1] "tbl2"
               cls
clus            [,1] [,2]
  SF1 MUTATED      0    9
  SF1 WILD-TYPE   96  271
        clus
vv       SF1 MUTATED SF1 WILD-TYPE
  FEMALE           0            96
  MALE             9           271
[1] 2 2
[1] FALSE
D40V8, continuous
D40V9, continuous
D40V10, continuous
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SF1 MUTATED       1                         1     7
  SF1 WILD-TYPE    37                        20   294
D40V11, multiclass
                           clus
vv                          SF1 MUTATED SF1 WILD-TYPE
  ASIAN                               1            37
  BLACK OR AFRICAN AMERICAN           1            20
  WHITE                               7           294
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V12, binary
               cls
clus              0   1
  SF1 MUTATED     0   7
  SF1 WILD-TYPE   8 331
[1] "tbl2"
               cls
clus            [,1] [,2]
  SF1 MUTATED      0    7
  SF1 WILD-TYPE    8  331
                        clus
vv                       SF1 MUTATED SF1 WILD-TYPE
  HISPANIC OR LATINO               0             8
  NOT HISPANIC OR LATINO           7           331
[1] 2 2
[1] FALSE

Clustering(41) Variable = DNAH6 MUTATION ANALYSIS
D41V1, survival
                 sevent
clus2               0   1
  DNAH6 MUTATED    11   4
  DNAH6 WILD-TYPE 208 147
  DNAH6 MUTATED DNAH6 WILD-TYPE 
             15             355 
  DNAH6 MUTATED DNAH6 WILD-TYPE 
              4             147 
$`DNAH6 MUTATED`
TCGA-4Z-AA80 TCGA-CF-A47V TCGA-CU-A3QU TCGA-DK-A6B6 TCGA-DK-AA6P TCGA-E7-A541 
        0.62        12.46         5.19        30.67        15.02        17.39 
TCGA-FD-A3B8 TCGA-GD-A3OP TCGA-GV-A3QF TCGA-GV-A6ZA TCGA-K4-A83P TCGA-MV-A51V 
       12.62         2.10        20.28        22.72         6.38        13.48 
TCGA-UY-A9PD TCGA-XF-A8HI TCGA-XF-A9SW 
       17.82        17.88        11.90 

$`DNAH6 WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        91.63       103.50       105.70         8.35 
TCGA-4Z-AA7M TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7S 
       16.27        44.94        16.83        16.77        17.16        34.98 
TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA84 
       27.62        49.12        41.75        51.16        66.54        15.12 
TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J 
       10.22        47.80        33.83        40.08         7.33         2.66 
TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N 
        6.74        12.39         6.58        13.15        19.04        32.84 
TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U 
       12.16        17.88        19.50         5.06        14.89        14.96 
TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A2LD 
        5.06         8.35         8.25        17.16        16.18        20.48 
TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E 
        4.67        12.82         9.96        17.56        28.70        24.26 
TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-C4-A0F6 TCGA-C4-A0F7 
       28.41         8.98         1.94         2.93        23.01         2.04 
TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47W 
        0.46         0.43         0.69        10.95        12.66        12.10 
TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A9FF 
       12.62        12.26        13.12        12.00        12.10        11.87 
TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3YL 
       13.08        12.92         4.90         7.20         5.46        16.31 
TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 
        1.84        13.58        21.86         2.14        66.41        18.41 
TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF 
       19.00        16.70       130.88       112.44        16.14        17.62 
TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A2I6 
       15.62         1.81        10.59         7.79       123.85        87.32 
TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS 
        2.20        13.58         7.82         8.22        17.72        50.27 
TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY 
       21.30        23.21         9.67        20.81        10.55       140.81 
TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 
       48.00        17.98        64.18        41.56        76.60        67.36 
TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-AA6L TCGA-DK-AA6Q TCGA-DK-AA6S TCGA-DK-AA6T 
       15.68        41.06        38.24        13.58       166.03        12.36 
TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA76 
       10.49         8.65         7.53        13.64        43.50        12.03 
TCGA-DK-AA77 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 
       10.62        43.59        15.35        38.83        24.66         0.10 
TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 
        0.49         2.24        16.70         0.56         0.66        14.56 
TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7DV TCGA-E7-A7PW 
       13.97        12.99        14.33         0.92         1.22        13.68 
TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 
       14.07        12.95        14.37         8.09        32.02        16.77 
TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA 
        8.94        33.04         4.01        22.52        27.98        60.66 
TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP 
       24.30        23.41        17.98        29.16         5.52        25.74 
TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S 
       46.78        19.79        12.85        22.98        27.35        14.96 
TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU 
       20.91         3.62        26.73        53.88        11.01        19.33 
TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 
        5.36         5.69         8.25        27.45        18.08        58.92 
TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB 
        2.70         7.10         6.28        13.35        62.86        18.81 
TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH 
        6.15        12.69        12.36         2.27         3.06         4.31 
TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF 
        9.67        10.85        31.07         7.13        10.65        17.23 
TCGA-FJ-A871 TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EC TCGA-G2-A2EF TCGA-G2-A2EJ 
        8.94         3.25         6.48        22.88        61.94        30.61 
TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE 
       15.95        26.93        35.24        33.01         7.23        20.12 
TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3BM 
       17.62        66.02         6.94        64.44        19.46        21.40 
TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC 
        2.24        15.81         4.50        15.91        14.07        17.75 
TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OQ TCGA-GD-A3OS 
       24.92         8.94        13.91         7.73         3.12        20.98 
TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 
        2.20         7.36        10.92        11.31        11.31         7.63 
TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATO TCGA-GU-AATP 
       27.09        20.05         5.62         4.73        10.65        32.98 
TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QH 
        7.00        14.27        21.34        19.10        19.82         8.48 
TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-H4-A2HO TCGA-H4-A2HQ 
       10.59        27.35         8.58        19.07         1.51        19.40 
TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU 
       38.60         3.06         9.01         8.22        25.02         3.45 
TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RH TCGA-K4-A5RI 
       21.24         2.76         9.14        27.68         9.07        11.70 
TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-AAQO TCGA-LC-A66R TCGA-LT-A5Z6 
        1.74         1.81        15.42        11.80        15.32        15.58 
TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 TCGA-SY-A9G0 
       12.23        16.67        14.24         1.84         3.75        12.43 
TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78N TCGA-UY-A78O 
       31.56        17.62        37.05        22.68        86.83        76.01 
TCGA-UY-A8OB TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HH 
       65.75        35.24        29.56         4.54         1.64         1.87 
TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SL TCGA-XF-A9SV 
       48.62        64.80        79.66         3.22        66.41        12.76 
TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 
       23.64        21.04        28.24        26.27        18.90         2.24 
TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMF 
       16.27        66.64         2.10        13.74        92.98        10.82 
TCGA-XF-AAMG TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR 
      110.60        11.31        54.90         7.63        71.57        91.73 
TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN0 
        2.96         8.32         6.77        98.99        44.32        56.48 
TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN7 
       30.94        61.45        86.30        27.06        75.39        18.81 
TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R0 
        3.88         9.63         0.66        11.97        13.64        18.64 
TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R7 
        7.36        21.11        24.13        30.28        27.19        21.86 
TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RG 
       28.41        74.56        13.41         3.48        52.73        52.60 
TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4R TCGA-ZF-AA4T 
       82.49        47.84        20.22         2.89        34.06        19.69 
TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 
        8.61        59.38        60.16        63.02        38.73        35.41 
TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N 
       57.90        19.40         8.52        47.15        19.17         5.52 
TCGA-ZF-AA5P 
       10.13 

  DNAH6 MUTATED DNAH6 WILD-TYPE 
           0.62            0.10 
  DNAH6 MUTATED DNAH6 WILD-TYPE 
          30.67          166.03 
  DNAH6 MUTATED DNAH6 WILD-TYPE 
          13.48           15.81 
[1] "0.6 - 30.7 (13.5)"  "0.1 - 166.0 (15.8)"
[1] "hr=" "1.1"
D41V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  DNAH6 MUTATED         0        7         2        6
  DNAH6 WILD-TYPE       4      110       120      122
D41V3, multiclass
           clus
vv          DNAH6 MUTATED DNAH6 WILD-TYPE
  STAGE I               0               4
  STAGE II              7             110
  STAGE III             2             120
  STAGE IV              6             122
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1+T2  T3  T4
  DNAH6 MUTATED          7   4   2
  DNAH6 WILD-TYPE      107 175  50
D41V4, multiclass
          clus
vv         DNAH6 MUTATED DNAH6 WILD-TYPE
  T0+T1+T2             7             107
  T3                   4             175
  T4                   2              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"
                 vv
clus               N0  N1  N2  N3
  DNAH6 MUTATED     8   2   4   0
  DNAH6 WILD-TYPE 205  39  71   8
D41V5, multiclass
    clus
vv   DNAH6 MUTATED DNAH6 WILD-TYPE
  N0             8             205
  N1             2              39
  N2             4              71
  N3             0               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"
D41V6, binary
                 cls
clus                0   1
  DNAH6 MUTATED     5   0
  DNAH6 WILD-TYPE 177  10
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DNAH6 MUTATED      5    0
  DNAH6 WILD-TYPE  177   10
   clus
vv  DNAH6 MUTATED DNAH6 WILD-TYPE
  0             5             177
  1             0              10
[1] 2 2
[1] FALSE
D41V7, binary
                 cls
clus                0   1
  DNAH6 MUTATED     3  12
  DNAH6 WILD-TYPE  93 268
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DNAH6 MUTATED      3   12
  DNAH6 WILD-TYPE   93  268
        clus
vv       DNAH6 MUTATED DNAH6 WILD-TYPE
  FEMALE             3              93
  MALE              12             268
[1] 2 2
[1] FALSE
D41V8, continuous
D41V9, continuous
D41V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DNAH6 MUTATED       1                         0    14
  DNAH6 WILD-TYPE    37                        21   287
D41V11, multiclass
                           clus
vv                          DNAH6 MUTATED DNAH6 WILD-TYPE
  ASIAN                                 1              37
  BLACK OR AFRICAN AMERICAN             0              21
  WHITE                                14             287
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V12, binary
                 cls
clus                0   1
  DNAH6 MUTATED     1  13
  DNAH6 WILD-TYPE   7 325
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DNAH6 MUTATED      1   13
  DNAH6 WILD-TYPE    7  325
                        clus
vv                       DNAH6 MUTATED DNAH6 WILD-TYPE
  HISPANIC OR LATINO                 1               7
  NOT HISPANIC OR LATINO            13             325
[1] 2 2
[1] FALSE

Clustering(42) Variable = ZNF185 MUTATION ANALYSIS
D42V1, survival
                  sevent
clus2                0   1
  ZNF185 MUTATED     4   1
  ZNF185 WILD-TYPE 215 150
  ZNF185 MUTATED ZNF185 WILD-TYPE 
               5              365 
  ZNF185 MUTATED ZNF185 WILD-TYPE 
               1              150 
$`ZNF185 MUTATED`
TCGA-FJ-A3Z9 TCGA-G2-A2ES TCGA-GC-A3I6 TCGA-K4-A5RJ TCGA-ZF-A9RC 
        7.13        33.01         2.24         1.74        74.56 

$`ZNF185 WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        91.63       103.50       105.70         8.35 
TCGA-4Z-AA7M TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7S 
       16.27        44.94        16.83        16.77        17.16        34.98 
TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 
       27.62        49.12         0.62        41.75        51.16        66.54 
TCGA-4Z-AA84 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BL-A13I 
       15.12        10.22        47.80        33.83        40.08         7.33 
TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J 
        2.66         6.74        12.39         6.58        13.15        19.04 
TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T 
       32.84        12.16        17.88        19.50         5.06        14.89 
TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB 
       14.96         5.06         8.35         8.25        17.16        16.18 
TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C 
       20.48         4.67        12.82         9.96        17.56        28.70 
TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-C4-A0F6 
       24.26        28.41         8.98         1.94         2.93        23.01 
TCGA-C4-A0F7 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T 
        2.04         0.46         0.43         0.69        10.95        12.66 
TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA 
       12.46        12.10        12.62        12.26        13.12        12.00 
TCGA-CF-A7I0 TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR 
       12.10        11.87        13.08        12.92         4.90         7.20 
TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 
        5.46         5.19        16.31         1.84        13.58        21.86 
TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC 
        2.14        66.41        18.41        19.00        16.70       130.88 
TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 
      112.44        16.14        17.62        15.62         1.81        10.59 
TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM 
        7.79       123.85        87.32         2.20        13.58         7.82 
TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV 
        8.22        17.72        50.27        21.30        23.21         9.67 
TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV 
       20.81        10.55       140.81        48.00        17.98        64.18 
TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 
       41.56        76.60        67.36        15.68        41.06        30.67 
TCGA-DK-AA6L TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6U 
       38.24        15.02        13.58       166.03        12.36        10.49 
TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA76 TCGA-DK-AA77 
        8.65         7.53        13.64        43.50        12.03        10.62 
TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ 
       43.59        15.35        38.83        24.66         0.10         0.49 
TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 
        2.24        16.70        17.39         0.56         0.66        14.56 
TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7DV TCGA-E7-A7PW 
       13.97        12.99        14.33         0.92         1.22        13.68 
TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 
       14.07        12.95        14.37         8.09        32.02        16.77 
TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 
        8.94        33.04         4.01        12.62        22.52        27.98 
TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO 
       60.66        24.30        23.41        17.98        29.16         5.52 
TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P 
       25.74        46.78        19.79        12.85        22.98        27.35 
TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT 
       14.96        20.91         3.62        26.73        53.88        11.01 
TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 
       19.33         5.36         5.69         8.25        27.45        18.08 
TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA 
       58.92         2.70         7.10         6.28        13.35        62.86 
TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TG 
       18.81         6.15        12.69        12.36         2.27         3.06 
TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3ZE TCGA-FJ-A3ZF 
        4.31         9.67        10.85        31.07        10.65        17.23 
TCGA-FJ-A871 TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EC TCGA-G2-A2EF TCGA-G2-A2EJ 
        8.94         3.25         6.48        22.88        61.94        30.61 
TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY 
       15.95        26.93        35.24         7.23        20.12        17.62 
TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3OO 
       66.02         6.94        64.44        19.46        21.40        15.81 
TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A6I1 
        4.50        15.91        14.07        17.75        24.92         8.94 
TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 
       13.91         7.73         2.10         3.12        20.98         2.20 
TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 
        7.36        10.92        11.31        11.31         7.63        27.09 
TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATO TCGA-GU-AATP TCGA-GU-AATQ 
       20.05         5.62         4.73        10.65        32.98         7.00 
TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH 
       14.27        21.34        19.10        19.82        20.28         8.48 
TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO 
       10.59        27.35         8.58        19.07        22.72         1.51 
TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS 
       19.40        38.60         3.06         9.01         8.22        25.02 
TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RH 
        3.45        21.24         2.76         9.14        27.68         9.07 
TCGA-K4-A5RI TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO TCGA-LC-A66R 
       11.70         1.81        15.42         6.38        11.80        15.32 
TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX 
       15.58        13.48        12.23        16.67        14.24         1.84 
TCGA-S5-AA26 TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M 
        3.75        12.43        31.56        17.62        37.05        22.68 
TCGA-UY-A78N TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD 
       86.83        76.01        65.75        35.24        29.56        17.82 
TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH 
        4.54         1.64         1.87        17.88        48.62        64.80 
TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SL TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SX 
       79.66         3.22        66.41        12.76        11.90        23.64 
TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 
       21.04        28.24        26.27        18.90         2.24        16.27 
TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMG 
       66.64         2.10        13.74        92.98        10.82       110.60 
TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMT 
       11.31        54.90         7.63        71.57        91.73         2.96 
TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN0 TCGA-XF-AAN1 
        8.32         6.77        98.99        44.32        56.48        30.94 
TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN7 TCGA-XF-AAN8 
       61.45        86.30        27.06        75.39        18.81         3.88 
TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R0 TCGA-ZF-A9R1 
        9.63         0.66        11.97        13.64        18.64         7.36 
TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 
       21.11        24.13        30.28        27.19        21.86        28.41 
TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-A9RM 
       13.41         3.48        52.73        52.60        82.49        47.84 
TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4U TCGA-ZF-AA4V 
       20.22         2.89        34.06        19.69         8.61        59.38 
TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA53 TCGA-ZF-AA54 
       60.16        63.02        38.73        35.41        57.90        19.40 
TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-ZF-AA5P 
        8.52        47.15        19.17         5.52        10.13 

  ZNF185 MUTATED ZNF185 WILD-TYPE 
            1.74             0.10 
  ZNF185 MUTATED ZNF185 WILD-TYPE 
           74.56           166.03 
  ZNF185 MUTATED ZNF185 WILD-TYPE 
            7.13            15.68 
[1] "1.7 - 74.6 (7.1)"   "0.1 - 166.0 (15.7)"
[1] "hr=" "1.8"
D42V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  ZNF185 MUTATED         1        2         2        0
  ZNF185 WILD-TYPE       3      115       120      128
D42V3, multiclass
           clus
vv          ZNF185 MUTATED ZNF185 WILD-TYPE
  STAGE I                1                3
  STAGE II               2              115
  STAGE III              2              120
  STAGE IV               0              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"
                  vv
clus               T0+T1+T2  T3  T4
  ZNF185 MUTATED          2   3   0
  ZNF185 WILD-TYPE      112 176  52
D42V4, multiclass
          clus
vv         ZNF185 MUTATED ZNF185 WILD-TYPE
  T0+T1+T2              2              112
  T3                    3              176
  T4                    0               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"
                  vv
clus                N0  N1  N2  N3
  ZNF185 MUTATED     5   0   0   0
  ZNF185 WILD-TYPE 208  41  75   8
D42V5, multiclass
    clus
vv   ZNF185 MUTATED ZNF185 WILD-TYPE
  N0              5              208
  N1              0               41
  N2              0               75
  N3              0                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"
D42V6, binary
                  cls
clus                 0   1
  ZNF185 MUTATED     3   0
  ZNF185 WILD-TYPE 179  10
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF185 MUTATED      3    0
  ZNF185 WILD-TYPE  179   10
   clus
vv  ZNF185 MUTATED ZNF185 WILD-TYPE
  0              3              179
  1              0               10
[1] 2 2
[1] FALSE
D42V7, binary
                  cls
clus                 0   1
  ZNF185 MUTATED     0   5
  ZNF185 WILD-TYPE  96 275
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF185 MUTATED      0    5
  ZNF185 WILD-TYPE   96  275
        clus
vv       ZNF185 MUTATED ZNF185 WILD-TYPE
  FEMALE              0               96
  MALE                5              275
[1] 2 2
[1] FALSE
D42V8, continuous
[1] "Remove cluster labels:" "ZNF185 MUTATED"        
clus
  ZNF185 MUTATED ZNF185 WILD-TYPE 
               2              118 
      TCGA-2F-A9KO       TCGA-2F-A9KP       TCGA-2F-A9KQ       TCGA-2F-A9KR 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-2F-A9KT       TCGA-2F-A9KW       TCGA-CF-A1HS       TCGA-CF-A27C 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-CF-A3MF       TCGA-CF-A3MG       TCGA-CF-A3MH       TCGA-CF-A3MI 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-CF-A47S       TCGA-CF-A47T       TCGA-CF-A47V       TCGA-CF-A47W 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-CF-A47X       TCGA-CF-A47Y       TCGA-CF-A5U8       TCGA-CF-A5UA 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-CF-A7I0       TCGA-DK-A2HX       TCGA-DK-A3IN       TCGA-DK-A3IV 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-DK-A3WX       TCGA-DK-A3X2       TCGA-DK-A6B2       TCGA-DK-A6B5 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-DK-A6B6       TCGA-DK-AA6P       TCGA-DK-AA6S       TCGA-DK-AA6U 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-DK-AA6W       TCGA-DK-AA76       TCGA-E5-A2PC       TCGA-E5-A4TZ 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-E5-A4U1       TCGA-E7-A519       TCGA-E7-A541       TCGA-E7-A7DU 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-E7-A7DV       TCGA-FT-A61P       TCGA-G2-A2EC       TCGA-G2-A2EF 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-G2-A2EJ       TCGA-G2-A2EK       TCGA-G2-A2EL       TCGA-G2-A2EO 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-G2-A3IB       TCGA-G2-A3IE       TCGA-G2-A3VY       TCGA-GC-A3BM 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-GC-A3OO       TCGA-GC-A3RC       TCGA-GC-A3RD       TCGA-GC-A3YS 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-GC-A6I1       TCGA-GC-A6I3       TCGA-GD-A3OS       TCGA-GD-A6C6 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-GV-A3JV       TCGA-GV-A3JW       TCGA-GV-A3JX       TCGA-GV-A3JZ 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-GV-A3QF       TCGA-GV-A3QH       TCGA-GV-A3QI       TCGA-GV-A3QK 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-GV-A40E       TCGA-GV-A40G       TCGA-GV-A6ZA       TCGA-SY-A9G0 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-SY-A9G5       TCGA-UY-A78L       TCGA-UY-A78M       TCGA-UY-A78N 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-XF-A8HH       TCGA-XF-A8HI       TCGA-XF-A9SG       TCGA-XF-A9SH 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-XF-A9SI       TCGA-XF-A9SJ       TCGA-XF-A9SL       TCGA-XF-A9SV 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-XF-A9SW       TCGA-XF-A9SX       TCGA-XF-A9SY       TCGA-XF-A9SZ 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-XF-A9T0       TCGA-XF-A9T2       TCGA-XF-A9T3       TCGA-XF-A9T4 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-XF-A9T5       TCGA-XF-A9T6       TCGA-XF-A9T8       TCGA-XF-AAME 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-XF-AAMF       TCGA-XF-AAMG       TCGA-XF-AAMH       TCGA-XF-AAMJ 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-XF-AAML       TCGA-XF-AAMQ       TCGA-XF-AAMR       TCGA-XF-AAMT 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-XF-AAMW       TCGA-XF-AAMX       TCGA-XF-AAMY       TCGA-XF-AAMZ 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-XF-AAN0       TCGA-XF-AAN1       TCGA-XF-AAN2       TCGA-XF-AAN3 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-XF-AAN4       TCGA-XF-AAN5       TCGA-XF-AAN7       TCGA-XF-AAN8 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-YF-AA3L       TCGA-YF-AA3M 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
D42V9, continuous
[1] "Remove cluster labels:" "ZNF185 MUTATED"        
clus
  ZNF185 MUTATED ZNF185 WILD-TYPE 
               2              203 
      TCGA-2F-A9KO       TCGA-2F-A9KP       TCGA-2F-A9KR       TCGA-4Z-AA7M 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-4Z-AA89       TCGA-BL-A0C8       TCGA-BL-A13I       TCGA-BL-A13J 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-BL-A3JM       TCGA-BL-A5ZZ       TCGA-BT-A20J       TCGA-BT-A20N 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-BT-A2LA       TCGA-BT-A42B       TCGA-BT-A42C       TCGA-BT-A42E 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-C4-A0EZ       TCGA-C4-A0F0       TCGA-C4-A0F1       TCGA-C4-A0F6 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-CF-A3MH       TCGA-CF-A3MI       TCGA-CF-A47W       TCGA-CF-A47X 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-CF-A5UA       TCGA-CF-A9FH       TCGA-CU-A0YN       TCGA-CU-A0YR 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-CU-A3KJ       TCGA-CU-A3QU       TCGA-CU-A3YL       TCGA-CU-A5W6 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-CU-A72E       TCGA-DK-A1A3       TCGA-DK-A1A5       TCGA-DK-A1A6 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-DK-A1AA       TCGA-DK-A1AC       TCGA-DK-A1AE       TCGA-DK-A2HX 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-DK-A2I6       TCGA-DK-A3IL       TCGA-DK-A3IM       TCGA-DK-A3IN 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-DK-A3IQ       TCGA-DK-A3IU       TCGA-DK-A3IV       TCGA-DK-A3WX 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-DK-A3X1       TCGA-DK-A3X2       TCGA-DK-A6AV       TCGA-DK-A6AW 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-DK-A6B0       TCGA-DK-A6B2       TCGA-DK-A6B6       TCGA-DK-AA6L 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-DK-AA6P       TCGA-DK-AA6T       TCGA-DK-AA6U       TCGA-DK-AA74 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-DK-AA76       TCGA-E5-A4TZ       TCGA-E7-A4XJ       TCGA-E7-A519 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-E7-A5KF       TCGA-E7-A678       TCGA-E7-A6ME       TCGA-E7-A6MF 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-E7-A7PW       TCGA-E7-A7XN       TCGA-E7-A85H       TCGA-E7-A97Q 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-FD-A3B3       TCGA-FD-A3B4       TCGA-FD-A3B5       TCGA-FD-A3B6 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-FD-A3B7       TCGA-FD-A3B8       TCGA-FD-A3N5       TCGA-FD-A3N6 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-FD-A3NA       TCGA-FD-A3SJ       TCGA-FD-A3SM       TCGA-FD-A3SN 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-FD-A3SO       TCGA-FD-A3SP       TCGA-FD-A3SQ       TCGA-FD-A3SR 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-FD-A3SS       TCGA-FD-A43N       TCGA-FD-A43P       TCGA-FD-A43S 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-FD-A43U       TCGA-FD-A43X       TCGA-FD-A5BT       TCGA-FD-A5BU 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-FD-A5BV       TCGA-FD-A5BX       TCGA-FD-A5C0       TCGA-FD-A62N 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-FD-A6TB       TCGA-FD-A6TC       TCGA-FD-A6TE       TCGA-FD-A6TG 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-FD-A6TH       TCGA-FD-A6TK       TCGA-FJ-A3ZE       TCGA-FJ-A3ZF 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-FJ-A871       TCGA-FT-A61P       TCGA-G2-A2EF       TCGA-G2-A2EJ 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-G2-A2EL       TCGA-G2-A3IE       TCGA-G2-AA3B       TCGA-G2-AA3C 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-G2-AA3D       TCGA-G2-AA3F       TCGA-GC-A3BM       TCGA-GC-A3RB 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-GC-A3WC       TCGA-GC-A3YS       TCGA-GD-A2C5       TCGA-GD-A3OQ 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-GD-A3OS       TCGA-GD-A6C6       TCGA-GU-A42P       TCGA-GU-A42Q 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-GU-A42R       TCGA-GU-A763       TCGA-GU-A764       TCGA-GU-AATO 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-GU-AATP       TCGA-GU-AATQ       TCGA-GV-A3JV       TCGA-GV-A3JX 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-GV-A3JZ       TCGA-GV-A3QF       TCGA-GV-A3QG       TCGA-GV-A3QH 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-GV-A3QI       TCGA-GV-A3QK       TCGA-GV-A40E       TCGA-GV-A40G 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-H4-A2HO       TCGA-H4-A2HQ       TCGA-HQ-A5ND       TCGA-HQ-A5NE 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-K4-A3WS       TCGA-K4-A3WV       TCGA-K4-A5RH       TCGA-K4-A5RI 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-K4-A83P       TCGA-K4-AAQO       TCGA-PQ-A6FI       TCGA-PQ-A6FN 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-R3-A69X       TCGA-S5-A6DX       TCGA-SY-A9G0       TCGA-UY-A78N 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-UY-A8OB       TCGA-UY-A9PB       TCGA-UY-A9PE       TCGA-UY-A9PF 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-XF-A9SJ       TCGA-XF-A9SL       TCGA-XF-A9SV       TCGA-XF-A9SX 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-XF-A9SY       TCGA-XF-A9SZ       TCGA-XF-A9T3       TCGA-XF-A9T8 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-XF-AAMF       TCGA-XF-AAMH       TCGA-XF-AAMQ       TCGA-XF-AAMT 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-XF-AAN0       TCGA-XF-AAN1       TCGA-XF-AAN2       TCGA-XF-AAN4 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-XF-AAN5       TCGA-XF-AAN7       TCGA-XF-AAN8       TCGA-YF-AA3L 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-YF-AA3M       TCGA-ZF-A9R0       TCGA-ZF-A9R2       TCGA-ZF-A9R3 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-ZF-A9R5       TCGA-ZF-A9R7       TCGA-ZF-A9R9       TCGA-ZF-A9RD 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-ZF-A9RF       TCGA-ZF-A9RL       TCGA-ZF-A9RM       TCGA-ZF-AA4U 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-ZF-AA4V       TCGA-ZF-AA51       TCGA-ZF-AA52       TCGA-ZF-AA58 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-ZF-AA5H       TCGA-ZF-AA5N       TCGA-ZF-AA5P 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
D42V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ZNF185 MUTATED       0                         0     5
  ZNF185 WILD-TYPE    38                        21   296
D42V11, multiclass
                           clus
vv                          ZNF185 MUTATED ZNF185 WILD-TYPE
  ASIAN                                  0               38
  BLACK OR AFRICAN AMERICAN              0               21
  WHITE                                  5              296
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V12, binary
                  cls
clus                 0   1
  ZNF185 MUTATED     0   5
  ZNF185 WILD-TYPE   8 333
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF185 MUTATED      0    5
  ZNF185 WILD-TYPE    8  333
                        clus
vv                       ZNF185 MUTATED ZNF185 WILD-TYPE
  HISPANIC OR LATINO                  0                8
  NOT HISPANIC OR LATINO              5              333
[1] 2 2
[1] FALSE

Clustering(43) Variable = ATM MUTATION ANALYSIS
D43V1, survival
               sevent
clus2             0   1
  ATM MUTATED    30  18
  ATM WILD-TYPE 189 133
  ATM MUTATED ATM WILD-TYPE 
           48           322 
  ATM MUTATED ATM WILD-TYPE 
           18           133 
$`ATM MUTATED`
TCGA-2F-A9KO TCGA-4Z-AA84 TCGA-BT-A0YX TCGA-BT-A20U TCGA-BT-A3PH TCGA-BT-A3PK 
       22.29        15.12        13.15        14.96         4.67         9.96 
TCGA-BT-A42E TCGA-CU-A0YR TCGA-DK-A1AG TCGA-DK-A3IK TCGA-DK-A3WW TCGA-DK-A6AW 
       24.26         7.20        15.62         2.20        20.81        41.56 
TCGA-E7-A4XJ TCGA-E7-A5KF TCGA-E7-A85H TCGA-FD-A3B5 TCGA-FD-A3N6 TCGA-FD-A43N 
        2.24         0.66        12.95         8.94        27.98        22.98 
TCGA-FD-A43P TCGA-FD-A6TI TCGA-FT-A3EE TCGA-G2-A3IE TCGA-G2-AA3B TCGA-G2-AA3C 
       27.35         9.67         3.25        20.12        66.02         6.94 
TCGA-GD-A6C6 TCGA-GV-A40E TCGA-GV-A6ZA TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A6MB 
        2.20         8.58        22.72        25.02         3.45        15.42 
TCGA-MV-A51V TCGA-R3-A69X TCGA-S5-AA26 TCGA-SY-A9G5 TCGA-UY-A8OB TCGA-UY-A9PB 
       13.48        14.24         3.75        31.56        65.75        29.56 
TCGA-UY-A9PF TCGA-XF-A8HI TCGA-XF-A9SI TCGA-XF-A9T5 TCGA-XF-A9T8 TCGA-XF-AAME 
        1.64        17.88        79.66        66.64        13.74        92.98 
TCGA-XF-AAMG TCGA-XF-AAML TCGA-YC-A9TC TCGA-ZF-A9RC TCGA-ZF-A9RF TCGA-ZF-AA4X 
      110.60         7.63         0.66        74.56        52.73        63.02 

$`ATM WILD-TYPE`
TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW TCGA-4Z-AA7M 
       11.97        91.63       103.50       105.70         8.35        16.27 
TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7W 
       44.94        16.83        16.77        17.16        34.98        27.62 
TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA86 
       49.12         0.62        41.75        51.16        66.54        10.22 
TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM 
       47.80        33.83        40.08         7.33         2.66         6.74 
TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P 
       12.39         6.58        19.04        32.84        12.16        17.88 
TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X 
       19.50         5.06        14.89         5.06         8.35         8.25 
TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A42B TCGA-BT-A42C 
       17.16        16.18        20.48        12.82        17.56        28.70 
TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-C4-A0F6 TCGA-C4-A0F7 
       28.41         8.98         1.94         2.93        23.01         2.04 
TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V 
        0.46         0.43         0.69        10.95        12.66        12.46 
TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 
       12.10        12.62        12.26        13.12        12.00        12.10 
TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A3KJ TCGA-CU-A3QU 
       11.87        13.08        12.92         4.90         5.46         5.19 
TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 
       16.31         1.84        13.58        21.86         2.14        66.41 
TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE 
       18.41        19.00        16.70       130.88       112.44        16.14 
TCGA-DK-A1AF TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A2I6 
       17.62         1.81        10.59         7.79       123.85        87.32 
TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT 
       13.58         7.82         8.22        17.72        50.27        21.30 
TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A3X2 
       23.21         9.67        10.55       140.81        48.00        17.98 
TCGA-DK-A6AV TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 
       64.18        76.60        67.36        15.68        41.06        30.67 
TCGA-DK-AA6L TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6U 
       38.24        15.02        13.58       166.03        12.36        10.49 
TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA76 TCGA-DK-AA77 
        8.65         7.53        13.64        43.50        12.03        10.62 
TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ 
       43.59        15.35        38.83        24.66         0.10         0.49 
TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME 
       16.70        17.39         0.56        14.56        13.97        12.99 
TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A97P 
       14.33         0.92         1.22        13.68        14.07        14.37 
TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 
        8.09        32.02        16.77        33.04         4.01        12.62 
TCGA-FD-A3N5 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN 
       22.52        60.66        24.30        23.41        17.98        29.16 
TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43S 
        5.52        25.74        46.78        19.79        12.85        14.96 
TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU 
       20.91         3.62        26.73        53.88        11.01        19.33 
TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 
        5.36         5.69         8.25        27.45        18.08        58.92 
TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB 
        2.70         7.10         6.28        13.35        62.86        18.81 
TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH 
        6.15        12.69        12.36         2.27         3.06         4.31 
TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FJ-A871 
       10.85        31.07         7.13        10.65        17.23         8.94 
TCGA-FT-A61P TCGA-G2-A2EC TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL 
        6.48        22.88        61.94        30.61        15.95        26.93 
TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3VY TCGA-G2-AA3D TCGA-G2-AA3F 
       35.24        33.01         7.23        17.62        64.44        19.46 
TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD 
       21.40         2.24        15.81         4.50        15.91        14.07 
TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP 
       17.75        24.92         8.94        13.91         7.73         2.10 
TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R 
        3.12        20.98         7.36        10.92        11.31        11.31 
TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATO 
        7.63        27.09        20.05         5.62         4.73        10.65 
TCGA-GU-AATP TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ 
       32.98         7.00        14.27        21.34        19.10        19.82 
TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40G TCGA-H4-A2HO 
       20.28         8.48        10.59        27.35        19.07         1.51 
TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WV 
       19.40        38.60         3.06         9.01         8.22        21.24 
TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ 
        2.76         9.14        27.68         9.07        11.70         1.74 
TCGA-K4-A6FZ TCGA-K4-A83P TCGA-K4-AAQO TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-PQ-A6FI 
        1.81         6.38        11.80        15.32        15.58        12.23 
TCGA-PQ-A6FN TCGA-S5-A6DX TCGA-SY-A9G0 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M 
       16.67         1.84        12.43        17.62        37.05        22.68 
TCGA-UY-A78N TCGA-UY-A78O TCGA-UY-A9PA TCGA-UY-A9PD TCGA-UY-A9PE TCGA-XF-A8HH 
       86.83        76.01        35.24        17.82         4.54         1.87 
TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SJ TCGA-XF-A9SL TCGA-XF-A9SV TCGA-XF-A9SW 
       48.62        64.80         3.22        66.41        12.76        11.90 
TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 
       23.64        21.04        28.24        26.27        18.90         2.24 
TCGA-XF-A9T4 TCGA-XF-A9T6 TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAMQ 
       16.27         2.10        10.82        11.31        54.90        71.57 
TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAMZ 
       91.73         2.96         8.32         6.77        98.99        44.32 
TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN5 
       56.48        30.94        61.45        86.30        27.06        75.39 
TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R0 
       18.81         3.88         9.63        11.97        13.64        18.64 
TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R7 
        7.36        21.11        24.13        30.28        27.19        21.86 
TCGA-ZF-A9R9 TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-A9RM 
       28.41        13.41         3.48        52.60        82.49        47.84 
TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4U TCGA-ZF-AA4V 
       20.22         2.89        34.06        19.69         8.61        59.38 
TCGA-ZF-AA4W TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA56 
       60.16        38.73        35.41        57.90        19.40         8.52 
TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-ZF-AA5P 
       47.15        19.17         5.52        10.13 

  ATM MUTATED ATM WILD-TYPE 
         0.66          0.10 
  ATM MUTATED ATM WILD-TYPE 
       110.60        166.03 
  ATM MUTATED ATM WILD-TYPE 
        15.27         15.86 
[1] "0.7 - 110.6 (15.3)" "0.1 - 166.0 (15.9)"
[1] "hr=" "1.2"
D43V2, continuous
               vv
clus            STAGE I STAGE II STAGE III STAGE IV
  ATM MUTATED         0       15        19       15
  ATM WILD-TYPE       4      102       103      113
D43V3, multiclass
           clus
vv          ATM MUTATED ATM WILD-TYPE
  STAGE I             0             4
  STAGE II           15           102
  STAGE III          19           103
  STAGE IV           15           113
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            T0+T1+T2  T3  T4
  ATM MUTATED         16  25   5
  ATM WILD-TYPE       98 154  47
D43V4, multiclass
          clus
vv         ATM MUTATED ATM WILD-TYPE
  T0+T1+T2          16            98
  T3                25           154
  T4                 5            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"
               vv
clus             N0  N1  N2  N3
  ATM MUTATED    30   7   6   1
  ATM WILD-TYPE 183  34  69   7
D43V5, multiclass
    clus
vv   ATM MUTATED ATM WILD-TYPE
  N0          30           183
  N1           7            34
  N2           6            69
  N3           1             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"
D43V6, binary
               cls
clus              0   1
  ATM MUTATED    19   2
  ATM WILD-TYPE 163   8
[1] "tbl2"
               cls
clus            [,1] [,2]
  ATM MUTATED     19    2
  ATM WILD-TYPE  163    8
   clus
vv  ATM MUTATED ATM WILD-TYPE
  0          19           163
  1           2             8
[1] 2 2
[1] FALSE
D43V7, binary
               cls
clus              0   1
  ATM MUTATED     9  40
  ATM WILD-TYPE  87 240
[1] "tbl2"
               cls
clus            [,1] [,2]
  ATM MUTATED      9   40
  ATM WILD-TYPE   87  240
        clus
vv       ATM MUTATED ATM WILD-TYPE
  FEMALE           9            87
  MALE            40           240
[1] 2 2
[1] FALSE
D43V8, continuous
D43V9, continuous
D43V10, continuous
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ATM MUTATED       4                         4    41
  ATM WILD-TYPE    34                        17   260
D43V11, multiclass
                           clus
vv                          ATM MUTATED ATM WILD-TYPE
  ASIAN                               4            34
  BLACK OR AFRICAN AMERICAN           4            17
  WHITE                              41           260
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V12, binary
               cls
clus              0   1
  ATM MUTATED     2  46
  ATM WILD-TYPE   6 292
[1] "tbl2"
               cls
clus            [,1] [,2]
  ATM MUTATED      2   46
  ATM WILD-TYPE    6  292
                        clus
vv                       ATM MUTATED ATM WILD-TYPE
  HISPANIC OR LATINO               2             6
  NOT HISPANIC OR LATINO          46           292
[1] 2 2
[1] FALSE

Clustering(44) Variable = UNC93B1 MUTATION ANALYSIS
D44V1, survival
                   sevent
clus2                 0   1
  UNC93B1 MUTATED     2   5
  UNC93B1 WILD-TYPE 217 146
  UNC93B1 MUTATED UNC93B1 WILD-TYPE 
                7               363 
  UNC93B1 MUTATED UNC93B1 WILD-TYPE 
                5               146 
$`UNC93B1 MUTATED`
TCGA-4Z-AA7W TCGA-BT-A3PH TCGA-FD-A3SJ TCGA-XF-AAML TCGA-XF-AAN0 TCGA-ZF-AA4N 
       27.62         4.67        24.30         7.63        56.48         2.89 
TCGA-ZF-AA4W 
       60.16 

$`UNC93B1 WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        91.63       103.50       105.70         8.35 
TCGA-4Z-AA7M TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7S 
       16.27        44.94        16.83        16.77        17.16        34.98 
TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA84 
       49.12         0.62        41.75        51.16        66.54        15.12 
TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J 
       10.22        47.80        33.83        40.08         7.33         2.66 
TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N 
        6.74        12.39         6.58        13.15        19.04        32.84 
TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U 
       12.16        17.88        19.50         5.06        14.89        14.96 
TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A2LD 
        5.06         8.35         8.25        17.16        16.18        20.48 
TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E TCGA-BT-A42F 
       12.82         9.96        17.56        28.70        24.26        28.41 
TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-C4-A0F6 TCGA-C4-A0F7 TCGA-CF-A1HR 
        8.98         1.94         2.93        23.01         2.04         0.46 
TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W 
        0.43         0.69        10.95        12.66        12.46        12.10 
TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A9FF 
       12.62        12.26        13.12        12.00        12.10        11.87 
TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3QU 
       13.08        12.92         4.90         7.20         5.46         5.19 
TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 
       16.31         1.84        13.58        21.86         2.14        66.41 
TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE 
       18.41        19.00        16.70       130.88       112.44        16.14 
TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 
       17.62        15.62         1.81        10.59         7.79       123.85 
TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ 
       87.32         2.20        13.58         7.82         8.22        17.72 
TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX 
       50.27        21.30        23.21         9.67        20.81        10.55 
TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 
      140.81        48.00        17.98        64.18        41.56        76.60 
TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6P 
       67.36        15.68        41.06        30.67        38.24        15.02 
TCGA-DK-AA6Q TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA6X 
       13.58       166.03        12.36        10.49         8.65         7.53 
TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A2PC TCGA-E5-A4TZ 
       13.64        43.50        12.03        10.62        43.59        15.35 
TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 
       38.83        24.66         0.10         0.49         2.24        16.70 
TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME 
       17.39         0.56         0.66        14.56        13.97        12.99 
TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H 
       14.33         0.92         1.22        13.68        14.07        12.95 
TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 
       14.37         8.09        32.02        16.77         8.94        33.04 
TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SL 
        4.01        12.62        22.52        27.98        60.66        23.41 
TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR 
       17.98        29.16         5.52        25.74        46.78        19.79 
TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X 
       12.85        22.98        27.35        14.96        20.91         3.62 
TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX 
       26.73        53.88        11.01        19.33         5.36         5.69 
TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O 
        8.25        27.45        18.08        58.92         2.70         7.10 
TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD 
        6.28        13.35        62.86        18.81         6.15        12.69 
TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FD-A6TK 
       12.36         2.27         3.06         4.31         9.67        10.85 
TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FJ-A871 TCGA-FT-A3EE 
       31.07         7.13        10.65        17.23         8.94         3.25 
TCGA-FT-A61P TCGA-G2-A2EC TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL 
        6.48        22.88        61.94        30.61        15.95        26.93 
TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B 
       35.24        33.01         7.23        20.12        17.62        66.02 
TCGA-G2-AA3C TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO 
        6.94        64.44        19.46        21.40         2.24        15.81 
TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A6I1 
        4.50        15.91        14.07        17.75        24.92         8.94 
TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 
       13.91         7.73         2.10         3.12        20.98         2.20 
TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 
        7.36        10.92        11.31        11.31         7.63        27.09 
TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATO TCGA-GU-AATP TCGA-GU-AATQ 
       20.05         5.62         4.73        10.65        32.98         7.00 
TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH 
       14.27        21.34        19.10        19.82        20.28         8.48 
TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO 
       10.59        27.35         8.58        19.07        22.72         1.51 
TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS 
       19.40        38.60         3.06         9.01         8.22        25.02 
TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RH 
        3.45        21.24         2.76         9.14        27.68         9.07 
TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO 
       11.70         1.74         1.81        15.42         6.38        11.80 
TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X 
       15.32        15.58        13.48        12.23        16.67        14.24 
TCGA-S5-A6DX TCGA-S5-AA26 TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L 
        1.84         3.75        12.43        31.56        17.62        37.05 
TCGA-UY-A78M TCGA-UY-A78N TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A9PA TCGA-UY-A9PB 
       22.68        86.83        76.01        65.75        35.24        29.56 
TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG 
       17.82         4.54         1.64         1.87        17.88        48.62 
TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SL TCGA-XF-A9SV TCGA-XF-A9SW 
       64.80        79.66         3.22        66.41        12.76        11.90 
TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 
       23.64        21.04        28.24        26.27        18.90         2.24 
TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMF 
       16.27        66.64         2.10        13.74        92.98        10.82 
TCGA-XF-AAMG TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMT 
      110.60        11.31        54.90        71.57        91.73         2.96 
TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN1 TCGA-XF-AAN2 
        8.32         6.77        98.99        44.32        30.94        61.45 
TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 
       86.30        27.06        75.39        18.81         3.88         9.63 
TCGA-YC-A9TC TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R2 
        0.66        11.97        13.64        18.64         7.36        21.11 
TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RC 
       24.13        30.28        27.19        21.86        28.41        74.56 
TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-A9RM 
       13.41         3.48        52.73        52.60        82.49        47.84 
TCGA-ZF-A9RN TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4X 
       20.22        34.06        19.69         8.61        59.38        63.02 
TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 
       38.73        35.41        57.90        19.40         8.52        47.15 
TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-ZF-AA5P 
       19.17         5.52        10.13 

  UNC93B1 MUTATED UNC93B1 WILD-TYPE 
             2.89              0.10 
  UNC93B1 MUTATED UNC93B1 WILD-TYPE 
            60.16            166.03 
  UNC93B1 MUTATED UNC93B1 WILD-TYPE 
            24.30             15.62 
[1] "2.9 - 60.2 (24.3)"  "0.1 - 166.0 (15.6)"
[1] "hr=" "1.6"
D44V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  UNC93B1 MUTATED         0        3         1        3
  UNC93B1 WILD-TYPE       4      114       121      125
D44V3, multiclass
           clus
vv          UNC93B1 MUTATED UNC93B1 WILD-TYPE
  STAGE I                 0                 4
  STAGE II                3               114
  STAGE III               1               121
  STAGE IV                3               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"
                   vv
clus                T0+T1+T2  T3  T4
  UNC93B1 MUTATED          3   2   1
  UNC93B1 WILD-TYPE      111 177  51
D44V4, multiclass
          clus
vv         UNC93B1 MUTATED UNC93B1 WILD-TYPE
  T0+T1+T2               3               111
  T3                     2               177
  T4                     1                51
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  UNC93B1 MUTATED     3   0   3   0
  UNC93B1 WILD-TYPE 210  41  72   8
D44V5, multiclass
    clus
vv   UNC93B1 MUTATED UNC93B1 WILD-TYPE
  N0               3               210
  N1               0                41
  N2               3                72
  N3               0                 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"
D44V6, binary
                   cls
clus                  0   1
  UNC93B1 MUTATED     2   0
  UNC93B1 WILD-TYPE 180  10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  UNC93B1 MUTATED      2    0
  UNC93B1 WILD-TYPE  180   10
   clus
vv  UNC93B1 MUTATED UNC93B1 WILD-TYPE
  0               2               180
  1               0                10
[1] 2 2
[1] FALSE
D44V7, binary
                   cls
clus                  0   1
  UNC93B1 MUTATED     0   7
  UNC93B1 WILD-TYPE  96 273
[1] "tbl2"
                   cls
clus                [,1] [,2]
  UNC93B1 MUTATED      0    7
  UNC93B1 WILD-TYPE   96  273
        clus
vv       UNC93B1 MUTATED UNC93B1 WILD-TYPE
  FEMALE               0                96
  MALE                 7               273
[1] 2 2
[1] FALSE
D44V8, continuous
[1] "Remove cluster labels:" "UNC93B1 MUTATED"       
clus
  UNC93B1 MUTATED UNC93B1 WILD-TYPE 
                2               118 
       TCGA-2F-A9KO        TCGA-2F-A9KP        TCGA-2F-A9KQ        TCGA-2F-A9KR 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
       TCGA-2F-A9KT        TCGA-2F-A9KW        TCGA-CF-A1HS        TCGA-CF-A27C 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
       TCGA-CF-A3MF        TCGA-CF-A3MG        TCGA-CF-A3MH        TCGA-CF-A3MI 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
       TCGA-CF-A47S        TCGA-CF-A47T        TCGA-CF-A47V        TCGA-CF-A47W 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
       TCGA-CF-A47X        TCGA-CF-A47Y        TCGA-CF-A5U8        TCGA-CF-A5UA 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
       TCGA-CF-A7I0        TCGA-DK-A2HX        TCGA-DK-A3IN        TCGA-DK-A3IV 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
       TCGA-DK-A3WX        TCGA-DK-A3X2        TCGA-DK-A6B2        TCGA-DK-A6B5 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
       TCGA-DK-A6B6        TCGA-DK-AA6P        TCGA-DK-AA6S        TCGA-DK-AA6U 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
       TCGA-DK-AA6W        TCGA-DK-AA76        TCGA-E5-A2PC        TCGA-E5-A4TZ 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
       TCGA-E5-A4U1        TCGA-E7-A519        TCGA-E7-A541        TCGA-E7-A7DU 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
       TCGA-E7-A7DV        TCGA-FT-A61P        TCGA-G2-A2EC        TCGA-G2-A2EF 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
       TCGA-G2-A2EJ        TCGA-G2-A2EK        TCGA-G2-A2EL        TCGA-G2-A2EO 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
       TCGA-G2-A2ES        TCGA-G2-A3IB        TCGA-G2-A3IE        TCGA-G2-A3VY 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
       TCGA-GC-A3BM        TCGA-GC-A3I6        TCGA-GC-A3OO        TCGA-GC-A3RC 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
       TCGA-GC-A3RD        TCGA-GC-A3YS        TCGA-GC-A6I1        TCGA-GC-A6I3 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
       TCGA-GD-A3OS        TCGA-GD-A6C6        TCGA-GV-A3JV        TCGA-GV-A3JW 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
       TCGA-GV-A3JX        TCGA-GV-A3JZ        TCGA-GV-A3QF        TCGA-GV-A3QH 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
       TCGA-GV-A3QI        TCGA-GV-A3QK        TCGA-GV-A40E        TCGA-GV-A40G 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
       TCGA-GV-A6ZA        TCGA-SY-A9G0        TCGA-SY-A9G5        TCGA-UY-A78L 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
       TCGA-UY-A78M        TCGA-UY-A78N        TCGA-XF-A8HH        TCGA-XF-A8HI 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
       TCGA-XF-A9SG        TCGA-XF-A9SH        TCGA-XF-A9SI        TCGA-XF-A9SJ 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
       TCGA-XF-A9SL        TCGA-XF-A9SV        TCGA-XF-A9SW        TCGA-XF-A9SX 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
       TCGA-XF-A9SY        TCGA-XF-A9SZ        TCGA-XF-A9T0        TCGA-XF-A9T2 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
       TCGA-XF-A9T3        TCGA-XF-A9T4        TCGA-XF-A9T5        TCGA-XF-A9T6 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
       TCGA-XF-A9T8        TCGA-XF-AAME        TCGA-XF-AAMF        TCGA-XF-AAMG 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
       TCGA-XF-AAMH        TCGA-XF-AAMJ        TCGA-XF-AAMQ        TCGA-XF-AAMR 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
       TCGA-XF-AAMT        TCGA-XF-AAMW        TCGA-XF-AAMX        TCGA-XF-AAMY 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
       TCGA-XF-AAMZ        TCGA-XF-AAN1        TCGA-XF-AAN2        TCGA-XF-AAN3 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
       TCGA-XF-AAN4        TCGA-XF-AAN5        TCGA-XF-AAN7        TCGA-XF-AAN8 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
       TCGA-YF-AA3L        TCGA-YF-AA3M 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
D44V9, continuous
[1] "Remove cluster labels:" "UNC93B1 MUTATED"       
clus
  UNC93B1 MUTATED UNC93B1 WILD-TYPE 
                2               203 
       TCGA-2F-A9KO        TCGA-2F-A9KP        TCGA-2F-A9KR        TCGA-4Z-AA7M 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
       TCGA-4Z-AA89        TCGA-BL-A0C8        TCGA-BL-A13I        TCGA-BL-A13J 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
       TCGA-BL-A3JM        TCGA-BL-A5ZZ        TCGA-BT-A20J        TCGA-BT-A20N 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
       TCGA-BT-A2LA        TCGA-BT-A42B        TCGA-BT-A42C        TCGA-BT-A42E 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
       TCGA-C4-A0EZ        TCGA-C4-A0F0        TCGA-C4-A0F1        TCGA-C4-A0F6 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
       TCGA-CF-A3MH        TCGA-CF-A3MI        TCGA-CF-A47W        TCGA-CF-A47X 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
       TCGA-CF-A5UA        TCGA-CF-A9FH        TCGA-CU-A0YN        TCGA-CU-A0YR 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
       TCGA-CU-A3KJ        TCGA-CU-A3QU        TCGA-CU-A3YL        TCGA-CU-A5W6 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
       TCGA-CU-A72E        TCGA-DK-A1A3        TCGA-DK-A1A5        TCGA-DK-A1A6 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
       TCGA-DK-A1AA        TCGA-DK-A1AC        TCGA-DK-A1AE        TCGA-DK-A2HX 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
       TCGA-DK-A2I6        TCGA-DK-A3IL        TCGA-DK-A3IM        TCGA-DK-A3IN 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
       TCGA-DK-A3IQ        TCGA-DK-A3IU        TCGA-DK-A3IV        TCGA-DK-A3WX 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
       TCGA-DK-A3X1        TCGA-DK-A3X2        TCGA-DK-A6AV        TCGA-DK-A6AW 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
       TCGA-DK-A6B0        TCGA-DK-A6B2        TCGA-DK-A6B6        TCGA-DK-AA6L 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
       TCGA-DK-AA6P        TCGA-DK-AA6T        TCGA-DK-AA6U        TCGA-DK-AA74 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
       TCGA-DK-AA76        TCGA-E5-A4TZ        TCGA-E7-A4XJ        TCGA-E7-A519 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
       TCGA-E7-A5KF        TCGA-E7-A678        TCGA-E7-A6ME        TCGA-E7-A6MF 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
       TCGA-E7-A7PW        TCGA-E7-A7XN        TCGA-E7-A85H        TCGA-E7-A97Q 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
       TCGA-FD-A3B3        TCGA-FD-A3B4        TCGA-FD-A3B5        TCGA-FD-A3B6 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
       TCGA-FD-A3B7        TCGA-FD-A3B8        TCGA-FD-A3N5        TCGA-FD-A3N6 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
       TCGA-FD-A3NA        TCGA-FD-A3SM        TCGA-FD-A3SN        TCGA-FD-A3SO 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
       TCGA-FD-A3SP        TCGA-FD-A3SQ        TCGA-FD-A3SR        TCGA-FD-A3SS 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
       TCGA-FD-A43N        TCGA-FD-A43P        TCGA-FD-A43S        TCGA-FD-A43U 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
       TCGA-FD-A43X        TCGA-FD-A5BT        TCGA-FD-A5BU        TCGA-FD-A5BV 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
       TCGA-FD-A5BX        TCGA-FD-A5C0        TCGA-FD-A62N        TCGA-FD-A6TB 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
       TCGA-FD-A6TC        TCGA-FD-A6TE        TCGA-FD-A6TG        TCGA-FD-A6TH 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
       TCGA-FD-A6TK        TCGA-FJ-A3Z9        TCGA-FJ-A3ZE        TCGA-FJ-A3ZF 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
       TCGA-FJ-A871        TCGA-FT-A61P        TCGA-G2-A2EF        TCGA-G2-A2EJ 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
       TCGA-G2-A2EL        TCGA-G2-A2ES        TCGA-G2-A3IE        TCGA-G2-AA3B 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
       TCGA-G2-AA3C        TCGA-G2-AA3D        TCGA-G2-AA3F        TCGA-GC-A3BM 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
       TCGA-GC-A3RB        TCGA-GC-A3WC        TCGA-GC-A3YS        TCGA-GD-A2C5 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
       TCGA-GD-A3OQ        TCGA-GD-A3OS        TCGA-GD-A6C6        TCGA-GU-A42P 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
       TCGA-GU-A42Q        TCGA-GU-A42R        TCGA-GU-A763        TCGA-GU-A764 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
       TCGA-GU-AATO        TCGA-GU-AATP        TCGA-GU-AATQ        TCGA-GV-A3JV 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
       TCGA-GV-A3JX        TCGA-GV-A3JZ        TCGA-GV-A3QF        TCGA-GV-A3QG 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
       TCGA-GV-A3QH        TCGA-GV-A3QI        TCGA-GV-A3QK        TCGA-GV-A40E 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
       TCGA-GV-A40G        TCGA-H4-A2HO        TCGA-H4-A2HQ        TCGA-HQ-A5ND 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
       TCGA-HQ-A5NE        TCGA-K4-A3WS        TCGA-K4-A3WV        TCGA-K4-A5RH 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
       TCGA-K4-A5RI        TCGA-K4-A83P        TCGA-K4-AAQO        TCGA-PQ-A6FI 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
       TCGA-PQ-A6FN        TCGA-R3-A69X        TCGA-S5-A6DX        TCGA-SY-A9G0 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
       TCGA-UY-A78N        TCGA-UY-A8OB        TCGA-UY-A9PB        TCGA-UY-A9PE 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
       TCGA-UY-A9PF        TCGA-XF-A9SJ        TCGA-XF-A9SL        TCGA-XF-A9SV 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
       TCGA-XF-A9SX        TCGA-XF-A9SY        TCGA-XF-A9SZ        TCGA-XF-A9T3 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
       TCGA-XF-A9T8        TCGA-XF-AAMF        TCGA-XF-AAMH        TCGA-XF-AAMQ 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
       TCGA-XF-AAMT        TCGA-XF-AAN1        TCGA-XF-AAN2        TCGA-XF-AAN4 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
       TCGA-XF-AAN5        TCGA-XF-AAN7        TCGA-XF-AAN8        TCGA-YF-AA3L 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
       TCGA-YF-AA3M        TCGA-ZF-A9R0        TCGA-ZF-A9R2        TCGA-ZF-A9R3 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
       TCGA-ZF-A9R5        TCGA-ZF-A9R7        TCGA-ZF-A9R9        TCGA-ZF-A9RD 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
       TCGA-ZF-A9RF        TCGA-ZF-A9RL        TCGA-ZF-A9RM        TCGA-ZF-AA4U 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
       TCGA-ZF-AA4V        TCGA-ZF-AA51        TCGA-ZF-AA52        TCGA-ZF-AA58 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
       TCGA-ZF-AA5H        TCGA-ZF-AA5N        TCGA-ZF-AA5P 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
D44V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  UNC93B1 MUTATED       0                         0     7
  UNC93B1 WILD-TYPE    38                        21   294
D44V11, multiclass
                           clus
vv                          UNC93B1 MUTATED UNC93B1 WILD-TYPE
  ASIAN                                   0                38
  BLACK OR AFRICAN AMERICAN               0                21
  WHITE                                   7               294
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V12, binary
                   cls
clus                  0   1
  UNC93B1 MUTATED     0   6
  UNC93B1 WILD-TYPE   8 332
[1] "tbl2"
                   cls
clus                [,1] [,2]
  UNC93B1 MUTATED      0    6
  UNC93B1 WILD-TYPE    8  332
                        clus
vv                       UNC93B1 MUTATED UNC93B1 WILD-TYPE
  HISPANIC OR LATINO                   0                 8
  NOT HISPANIC OR LATINO               6               332
[1] 2 2
[1] FALSE

Clustering(45) Variable = UBA52 MUTATION ANALYSIS
D45V1, survival
                 sevent
clus2               0   1
  UBA52 MUTATED     5   1
  UBA52 WILD-TYPE 214 150
  UBA52 MUTATED UBA52 WILD-TYPE 
              6             364 
  UBA52 MUTATED UBA52 WILD-TYPE 
              1             150 
$`UBA52 MUTATED`
TCGA-DK-A6AW TCGA-DK-A6B6 TCGA-G2-A2EO TCGA-GC-A6I1 TCGA-K4-A54R TCGA-XF-AAMR 
       41.56        30.67        35.24         8.94        27.68        91.73 

$`UBA52 WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        91.63       103.50       105.70         8.35 
TCGA-4Z-AA7M TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7S 
       16.27        44.94        16.83        16.77        17.16        34.98 
TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 
       27.62        49.12         0.62        41.75        51.16        66.54 
TCGA-4Z-AA84 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BL-A13I 
       15.12        10.22        47.80        33.83        40.08         7.33 
TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J 
        2.66         6.74        12.39         6.58        13.15        19.04 
TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T 
       32.84        12.16        17.88        19.50         5.06        14.89 
TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB 
       14.96         5.06         8.35         8.25        17.16        16.18 
TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C 
       20.48         4.67        12.82         9.96        17.56        28.70 
TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-C4-A0F6 
       24.26        28.41         8.98         1.94         2.93        23.01 
TCGA-C4-A0F7 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T 
        2.04         0.46         0.43         0.69        10.95        12.66 
TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA 
       12.46        12.10        12.62        12.26        13.12        12.00 
TCGA-CF-A7I0 TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR 
       12.10        11.87        13.08        12.92         4.90         7.20 
TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 
        5.46         5.19        16.31         1.84        13.58        21.86 
TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC 
        2.14        66.41        18.41        19.00        16.70       130.88 
TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 
      112.44        16.14        17.62        15.62         1.81        10.59 
TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM 
        7.79       123.85        87.32         2.20        13.58         7.82 
TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV 
        8.22        17.72        50.27        21.30        23.21         9.67 
TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV 
       20.81        10.55       140.81        48.00        17.98        64.18 
TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-AA6L TCGA-DK-AA6P 
       76.60        67.36        15.68        41.06        38.24        15.02 
TCGA-DK-AA6Q TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA6X 
       13.58       166.03        12.36        10.49         8.65         7.53 
TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A2PC TCGA-E5-A4TZ 
       13.64        43.50        12.03        10.62        43.59        15.35 
TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 
       38.83        24.66         0.10         0.49         2.24        16.70 
TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME 
       17.39         0.56         0.66        14.56        13.97        12.99 
TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H 
       14.33         0.92         1.22        13.68        14.07        12.95 
TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 
       14.37         8.09        32.02        16.77         8.94        33.04 
TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ 
        4.01        12.62        22.52        27.98        60.66        24.30 
TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ 
       23.41        17.98        29.16         5.52        25.74        46.78 
TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U 
       19.79        12.85        22.98        27.35        14.96        20.91 
TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV 
        3.62        26.73        53.88        11.01        19.33         5.36 
TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N 
        5.69         8.25        27.45        18.08        58.92         2.70 
TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC 
        7.10         6.28        13.35        62.86        18.81         6.15 
TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI 
       12.69        12.36         2.27         3.06         4.31         9.67 
TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FJ-A871 
       10.85        31.07         7.13        10.65        17.23         8.94 
TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EC TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK 
        3.25         6.48        22.88        61.94        30.61        15.95 
TCGA-G2-A2EL TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B 
       26.93        33.01         7.23        20.12        17.62        66.02 
TCGA-G2-AA3C TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO 
        6.94        64.44        19.46        21.40         2.24        15.81 
TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A6I3 
        4.50        15.91        14.07        17.75        24.92        13.91 
TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GD-A76B 
        7.73         2.10         3.12        20.98         2.20         7.36 
TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A764 
       10.92        11.31        11.31         7.63        27.09        20.05 
TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATO TCGA-GU-AATP TCGA-GU-AATQ TCGA-GV-A3JV 
        5.62         4.73        10.65        32.98         7.00        14.27 
TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI 
       21.34        19.10        19.82        20.28         8.48        10.59 
TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-H4-A2HQ 
       27.35         8.58        19.07        22.72         1.51        19.40 
TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU 
       38.60         3.06         9.01         8.22        25.02         3.45 
TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ 
       21.24         2.76         9.14         9.07        11.70         1.74 
TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO TCGA-LC-A66R TCGA-LT-A5Z6 
        1.81        15.42         6.38        11.80        15.32        15.58 
TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 
       13.48        12.23        16.67        14.24         1.84         3.75 
TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78N 
       12.43        31.56        17.62        37.05        22.68        86.83 
TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE 
       76.01        65.75        35.24        29.56        17.82         4.54 
TCGA-UY-A9PF TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI 
        1.64         1.87        17.88        48.62        64.80        79.66 
TCGA-XF-A9SJ TCGA-XF-A9SL TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY 
        3.22        66.41        12.76        11.90        23.64        21.04 
TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T5 
       28.24        26.27        18.90         2.24        16.27        66.64 
TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMG TCGA-XF-AAMH 
        2.10        13.74        92.98        10.82       110.60        11.31 
TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX 
       54.90         7.63        71.57         2.96         8.32         6.77 
TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 
       98.99        44.32        56.48        30.94        61.45        86.30 
TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YC-A9TC 
       27.06        75.39        18.81         3.88         9.63         0.66 
TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R3 
       11.97        13.64        18.64         7.36        21.11        24.13 
TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RD 
       30.28        27.19        21.86        28.41        74.56        13.41 
TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-A9RN 
        3.48        52.73        52.60        82.49        47.84        20.22 
TCGA-ZF-AA4N TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W 
        2.89        34.06        19.69         8.61        59.38        60.16 
TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA56 
       63.02        38.73        35.41        57.90        19.40         8.52 
TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-ZF-AA5P 
       47.15        19.17         5.52        10.13 

  UBA52 MUTATED UBA52 WILD-TYPE 
           8.94            0.10 
  UBA52 MUTATED UBA52 WILD-TYPE 
          91.73          166.03 
  UBA52 MUTATED UBA52 WILD-TYPE 
         32.955          15.500 
[1] "8.9 - 91.7 (33.0)"  "0.1 - 166.0 (15.5)"
[1] "hr=" "4"  
D45V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  UBA52 MUTATED         0        4         2        0
  UBA52 WILD-TYPE       4      113       120      128
D45V3, multiclass
           clus
vv          UBA52 MUTATED UBA52 WILD-TYPE
  STAGE I               0               4
  STAGE II              4             113
  STAGE III             2             120
  STAGE IV              0             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"
                 vv
clus              T0+T1+T2  T3  T4
  UBA52 MUTATED          3   2   0
  UBA52 WILD-TYPE      111 177  52
D45V4, multiclass
          clus
vv         UBA52 MUTATED UBA52 WILD-TYPE
  T0+T1+T2             3             111
  T3                   2             177
  T4                   0              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"
                 vv
clus               N0  N1  N2  N3
  UBA52 MUTATED     5   0   0   0
  UBA52 WILD-TYPE 208  41  75   8
D45V5, multiclass
    clus
vv   UBA52 MUTATED UBA52 WILD-TYPE
  N0             5             208
  N1             0              41
  N2             0              75
  N3             0               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"
D45V6, binary
                 cls
clus                0   1
  UBA52 MUTATED     2   0
  UBA52 WILD-TYPE 180  10
[1] "tbl2"
                 cls
clus              [,1] [,2]
  UBA52 MUTATED      2    0
  UBA52 WILD-TYPE  180   10
   clus
vv  UBA52 MUTATED UBA52 WILD-TYPE
  0             2             180
  1             0              10
[1] 2 2
[1] FALSE
D45V7, binary
                 cls
clus                0   1
  UBA52 MUTATED     1   5
  UBA52 WILD-TYPE  95 275
[1] "tbl2"
                 cls
clus              [,1] [,2]
  UBA52 MUTATED      1    5
  UBA52 WILD-TYPE   95  275
        clus
vv       UBA52 MUTATED UBA52 WILD-TYPE
  FEMALE             1              95
  MALE               5             275
[1] 2 2
[1] FALSE
D45V8, continuous
D45V9, continuous
[1] "Remove cluster labels:" "UBA52 MUTATED"         
clus
  UBA52 MUTATED UBA52 WILD-TYPE 
              2             203 
     TCGA-2F-A9KO      TCGA-2F-A9KP      TCGA-2F-A9KR      TCGA-4Z-AA7M 
"UBA52 WILD-TYPE" "UBA52 WILD-TYPE" "UBA52 WILD-TYPE" "UBA52 WILD-TYPE" 
     TCGA-4Z-AA89      TCGA-BL-A0C8      TCGA-BL-A13I      TCGA-BL-A13J 
"UBA52 WILD-TYPE" "UBA52 WILD-TYPE" "UBA52 WILD-TYPE" "UBA52 WILD-TYPE" 
     TCGA-BL-A3JM      TCGA-BL-A5ZZ      TCGA-BT-A20J      TCGA-BT-A20N 
"UBA52 WILD-TYPE" "UBA52 WILD-TYPE" "UBA52 WILD-TYPE" "UBA52 WILD-TYPE" 
     TCGA-BT-A2LA      TCGA-BT-A42B      TCGA-BT-A42C      TCGA-BT-A42E 
"UBA52 WILD-TYPE" "UBA52 WILD-TYPE" "UBA52 WILD-TYPE" "UBA52 WILD-TYPE" 
     TCGA-C4-A0EZ      TCGA-C4-A0F0      TCGA-C4-A0F1      TCGA-C4-A0F6 
"UBA52 WILD-TYPE" "UBA52 WILD-TYPE" "UBA52 WILD-TYPE" "UBA52 WILD-TYPE" 
     TCGA-CF-A3MH      TCGA-CF-A3MI      TCGA-CF-A47W      TCGA-CF-A47X 
"UBA52 WILD-TYPE" "UBA52 WILD-TYPE" "UBA52 WILD-TYPE" "UBA52 WILD-TYPE" 
     TCGA-CF-A5UA      TCGA-CF-A9FH      TCGA-CU-A0YN      TCGA-CU-A0YR 
"UBA52 WILD-TYPE" "UBA52 WILD-TYPE" "UBA52 WILD-TYPE" "UBA52 WILD-TYPE" 
     TCGA-CU-A3KJ      TCGA-CU-A3QU      TCGA-CU-A3YL      TCGA-CU-A5W6 
"UBA52 WILD-TYPE" "UBA52 WILD-TYPE" "UBA52 WILD-TYPE" "UBA52 WILD-TYPE" 
     TCGA-CU-A72E      TCGA-DK-A1A3      TCGA-DK-A1A5      TCGA-DK-A1A6 
"UBA52 WILD-TYPE" "UBA52 WILD-TYPE" "UBA52 WILD-TYPE" "UBA52 WILD-TYPE" 
     TCGA-DK-A1AA      TCGA-DK-A1AC      TCGA-DK-A1AE      TCGA-DK-A2HX 
"UBA52 WILD-TYPE" "UBA52 WILD-TYPE" "UBA52 WILD-TYPE" "UBA52 WILD-TYPE" 
     TCGA-DK-A2I6      TCGA-DK-A3IL      TCGA-DK-A3IM      TCGA-DK-A3IN 
"UBA52 WILD-TYPE" "UBA52 WILD-TYPE" "UBA52 WILD-TYPE" "UBA52 WILD-TYPE" 
     TCGA-DK-A3IQ      TCGA-DK-A3IU      TCGA-DK-A3IV      TCGA-DK-A3WX 
"UBA52 WILD-TYPE" "UBA52 WILD-TYPE" "UBA52 WILD-TYPE" "UBA52 WILD-TYPE" 
     TCGA-DK-A3X1      TCGA-DK-A3X2      TCGA-DK-A6AV      TCGA-DK-A6B0 
"UBA52 WILD-TYPE" "UBA52 WILD-TYPE" "UBA52 WILD-TYPE" "UBA52 WILD-TYPE" 
     TCGA-DK-A6B2      TCGA-DK-AA6L      TCGA-DK-AA6P      TCGA-DK-AA6T 
"UBA52 WILD-TYPE" "UBA52 WILD-TYPE" "UBA52 WILD-TYPE" "UBA52 WILD-TYPE" 
     TCGA-DK-AA6U      TCGA-DK-AA74      TCGA-DK-AA76      TCGA-E5-A4TZ 
"UBA52 WILD-TYPE" "UBA52 WILD-TYPE" "UBA52 WILD-TYPE" "UBA52 WILD-TYPE" 
     TCGA-E7-A4XJ      TCGA-E7-A519      TCGA-E7-A5KF      TCGA-E7-A678 
"UBA52 WILD-TYPE" "UBA52 WILD-TYPE" "UBA52 WILD-TYPE" "UBA52 WILD-TYPE" 
     TCGA-E7-A6ME      TCGA-E7-A6MF      TCGA-E7-A7PW      TCGA-E7-A7XN 
"UBA52 WILD-TYPE" "UBA52 WILD-TYPE" "UBA52 WILD-TYPE" "UBA52 WILD-TYPE" 
     TCGA-E7-A85H      TCGA-E7-A97Q      TCGA-FD-A3B3      TCGA-FD-A3B4 
"UBA52 WILD-TYPE" "UBA52 WILD-TYPE" "UBA52 WILD-TYPE" "UBA52 WILD-TYPE" 
     TCGA-FD-A3B5      TCGA-FD-A3B6      TCGA-FD-A3B7      TCGA-FD-A3B8 
"UBA52 WILD-TYPE" "UBA52 WILD-TYPE" "UBA52 WILD-TYPE" "UBA52 WILD-TYPE" 
     TCGA-FD-A3N5      TCGA-FD-A3N6      TCGA-FD-A3NA      TCGA-FD-A3SJ 
"UBA52 WILD-TYPE" "UBA52 WILD-TYPE" "UBA52 WILD-TYPE" "UBA52 WILD-TYPE" 
     TCGA-FD-A3SM      TCGA-FD-A3SN      TCGA-FD-A3SO      TCGA-FD-A3SP 
"UBA52 WILD-TYPE" "UBA52 WILD-TYPE" "UBA52 WILD-TYPE" "UBA52 WILD-TYPE" 
     TCGA-FD-A3SQ      TCGA-FD-A3SR      TCGA-FD-A3SS      TCGA-FD-A43N 
"UBA52 WILD-TYPE" "UBA52 WILD-TYPE" "UBA52 WILD-TYPE" "UBA52 WILD-TYPE" 
     TCGA-FD-A43P      TCGA-FD-A43S      TCGA-FD-A43U      TCGA-FD-A43X 
"UBA52 WILD-TYPE" "UBA52 WILD-TYPE" "UBA52 WILD-TYPE" "UBA52 WILD-TYPE" 
     TCGA-FD-A5BT      TCGA-FD-A5BU      TCGA-FD-A5BV      TCGA-FD-A5BX 
"UBA52 WILD-TYPE" "UBA52 WILD-TYPE" "UBA52 WILD-TYPE" "UBA52 WILD-TYPE" 
     TCGA-FD-A5C0      TCGA-FD-A62N      TCGA-FD-A6TB      TCGA-FD-A6TC 
"UBA52 WILD-TYPE" "UBA52 WILD-TYPE" "UBA52 WILD-TYPE" "UBA52 WILD-TYPE" 
     TCGA-FD-A6TE      TCGA-FD-A6TG      TCGA-FD-A6TH      TCGA-FD-A6TK 
"UBA52 WILD-TYPE" "UBA52 WILD-TYPE" "UBA52 WILD-TYPE" "UBA52 WILD-TYPE" 
     TCGA-FJ-A3Z9      TCGA-FJ-A3ZE      TCGA-FJ-A3ZF      TCGA-FJ-A871 
"UBA52 WILD-TYPE" "UBA52 WILD-TYPE" "UBA52 WILD-TYPE" "UBA52 WILD-TYPE" 
     TCGA-FT-A61P      TCGA-G2-A2EF      TCGA-G2-A2EJ      TCGA-G2-A2EL 
"UBA52 WILD-TYPE" "UBA52 WILD-TYPE" "UBA52 WILD-TYPE" "UBA52 WILD-TYPE" 
     TCGA-G2-A2ES      TCGA-G2-A3IE      TCGA-G2-AA3B      TCGA-G2-AA3C 
"UBA52 WILD-TYPE" "UBA52 WILD-TYPE" "UBA52 WILD-TYPE" "UBA52 WILD-TYPE" 
     TCGA-G2-AA3D      TCGA-G2-AA3F      TCGA-GC-A3BM      TCGA-GC-A3RB 
"UBA52 WILD-TYPE" "UBA52 WILD-TYPE" "UBA52 WILD-TYPE" "UBA52 WILD-TYPE" 
     TCGA-GC-A3WC      TCGA-GC-A3YS      TCGA-GD-A2C5      TCGA-GD-A3OQ 
"UBA52 WILD-TYPE" "UBA52 WILD-TYPE" "UBA52 WILD-TYPE" "UBA52 WILD-TYPE" 
     TCGA-GD-A3OS      TCGA-GD-A6C6      TCGA-GU-A42P      TCGA-GU-A42Q 
"UBA52 WILD-TYPE" "UBA52 WILD-TYPE" "UBA52 WILD-TYPE" "UBA52 WILD-TYPE" 
     TCGA-GU-A42R      TCGA-GU-A763      TCGA-GU-A764      TCGA-GU-AATO 
"UBA52 WILD-TYPE" "UBA52 WILD-TYPE" "UBA52 WILD-TYPE" "UBA52 WILD-TYPE" 
     TCGA-GU-AATP      TCGA-GU-AATQ      TCGA-GV-A3JV      TCGA-GV-A3JX 
"UBA52 WILD-TYPE" "UBA52 WILD-TYPE" "UBA52 WILD-TYPE" "UBA52 WILD-TYPE" 
     TCGA-GV-A3JZ      TCGA-GV-A3QF      TCGA-GV-A3QG      TCGA-GV-A3QH 
"UBA52 WILD-TYPE" "UBA52 WILD-TYPE" "UBA52 WILD-TYPE" "UBA52 WILD-TYPE" 
     TCGA-GV-A3QI      TCGA-GV-A3QK      TCGA-GV-A40E      TCGA-GV-A40G 
"UBA52 WILD-TYPE" "UBA52 WILD-TYPE" "UBA52 WILD-TYPE" "UBA52 WILD-TYPE" 
     TCGA-H4-A2HO      TCGA-H4-A2HQ      TCGA-HQ-A5ND      TCGA-HQ-A5NE 
"UBA52 WILD-TYPE" "UBA52 WILD-TYPE" "UBA52 WILD-TYPE" "UBA52 WILD-TYPE" 
     TCGA-K4-A3WS      TCGA-K4-A3WV      TCGA-K4-A5RH      TCGA-K4-A5RI 
"UBA52 WILD-TYPE" "UBA52 WILD-TYPE" "UBA52 WILD-TYPE" "UBA52 WILD-TYPE" 
     TCGA-K4-A83P      TCGA-K4-AAQO      TCGA-PQ-A6FI      TCGA-PQ-A6FN 
"UBA52 WILD-TYPE" "UBA52 WILD-TYPE" "UBA52 WILD-TYPE" "UBA52 WILD-TYPE" 
     TCGA-R3-A69X      TCGA-S5-A6DX      TCGA-SY-A9G0      TCGA-UY-A78N 
"UBA52 WILD-TYPE" "UBA52 WILD-TYPE" "UBA52 WILD-TYPE" "UBA52 WILD-TYPE" 
     TCGA-UY-A8OB      TCGA-UY-A9PB      TCGA-UY-A9PE      TCGA-UY-A9PF 
"UBA52 WILD-TYPE" "UBA52 WILD-TYPE" "UBA52 WILD-TYPE" "UBA52 WILD-TYPE" 
     TCGA-XF-A9SJ      TCGA-XF-A9SL      TCGA-XF-A9SV      TCGA-XF-A9SX 
"UBA52 WILD-TYPE" "UBA52 WILD-TYPE" "UBA52 WILD-TYPE" "UBA52 WILD-TYPE" 
     TCGA-XF-A9SY      TCGA-XF-A9SZ      TCGA-XF-A9T3      TCGA-XF-A9T8 
"UBA52 WILD-TYPE" "UBA52 WILD-TYPE" "UBA52 WILD-TYPE" "UBA52 WILD-TYPE" 
     TCGA-XF-AAMF      TCGA-XF-AAMH      TCGA-XF-AAMQ      TCGA-XF-AAMT 
"UBA52 WILD-TYPE" "UBA52 WILD-TYPE" "UBA52 WILD-TYPE" "UBA52 WILD-TYPE" 
     TCGA-XF-AAN0      TCGA-XF-AAN1      TCGA-XF-AAN2      TCGA-XF-AAN4 
"UBA52 WILD-TYPE" "UBA52 WILD-TYPE" "UBA52 WILD-TYPE" "UBA52 WILD-TYPE" 
     TCGA-XF-AAN5      TCGA-XF-AAN7      TCGA-XF-AAN8      TCGA-YF-AA3L 
"UBA52 WILD-TYPE" "UBA52 WILD-TYPE" "UBA52 WILD-TYPE" "UBA52 WILD-TYPE" 
     TCGA-YF-AA3M      TCGA-ZF-A9R0      TCGA-ZF-A9R2      TCGA-ZF-A9R3 
"UBA52 WILD-TYPE" "UBA52 WILD-TYPE" "UBA52 WILD-TYPE" "UBA52 WILD-TYPE" 
     TCGA-ZF-A9R5      TCGA-ZF-A9R7      TCGA-ZF-A9R9      TCGA-ZF-A9RD 
"UBA52 WILD-TYPE" "UBA52 WILD-TYPE" "UBA52 WILD-TYPE" "UBA52 WILD-TYPE" 
     TCGA-ZF-A9RF      TCGA-ZF-A9RL      TCGA-ZF-A9RM      TCGA-ZF-AA4U 
"UBA52 WILD-TYPE" "UBA52 WILD-TYPE" "UBA52 WILD-TYPE" "UBA52 WILD-TYPE" 
     TCGA-ZF-AA4V      TCGA-ZF-AA51      TCGA-ZF-AA52      TCGA-ZF-AA58 
"UBA52 WILD-TYPE" "UBA52 WILD-TYPE" "UBA52 WILD-TYPE" "UBA52 WILD-TYPE" 
     TCGA-ZF-AA5H      TCGA-ZF-AA5N      TCGA-ZF-AA5P 
"UBA52 WILD-TYPE" "UBA52 WILD-TYPE" "UBA52 WILD-TYPE" 
D45V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  UBA52 MUTATED       0                         0     6
  UBA52 WILD-TYPE    38                        21   295
D45V11, multiclass
                           clus
vv                          UBA52 MUTATED UBA52 WILD-TYPE
  ASIAN                                 0              38
  BLACK OR AFRICAN AMERICAN             0              21
  WHITE                                 6             295
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V12, binary
                 cls
clus                0   1
  UBA52 MUTATED     0   6
  UBA52 WILD-TYPE   8 332
[1] "tbl2"
                 cls
clus              [,1] [,2]
  UBA52 MUTATED      0    6
  UBA52 WILD-TYPE    8  332
                        clus
vv                       UBA52 MUTATED UBA52 WILD-TYPE
  HISPANIC OR LATINO                 0               8
  NOT HISPANIC OR LATINO             6             332
[1] 2 2
[1] FALSE

Clustering(46) Variable = CNOT1 MUTATION ANALYSIS
D46V1, survival
                 sevent
clus2               0   1
  CNOT1 MUTATED    17   4
  CNOT1 WILD-TYPE 202 147
  CNOT1 MUTATED CNOT1 WILD-TYPE 
             21             349 
  CNOT1 MUTATED CNOT1 WILD-TYPE 
              4             147 
$`CNOT1 MUTATED`
TCGA-4Z-AA7M TCGA-DK-A1AE TCGA-DK-A2I1 TCGA-DK-A3X1 TCGA-DK-A6AW TCGA-DK-A6B0 
       16.27        16.14        10.59        48.00        41.56        76.60 
TCGA-DK-A6B6 TCGA-DK-AA71 TCGA-E7-A541 TCGA-FD-A3SN TCGA-FT-A61P TCGA-G2-A2ES 
       30.67        13.64        17.39        29.16         6.48        33.01 
TCGA-G2-A3VY TCGA-GV-A3QF TCGA-GV-A6ZA TCGA-K4-A4AB TCGA-UY-A8OB TCGA-XF-A9SG 
       17.62        20.28        22.72         2.76        65.75        48.62 
TCGA-XF-AAMR TCGA-ZF-A9RD TCGA-ZF-A9RL 
       91.73        13.41        82.49 

$`CNOT1 WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        91.63       103.50       105.70         8.35 
TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7W 
       44.94        16.83        16.77        17.16        34.98        27.62 
TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA84 
       49.12         0.62        41.75        51.16        66.54        15.12 
TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J 
       10.22        47.80        33.83        40.08         7.33         2.66 
TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N 
        6.74        12.39         6.58        13.15        19.04        32.84 
TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U 
       12.16        17.88        19.50         5.06        14.89        14.96 
TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A2LD 
        5.06         8.35         8.25        17.16        16.18        20.48 
TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E 
        4.67        12.82         9.96        17.56        28.70        24.26 
TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-C4-A0F6 TCGA-C4-A0F7 
       28.41         8.98         1.94         2.93        23.01         2.04 
TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V 
        0.46         0.43         0.69        10.95        12.66        12.46 
TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 
       12.10        12.62        12.26        13.12        12.00        12.10 
TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ 
       11.87        13.08        12.92         4.90         7.20         5.46 
TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 
        5.19        16.31         1.84        13.58        21.86         2.14 
TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD 
       66.41        18.41        19.00        16.70       130.88       112.44 
TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A2I6 
       17.62        15.62         1.81         7.79       123.85        87.32 
TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS 
        2.20        13.58         7.82         8.22        17.72        50.27 
TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY 
       21.30        23.21         9.67        20.81        10.55       140.81 
TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-AA6L 
       17.98        64.18        67.36        15.68        41.06        38.24 
TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6W 
       15.02        13.58       166.03        12.36        10.49         8.65 
TCGA-DK-AA6X TCGA-DK-AA74 TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A2PC TCGA-E5-A4TZ 
        7.53        43.50        12.03        10.62        43.59        15.35 
TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 
       38.83        24.66         0.10         0.49         2.24        16.70 
TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF 
        0.56         0.66        14.56        13.97        12.99        14.33 
TCGA-E7-A7DU TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A97P 
        0.92         1.22        13.68        14.07        12.95        14.37 
TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 
        8.09        32.02        16.77         8.94        33.04         4.01 
TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL 
       12.62        22.52        27.98        60.66        24.30        23.41 
TCGA-FD-A3SM TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS 
       17.98         5.52        25.74        46.78        19.79        12.85 
TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BR 
       22.98        27.35        14.96        20.91         3.62        26.73 
TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY 
       53.88        11.01        19.33         5.36         5.69         8.25 
TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P 
       27.45        18.08        58.92         2.70         7.10         6.28 
TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE 
       13.35        62.86        18.81         6.15        12.69        12.36 
TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z7 
        2.27         3.06         4.31         9.67        10.85        31.07 
TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FJ-A871 TCGA-FT-A3EE TCGA-G2-A2EC 
        7.13        10.65        17.23         8.94         3.25        22.88 
TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A3IB 
       61.94        30.61        15.95        26.93        35.24         7.23 
TCGA-G2-A3IE TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3BM 
       20.12        66.02         6.94        64.44        19.46        21.40 
TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC 
        2.24        15.81         4.50        15.91        14.07        17.75 
TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ 
       24.92         8.94        13.91         7.73         2.10         3.12 
TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R 
       20.98         2.20         7.36        10.92        11.31        11.31 
TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATO 
        7.63        27.09        20.05         5.62         4.73        10.65 
TCGA-GU-AATP TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ 
       32.98         7.00        14.27        21.34        19.10        19.82 
TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-H4-A2HO 
        8.48        10.59        27.35         8.58        19.07         1.51 
TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS 
       19.40        38.60         3.06         9.01         8.22        25.02 
TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RH TCGA-K4-A5RI 
        3.45        21.24         9.14        27.68         9.07        11.70 
TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO TCGA-LC-A66R 
        1.74         1.81        15.42         6.38        11.80        15.32 
TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX 
       15.58        13.48        12.23        16.67        14.24         1.84 
TCGA-S5-AA26 TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M 
        3.75        12.43        31.56        17.62        37.05        22.68 
TCGA-UY-A78N TCGA-UY-A78O TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE 
       86.83        76.01        35.24        29.56        17.82         4.54 
TCGA-UY-A9PF TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SJ 
        1.64         1.87        17.88        64.80        79.66         3.22 
TCGA-XF-A9SL TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ 
       66.41        12.76        11.90        23.64        21.04        28.24 
TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 
       26.27        18.90         2.24        16.27        66.64         2.10 
TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMG TCGA-XF-AAMH TCGA-XF-AAMJ 
       13.74        92.98        10.82       110.60        11.31        54.90 
TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAMY 
        7.63        71.57         2.96         8.32         6.77        98.99 
TCGA-XF-AAMZ TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN4 
       44.32        56.48        30.94        61.45        86.30        27.06 
TCGA-XF-AAN5 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L 
       75.39        18.81         3.88         9.63         0.66        11.97 
TCGA-YF-AA3M TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R4 
       13.64        18.64         7.36        21.11        24.13        30.28 
TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RE TCGA-ZF-A9RF 
       27.19        21.86        28.41        74.56         3.48        52.73 
TCGA-ZF-A9RG TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4R TCGA-ZF-AA4T 
       52.60        47.84        20.22         2.89        34.06        19.69 
TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 
        8.61        59.38        60.16        63.02        38.73        35.41 
TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N 
       57.90        19.40         8.52        47.15        19.17         5.52 
TCGA-ZF-AA5P 
       10.13 

  CNOT1 MUTATED CNOT1 WILD-TYPE 
           2.76            0.10 
  CNOT1 MUTATED CNOT1 WILD-TYPE 
          91.73          166.03 
  CNOT1 MUTATED CNOT1 WILD-TYPE 
          22.72           15.12 
[1] "2.8 - 91.7 (22.7)"  "0.1 - 166.0 (15.1)"
[1] "hr=" "3.1"
D46V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  CNOT1 MUTATED         0       11         6        4
  CNOT1 WILD-TYPE       4      106       116      124
D46V3, multiclass
           clus
vv          CNOT1 MUTATED CNOT1 WILD-TYPE
  STAGE I               0               4
  STAGE II             11             106
  STAGE III             6             116
  STAGE IV              4             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"
                 vv
clus              T0+T1+T2  T3  T4
  CNOT1 MUTATED          7  10   1
  CNOT1 WILD-TYPE      107 169  51
D46V4, multiclass
          clus
vv         CNOT1 MUTATED CNOT1 WILD-TYPE
  T0+T1+T2             7             107
  T3                  10             169
  T4                   1              51
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  CNOT1 MUTATED    14   1   3   0
  CNOT1 WILD-TYPE 199  40  72   8
D46V5, multiclass
    clus
vv   CNOT1 MUTATED CNOT1 WILD-TYPE
  N0            14             199
  N1             1              40
  N2             3              72
  N3             0               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"
D46V6, binary
                 cls
clus                0   1
  CNOT1 MUTATED     8   0
  CNOT1 WILD-TYPE 174  10
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CNOT1 MUTATED      8    0
  CNOT1 WILD-TYPE  174   10
   clus
vv  CNOT1 MUTATED CNOT1 WILD-TYPE
  0             8             174
  1             0              10
[1] 2 2
[1] FALSE
D46V7, binary
                 cls
clus                0   1
  CNOT1 MUTATED     3  18
  CNOT1 WILD-TYPE  93 262
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CNOT1 MUTATED      3   18
  CNOT1 WILD-TYPE   93  262
        clus
vv       CNOT1 MUTATED CNOT1 WILD-TYPE
  FEMALE             3              93
  MALE              18             262
[1] 2 2
[1] FALSE
D46V8, continuous
D46V9, continuous
D46V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CNOT1 MUTATED       1                         0    19
  CNOT1 WILD-TYPE    37                        21   282
D46V11, multiclass
                           clus
vv                          CNOT1 MUTATED CNOT1 WILD-TYPE
  ASIAN                                 1              37
  BLACK OR AFRICAN AMERICAN             0              21
  WHITE                                19             282
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V12, binary
                 cls
clus                0   1
  CNOT1 MUTATED     3  17
  CNOT1 WILD-TYPE   5 321
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CNOT1 MUTATED      3   17
  CNOT1 WILD-TYPE    5  321
                        clus
vv                       CNOT1 MUTATED CNOT1 WILD-TYPE
  HISPANIC OR LATINO                 3               5
  NOT HISPANIC OR LATINO            17             321
[1] 2 2
[1] FALSE

Clustering(47) Variable = ERBB2 MUTATION ANALYSIS
D47V1, survival
                 sevent
clus2               0   1
  ERBB2 MUTATED    30  15
  ERBB2 WILD-TYPE 189 136
  ERBB2 MUTATED ERBB2 WILD-TYPE 
             45             325 
  ERBB2 MUTATED ERBB2 WILD-TYPE 
             15             136 
$`ERBB2 MUTATED`
TCGA-2F-A9KP TCGA-2F-A9KT TCGA-4Z-AA7S TCGA-BT-A0YX TCGA-BT-A20T TCGA-CF-A5UA 
       11.97       105.70        34.98        13.15        14.89        12.00 
TCGA-CU-A3YL TCGA-DK-A1A3 TCGA-DK-A2I6 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-E7-A7XN 
       16.31        21.86        87.32        30.67        38.24        14.07 
TCGA-FD-A3SN TCGA-FD-A5BU TCGA-FD-A6TB TCGA-G2-AA3C TCGA-GC-A3OO TCGA-GC-A3YS 
       29.16        19.33        18.81         6.94        15.81        24.92 
TCGA-GU-A766 TCGA-GU-A767 TCGA-GV-A40G TCGA-GV-A6ZA TCGA-HQ-A2OF TCGA-K4-A5RJ 
        5.62         4.73        19.07        22.72         3.06         1.74 
TCGA-K4-A6FZ TCGA-K4-A83P TCGA-MV-A51V TCGA-SY-A9G5 TCGA-XF-A9SI TCGA-XF-A9SL 
        1.81         6.38        13.48        31.56        79.66        66.41 
TCGA-XF-A9T8 TCGA-XF-AAML TCGA-XF-AAMX TCGA-XF-AAN0 TCGA-XF-AAN2 TCGA-XF-AAN3 
       13.74         7.63         6.77        56.48        61.45        86.30 
TCGA-XF-AAN5 TCGA-ZF-A9R3 TCGA-ZF-A9R7 TCGA-ZF-A9RC TCGA-ZF-A9RF TCGA-ZF-A9RG 
       75.39        24.13        21.86        74.56        52.73        52.60 
TCGA-ZF-AA4R TCGA-ZF-AA4V TCGA-ZF-AA4X 
       34.06        59.38        63.02 

$`ERBB2 WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KW TCGA-4Z-AA7M TCGA-4Z-AA7N 
       22.29        91.63       103.50         8.35        16.27        44.94 
TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA80 
       16.83        16.77        17.16        27.62        49.12         0.62 
TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA84 TCGA-4Z-AA86 TCGA-4Z-AA87 
       41.75        51.16        66.54        15.12        10.22        47.80 
TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ 
       33.83        40.08         7.33         2.66         6.74        12.39 
TCGA-BT-A0S7 TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q 
        6.58        19.04        32.84        12.16        17.88        19.50 
TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA 
        5.06        14.96         5.06         8.35         8.25        17.16 
TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B 
       16.18        20.48         4.67        12.82         9.96        17.56 
TCGA-BT-A42C TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F1 
       28.70        24.26        28.41         8.98         1.94         2.93 
TCGA-C4-A0F6 TCGA-C4-A0F7 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47S 
       23.01         2.04         0.46         0.43         0.69        10.95 
TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 
       12.66        12.46        12.10        12.62        12.26        13.12 
TCGA-CF-A7I0 TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR 
       12.10        11.87        13.08        12.92         4.90         7.20 
TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1A6 
        5.46         5.19         1.84        13.58         2.14        66.41 
TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE 
       18.41        19.00        16.70       130.88       112.44        16.14 
TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 
       17.62        15.62         1.81        10.59         7.79       123.85 
TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS 
        2.20        13.58         7.82         8.22        17.72        50.27 
TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY 
       21.30        23.21         9.67        20.81        10.55       140.81 
TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 
       48.00        17.98        64.18        41.56        76.60        67.36 
TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6S TCGA-DK-AA6T 
       15.68        41.06        15.02        13.58       166.03        12.36 
TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA76 
       10.49         8.65         7.53        13.64        43.50        12.03 
TCGA-DK-AA77 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 
       10.62        43.59        15.35        38.83        24.66         0.10 
TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF 
        0.49         2.24        16.70        17.39         0.56         0.66 
TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7DV 
       14.56        13.97        12.99        14.33         0.92         1.22 
TCGA-E7-A7PW TCGA-E7-A85H TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 
       13.68        12.95        14.37         8.09        32.02        16.77 
TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 
        8.94        33.04         4.01        12.62        22.52        27.98 
TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SO TCGA-FD-A3SP 
       60.66        24.30        23.41        17.98         5.52        25.74 
TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S 
       46.78        19.79        12.85        22.98        27.35        14.96 
TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BV 
       20.91         3.62        26.73        53.88        11.01         5.36 
TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N 
        5.69         8.25        27.45        18.08        58.92         2.70 
TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TC TCGA-FD-A6TD 
        7.10         6.28        13.35        62.86         6.15        12.69 
TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FD-A6TK 
       12.36         2.27         3.06         4.31         9.67        10.85 
TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FJ-A871 TCGA-FT-A3EE 
       31.07         7.13        10.65        17.23         8.94         3.25 
TCGA-FT-A61P TCGA-G2-A2EC TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL 
        6.48        22.88        61.94        30.61        15.95        26.93 
TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B 
       35.24        33.01         7.23        20.12        17.62        66.02 
TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3RB TCGA-GC-A3RC 
       64.44        19.46        21.40         2.24         4.50        15.91 
TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP 
       14.07        17.75         8.94        13.91         7.73         2.10 
TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42Q 
        3.12        20.98         2.20         7.36        10.92        11.31 
TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-AATO TCGA-GU-AATP 
       11.31         7.63        27.09        20.05        10.65        32.98 
TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF 
        7.00        14.27        21.34        19.10        19.82        20.28 
TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E TCGA-H4-A2HO TCGA-H4-A2HQ 
        8.48        10.59        27.35         8.58         1.51        19.40 
TCGA-HQ-A2OE TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV 
       38.60         9.01         8.22        25.02         3.45        21.24 
TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A6MB 
        2.76         9.14        27.68         9.07        11.70        15.42 
TCGA-K4-AAQO TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X 
       11.80        15.32        15.58        12.23        16.67        14.24 
TCGA-S5-A6DX TCGA-S5-AA26 TCGA-SY-A9G0 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M 
        1.84         3.75        12.43        17.62        37.05        22.68 
TCGA-UY-A78N TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD 
       86.83        76.01        65.75        35.24        29.56        17.82 
TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH 
        4.54         1.64         1.87        17.88        48.62        64.80 
TCGA-XF-A9SJ TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ 
        3.22        12.76        11.90        23.64        21.04        28.24 
TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 
       26.27        18.90         2.24        16.27        66.64         2.10 
TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMG TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAMQ 
       92.98        10.82       110.60        11.31        54.90        71.57 
TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN1 
       91.73         2.96         8.32        98.99        44.32        30.94 
TCGA-XF-AAN4 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L 
       27.06        18.81         3.88         9.63         0.66        11.97 
TCGA-YF-AA3M TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R4 TCGA-ZF-A9R5 
       13.64        18.64         7.36        21.11        30.28        27.19 
TCGA-ZF-A9R9 TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-A9RN 
       28.41        13.41         3.48        82.49        47.84        20.22 
TCGA-ZF-AA4N TCGA-ZF-AA4T TCGA-ZF-AA4U TCGA-ZF-AA4W TCGA-ZF-AA51 TCGA-ZF-AA52 
        2.89        19.69         8.61        60.16        38.73        35.41 
TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N 
       57.90        19.40         8.52        47.15        19.17         5.52 
TCGA-ZF-AA5P 
       10.13 

  ERBB2 MUTATED ERBB2 WILD-TYPE 
           1.74            0.10 
  ERBB2 MUTATED ERBB2 WILD-TYPE 
         105.70          166.03 
  ERBB2 MUTATED ERBB2 WILD-TYPE 
          21.86           15.02 
[1] "1.7 - 105.7 (21.9)" "0.1 - 166.0 (15.0)"
[1] "hr=" "1.7"
D47V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  ERBB2 MUTATED         0       16        16       12
  ERBB2 WILD-TYPE       4      101       106      116
D47V3, multiclass
           clus
vv          ERBB2 MUTATED ERBB2 WILD-TYPE
  STAGE I               0               4
  STAGE II             16             101
  STAGE III            16             106
  STAGE IV             12             116
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1+T2  T3  T4
  ERBB2 MUTATED         15  23   5
  ERBB2 WILD-TYPE       99 156  47
D47V4, multiclass
          clus
vv         ERBB2 MUTATED ERBB2 WILD-TYPE
  T0+T1+T2            15              99
  T3                  23             156
  T4                   5              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"
                 vv
clus               N0  N1  N2  N3
  ERBB2 MUTATED    27   7   6   0
  ERBB2 WILD-TYPE 186  34  69   8
D47V5, multiclass
    clus
vv   ERBB2 MUTATED ERBB2 WILD-TYPE
  N0            27             186
  N1             7              34
  N2             6              69
  N3             0               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"
D47V6, binary
                 cls
clus                0   1
  ERBB2 MUTATED    20   0
  ERBB2 WILD-TYPE 162  10
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERBB2 MUTATED     20    0
  ERBB2 WILD-TYPE  162   10
   clus
vv  ERBB2 MUTATED ERBB2 WILD-TYPE
  0            20             162
  1             0              10
[1] 2 2
[1] FALSE
D47V7, binary
                 cls
clus                0   1
  ERBB2 MUTATED    10  35
  ERBB2 WILD-TYPE  86 245
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERBB2 MUTATED     10   35
  ERBB2 WILD-TYPE   86  245
        clus
vv       ERBB2 MUTATED ERBB2 WILD-TYPE
  FEMALE            10              86
  MALE              35             245
[1] 2 2
[1] FALSE
D47V8, continuous
D47V9, continuous
D47V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ERBB2 MUTATED       3                         3    38
  ERBB2 WILD-TYPE    35                        18   263
D47V11, multiclass
                           clus
vv                          ERBB2 MUTATED ERBB2 WILD-TYPE
  ASIAN                                 3              35
  BLACK OR AFRICAN AMERICAN             3              18
  WHITE                                38             263
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V12, binary
                 cls
clus                0   1
  ERBB2 MUTATED     1  42
  ERBB2 WILD-TYPE   7 296
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERBB2 MUTATED      1   42
  ERBB2 WILD-TYPE    7  296
                        clus
vv                       ERBB2 MUTATED ERBB2 WILD-TYPE
  HISPANIC OR LATINO                 1               7
  NOT HISPANIC OR LATINO            42             296
[1] 2 2
[1] FALSE

Clustering(48) Variable = FAM47C MUTATION ANALYSIS
D48V1, survival
                  sevent
clus2                0   1
  FAM47C MUTATED    10  10
  FAM47C WILD-TYPE 209 141
  FAM47C MUTATED FAM47C WILD-TYPE 
              20              350 
  FAM47C MUTATED FAM47C WILD-TYPE 
              10              141 
$`FAM47C MUTATED`
TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A3PJ TCGA-CU-A3KJ TCGA-DK-A2I2 TCGA-DK-A3IM 
        5.06        14.96        12.82         5.46         7.79         7.82 
TCGA-DK-AA71 TCGA-FD-A3N6 TCGA-FD-A5BV TCGA-FD-A62P TCGA-G2-A3IE TCGA-GC-A3I6 
       13.64        27.98         5.36         6.28        20.12         2.24 
TCGA-GC-A6I1 TCGA-K4-A5RI TCGA-K4-A83P TCGA-XF-A9SH TCGA-XF-AAMG TCGA-XF-AAML 
        8.94        11.70         6.38        64.80       110.60         7.63 
TCGA-ZF-A9R1 TCGA-ZF-AA51 
        7.36        38.73 

$`FAM47C WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        91.63       103.50       105.70         8.35 
TCGA-4Z-AA7M TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7S 
       16.27        44.94        16.83        16.77        17.16        34.98 
TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 
       27.62        49.12         0.62        41.75        51.16        66.54 
TCGA-4Z-AA84 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BL-A13I 
       15.12        10.22        47.80        33.83        40.08         7.33 
TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J 
        2.66         6.74        12.39         6.58        13.15        19.04 
TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20T TCGA-BT-A20V 
       32.84        12.16        17.88        19.50        14.89         5.06 
TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH 
        8.35         8.25        17.16        16.18        20.48         4.67 
TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ 
        9.96        17.56        28.70        24.26        28.41         8.98 
TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-C4-A0F6 TCGA-C4-A0F7 TCGA-CF-A1HR TCGA-CF-A1HS 
        1.94         2.93        23.01         2.04         0.46         0.43 
TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X 
        0.69        10.95        12.66        12.46        12.10        12.62 
TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A9FF TCGA-CF-A9FM 
       12.26        13.12        12.00        12.10        11.87        13.08 
TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 
       12.92         4.90         7.20         5.19        16.31         1.84 
TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA 
       13.58        21.86         2.14        66.41        18.41        19.00 
TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG 
       16.70       130.88       112.44        16.14        17.62        15.62 
TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL 
        1.81        10.59       123.85        87.32         2.20        13.58 
TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV 
        8.22        17.72        50.27        21.30        23.21         9.67 
TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV 
       20.81        10.55       140.81        48.00        17.98        64.18 
TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 
       41.56        76.60        67.36        15.68        41.06        30.67 
TCGA-DK-AA6L TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6U 
       38.24        15.02        13.58       166.03        12.36        10.49 
TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA74 TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A2PC 
        8.65         7.53        43.50        12.03        10.62        43.59 
TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ 
       15.35        38.83        24.66         0.10         0.49         2.24 
TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 
       16.70        17.39         0.56         0.66        14.56        13.97 
TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A7XN 
       12.99        14.33         0.92         1.22        13.68        14.07 
TCGA-E7-A85H TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 
       12.95        14.37         8.09        32.02        16.77         8.94 
TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3NA TCGA-FD-A3SJ 
       33.04         4.01        12.62        22.52        60.66        24.30 
TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ 
       23.41        17.98        29.16         5.52        25.74        46.78 
TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U 
       19.79        12.85        22.98        27.35        14.96        20.91 
TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BX 
        3.62        26.73        53.88        11.01        19.33         5.69 
TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O 
        8.25        27.45        18.08        58.92         2.70         7.10 
TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE 
       13.35        62.86        18.81         6.15        12.69        12.36 
TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z7 
        2.27         3.06         4.31         9.67        10.85        31.07 
TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FJ-A871 TCGA-FT-A3EE TCGA-FT-A61P 
        7.13        10.65        17.23         8.94         3.25         6.48 
TCGA-G2-A2EC TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO 
       22.88        61.94        30.61        15.95        26.93        35.24 
TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3D 
       33.01         7.23        17.62        66.02         6.94        64.44 
TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD 
       19.46        21.40        15.81         4.50        15.91        14.07 
TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ 
       17.75        24.92        13.91         7.73         2.10         3.12 
TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R 
       20.98         2.20         7.36        10.92        11.31        11.31 
TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATO 
        7.63        27.09        20.05         5.62         4.73        10.65 
TCGA-GU-AATP TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ 
       32.98         7.00        14.27        21.34        19.10        19.82 
TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G 
       20.28         8.48        10.59        27.35         8.58        19.07 
TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND 
       22.72         1.51        19.40        38.60         3.06         9.01 
TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC 
        8.22        25.02         3.45        21.24         2.76         9.14 
TCGA-K4-A54R TCGA-K4-A5RH TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-AAQO 
       27.68         9.07         1.74         1.81        15.42        11.80 
TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X 
       15.32        15.58        13.48        12.23        16.67        14.24 
TCGA-S5-A6DX TCGA-S5-AA26 TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L 
        1.84         3.75        12.43        31.56        17.62        37.05 
TCGA-UY-A78M TCGA-UY-A78N TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A9PA TCGA-UY-A9PB 
       22.68        86.83        76.01        65.75        35.24        29.56 
TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG 
       17.82         4.54         1.64         1.87        17.88        48.62 
TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SL TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SX 
       79.66         3.22        66.41        12.76        11.90        23.64 
TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 
       21.04        28.24        26.27        18.90         2.24        16.27 
TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMH 
       66.64         2.10        13.74        92.98        10.82        11.31 
TCGA-XF-AAMJ TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX 
       54.90        71.57        91.73         2.96         8.32         6.77 
TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 
       98.99        44.32        56.48        30.94        61.45        86.30 
TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YC-A9TC 
       27.06        75.39        18.81         3.88         9.63         0.66 
TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R0 TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R4 
       11.97        13.64        18.64        21.11        24.13        30.28 
TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RE 
       27.19        21.86        28.41        74.56        13.41         3.48 
TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N 
       52.73        52.60        82.49        47.84        20.22         2.89 
TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA4X 
       34.06        19.69         8.61        59.38        60.16        63.02 
TCGA-ZF-AA52 TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H 
       35.41        57.90        19.40         8.52        47.15        19.17 
TCGA-ZF-AA5N TCGA-ZF-AA5P 
        5.52        10.13 

  FAM47C MUTATED FAM47C WILD-TYPE 
            2.24             0.10 
  FAM47C MUTATED FAM47C WILD-TYPE 
          110.60           166.03 
  FAM47C MUTATED FAM47C WILD-TYPE 
            8.38            16.16 
[1] "2.2 - 110.6 (8.4)"  "0.1 - 166.0 (16.2)"
[1] "hr=" "1.7"
D48V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  FAM47C MUTATED         0        8         8        4
  FAM47C WILD-TYPE       4      109       114      124
D48V3, multiclass
           clus
vv          FAM47C MUTATED FAM47C WILD-TYPE
  STAGE I                0                4
  STAGE II               8              109
  STAGE III              8              114
  STAGE IV               4              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"
                  vv
clus               T0+T1+T2  T3  T4
  FAM47C MUTATED          7  10   2
  FAM47C WILD-TYPE      107 169  50
D48V4, multiclass
          clus
vv         FAM47C MUTATED FAM47C WILD-TYPE
  T0+T1+T2              7              107
  T3                   10              169
  T4                    2               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"
                  vv
clus                N0  N1  N2  N3
  FAM47C MUTATED    13   3   0   2
  FAM47C WILD-TYPE 200  38  75   6
D48V5, multiclass
    clus
vv   FAM47C MUTATED FAM47C WILD-TYPE
  N0             13              200
  N1              3               38
  N2              0               75
  N3              2                6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V6, binary
                  cls
clus                 0   1
  FAM47C MUTATED    11   0
  FAM47C WILD-TYPE 171  10
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM47C MUTATED     11    0
  FAM47C WILD-TYPE  171   10
   clus
vv  FAM47C MUTATED FAM47C WILD-TYPE
  0             11              171
  1              0               10
[1] 2 2
[1] FALSE
D48V7, binary
                  cls
clus                 0   1
  FAM47C MUTATED     9  11
  FAM47C WILD-TYPE  87 269
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM47C MUTATED      9   11
  FAM47C WILD-TYPE   87  269
        clus
vv       FAM47C MUTATED FAM47C WILD-TYPE
  FEMALE              9               87
  MALE               11              269
[1] 2 2
[1] FALSE
D48V8, continuous
D48V9, continuous
D48V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  FAM47C MUTATED       1                         1    18
  FAM47C WILD-TYPE    37                        20   283
D48V11, multiclass
                           clus
vv                          FAM47C MUTATED FAM47C WILD-TYPE
  ASIAN                                  1               37
  BLACK OR AFRICAN AMERICAN              1               20
  WHITE                                 18              283
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V12, binary
                  cls
clus                 0   1
  FAM47C MUTATED     1  19
  FAM47C WILD-TYPE   7 319
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM47C MUTATED      1   19
  FAM47C WILD-TYPE    7  319
                        clus
vv                       FAM47C MUTATED FAM47C WILD-TYPE
  HISPANIC OR LATINO                  1                7
  NOT HISPANIC OR LATINO             19              319
[1] 2 2
[1] FALSE

Clustering(49) Variable = SF3B1 MUTATION ANALYSIS
D49V1, survival
                 sevent
clus2               0   1
  SF3B1 MUTATED    15   9
  SF3B1 WILD-TYPE 204 142
  SF3B1 MUTATED SF3B1 WILD-TYPE 
             24             346 
  SF3B1 MUTATED SF3B1 WILD-TYPE 
              9             142 
$`SF3B1 MUTATED`
TCGA-4Z-AA7Q TCGA-BL-A0C8 TCGA-BL-A5ZZ TCGA-CU-A5W6 TCGA-DK-A1AE TCGA-DK-A2I4 
       16.77        40.08        12.39         1.84        16.14       123.85 
TCGA-DK-A3X1 TCGA-DK-AA6P TCGA-E5-A4TZ TCGA-E7-A541 TCGA-FD-A62P TCGA-FJ-A871 
       48.00        15.02        15.35        17.39         6.28         8.94 
TCGA-G2-A3VY TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GD-A3OQ TCGA-GV-A3QF TCGA-SY-A9G5 
       17.62        19.46        21.40         3.12        20.28        31.56 
TCGA-UY-A78N TCGA-UY-A9PD TCGA-XF-AAN3 TCGA-ZF-A9R4 TCGA-ZF-AA4R TCGA-ZF-AA5P 
       86.83        17.82        86.30        30.28        34.06        10.13 

$`SF3B1 WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        91.63       103.50       105.70         8.35 
TCGA-4Z-AA7M TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7W 
       16.27        44.94        16.83        17.16        34.98        27.62 
TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA84 
       49.12         0.62        41.75        51.16        66.54        15.12 
TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM 
       10.22        47.80        33.83         7.33         2.66         6.74 
TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P 
        6.58        13.15        19.04        32.84        12.16        17.88 
TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20W 
       19.50         5.06        14.89        14.96         5.06         8.35 
TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PJ 
        8.25        17.16        16.18        20.48         4.67        12.82 
TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ 
        9.96        17.56        28.70        24.26        28.41         8.98 
TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-C4-A0F6 TCGA-C4-A0F7 TCGA-CF-A1HR TCGA-CF-A1HS 
        1.94         2.93        23.01         2.04         0.46         0.43 
TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X 
        0.69        10.95        12.66        12.46        12.10        12.62 
TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A9FF TCGA-CF-A9FM 
       12.26        13.12        12.00        12.10        11.87        13.08 
TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL 
       12.92         4.90         7.20         5.46         5.19        16.31 
TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA 
       13.58        21.86         2.14        66.41        18.41        19.00 
TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX 
       16.70       130.88       112.44        17.62        15.62         1.81 
TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM 
       10.59         7.79        87.32         2.20        13.58         7.82 
TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV 
        8.22        17.72        50.27        21.30        23.21         9.67 
TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW 
       20.81        10.55       140.81        17.98        64.18        41.56 
TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L 
       76.60        67.36        15.68        41.06        30.67        38.24 
TCGA-DK-AA6Q TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA6X 
       13.58       166.03        12.36        10.49         8.65         7.53 
TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A2PC TCGA-E5-A4U1 
       13.64        43.50        12.03        10.62        43.59        38.83 
TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KE 
       24.66         0.10         0.49         2.24        16.70         0.56 
TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DU 
        0.66        14.56        13.97        12.99        14.33         0.92 
TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A97P TCGA-E7-A97Q 
        1.22        13.68        14.07        12.95        14.37         8.09 
TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 
       32.02        16.77         8.94        33.04         4.01        12.62 
TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM 
       22.52        27.98        60.66        24.30        23.41        17.98 
TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS 
       29.16         5.52        25.74        46.78        19.79        12.85 
TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BR 
       22.98        27.35        14.96        20.91         3.62        26.73 
TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY 
       53.88        11.01        19.33         5.36         5.69         8.25 
TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62S 
       27.45        18.08        58.92         2.70         7.10        13.35 
TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF 
       62.86        18.81         6.15        12.69        12.36         2.27 
TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 
        3.06         4.31         9.67        10.85        31.07         7.13 
TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EC TCGA-G2-A2EF 
       10.65        17.23         3.25         6.48        22.88        61.94 
TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB 
       30.61        15.95        26.93        35.24        33.01         7.23 
TCGA-G2-A3IE TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3D TCGA-GC-A3I6 TCGA-GC-A3OO 
       20.12        66.02         6.94        64.44         2.24        15.81 
TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A6I1 
        4.50        15.91        14.07        17.75        24.92         8.94 
TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GD-A76B 
       13.91         7.73         2.10        20.98         2.20         7.36 
TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A764 
       10.92        11.31        11.31         7.63        27.09        20.05 
TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATO TCGA-GU-AATP TCGA-GU-AATQ TCGA-GV-A3JV 
        5.62         4.73        10.65        32.98         7.00        14.27 
TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK 
       21.34        19.10        19.82         8.48        10.59        27.35 
TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE 
        8.58        19.07        22.72         1.51        19.40        38.60 
TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV 
        3.06         9.01         8.22        25.02         3.45        21.24 
TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ 
        2.76         9.14        27.68         9.07        11.70         1.74 
TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO TCGA-LC-A66R TCGA-LT-A5Z6 
        1.81        15.42         6.38        11.80        15.32        15.58 
TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 
       13.48        12.23        16.67        14.24         1.84         3.75 
TCGA-SY-A9G0 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78O TCGA-UY-A8OB 
       12.43        17.62        37.05        22.68        76.01        65.75 
TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HH TCGA-XF-A8HI 
       35.24        29.56         4.54         1.64         1.87        17.88 
TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SL TCGA-XF-A9SV 
       48.62        64.80        79.66         3.22        66.41        12.76 
TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 
       11.90        23.64        21.04        28.24        26.27        18.90 
TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAME 
        2.24        16.27        66.64         2.10        13.74        92.98 
TCGA-XF-AAMF TCGA-XF-AAMG TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ 
       10.82       110.60        11.31        54.90         7.63        71.57 
TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAMZ 
       91.73         2.96         8.32         6.77        98.99        44.32 
TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN7 
       56.48        30.94        61.45        27.06        75.39        18.81 
TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R0 
        3.88         9.63         0.66        11.97        13.64        18.64 
TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 
        7.36        21.11        24.13        27.19        21.86        28.41 
TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RL 
       74.56        13.41         3.48        52.73        52.60        82.49 
TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4T TCGA-ZF-AA4U TCGA-ZF-AA4V 
       47.84        20.22         2.89        19.69         8.61        59.38 
TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA53 TCGA-ZF-AA54 
       60.16        63.02        38.73        35.41        57.90        19.40 
TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N 
        8.52        47.15        19.17         5.52 

  SF3B1 MUTATED SF3B1 WILD-TYPE 
           1.84            0.10 
  SF3B1 MUTATED SF3B1 WILD-TYPE 
         123.85          166.03 
  SF3B1 MUTATED SF3B1 WILD-TYPE 
          17.72           15.22 
[1] "1.8 - 123.8 (17.7)" "0.1 - 166.0 (15.2)"
[1] "hr=" "1.3"
D49V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  SF3B1 MUTATED         1        6         9        8
  SF3B1 WILD-TYPE       3      111       113      120
D49V3, multiclass
           clus
vv          SF3B1 MUTATED SF3B1 WILD-TYPE
  STAGE I               1               3
  STAGE II              6             111
  STAGE III             9             113
  STAGE IV              8             120
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1+T2  T3  T4
  SF3B1 MUTATED          7  10   5
  SF3B1 WILD-TYPE      107 169  47
D49V4, multiclass
          clus
vv         SF3B1 MUTATED SF3B1 WILD-TYPE
  T0+T1+T2             7             107
  T3                  10             169
  T4                   5              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"
                 vv
clus               N0  N1  N2  N3
  SF3B1 MUTATED    11   4   4   0
  SF3B1 WILD-TYPE 202  37  71   8
D49V5, multiclass
    clus
vv   SF3B1 MUTATED SF3B1 WILD-TYPE
  N0            11             202
  N1             4              37
  N2             4              71
  N3             0               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"
D49V6, binary
                 cls
clus                0   1
  SF3B1 MUTATED    12   0
  SF3B1 WILD-TYPE 170  10
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SF3B1 MUTATED     12    0
  SF3B1 WILD-TYPE  170   10
   clus
vv  SF3B1 MUTATED SF3B1 WILD-TYPE
  0            12             170
  1             0              10
[1] 2 2
[1] FALSE
D49V7, binary
                 cls
clus                0   1
  SF3B1 MUTATED     3  21
  SF3B1 WILD-TYPE  93 259
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SF3B1 MUTATED      3   21
  SF3B1 WILD-TYPE   93  259
        clus
vv       SF3B1 MUTATED SF3B1 WILD-TYPE
  FEMALE             3              93
  MALE              21             259
[1] 2 2
[1] FALSE
D49V8, continuous
D49V9, continuous
D49V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SF3B1 MUTATED       1                         0    23
  SF3B1 WILD-TYPE    37                        21   278
D49V11, multiclass
                           clus
vv                          SF3B1 MUTATED SF3B1 WILD-TYPE
  ASIAN                                 1              37
  BLACK OR AFRICAN AMERICAN             0              21
  WHITE                                23             278
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V12, binary
                 cls
clus                0   1
  SF3B1 MUTATED     0  23
  SF3B1 WILD-TYPE   8 315
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SF3B1 MUTATED      0   23
  SF3B1 WILD-TYPE    8  315
                        clus
vv                       SF3B1 MUTATED SF3B1 WILD-TYPE
  HISPANIC OR LATINO                 0               8
  NOT HISPANIC OR LATINO            23             315
[1] 2 2
[1] FALSE

Clustering(50) Variable = EPS8 MUTATION ANALYSIS
D50V1, survival
                sevent
clus2              0   1
  EPS8 MUTATED     8   4
  EPS8 WILD-TYPE 211 147
  EPS8 MUTATED EPS8 WILD-TYPE 
            12            358 
  EPS8 MUTATED EPS8 WILD-TYPE 
             4            147 
$`EPS8 MUTATED`
TCGA-BL-A5ZZ TCGA-CF-A1HS TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-FD-A3SR TCGA-FT-A61P 
       12.39         0.43        30.67        38.24        19.79         6.48 
TCGA-MV-A51V TCGA-SY-A9G5 TCGA-UY-A78N TCGA-UY-A9PA TCGA-UY-A9PF TCGA-ZF-AA4W 
       13.48        31.56        86.83        35.24         1.64        60.16 

$`EPS8 WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        91.63       103.50       105.70         8.35 
TCGA-4Z-AA7M TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7S 
       16.27        44.94        16.83        16.77        17.16        34.98 
TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 
       27.62        49.12         0.62        41.75        51.16        66.54 
TCGA-4Z-AA84 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BL-A13I 
       15.12        10.22        47.80        33.83        40.08         7.33 
TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N 
        2.66         6.74         6.58        13.15        19.04        32.84 
TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U 
       12.16        17.88        19.50         5.06        14.89        14.96 
TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A2LD 
        5.06         8.35         8.25        17.16        16.18        20.48 
TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E 
        4.67        12.82         9.96        17.56        28.70        24.26 
TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-C4-A0F6 TCGA-C4-A0F7 
       28.41         8.98         1.94         2.93        23.01         2.04 
TCGA-CF-A1HR TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W 
        0.46         0.69        10.95        12.66        12.46        12.10 
TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A9FF 
       12.62        12.26        13.12        12.00        12.10        11.87 
TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3QU 
       13.08        12.92         4.90         7.20         5.46         5.19 
TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 
       16.31         1.84        13.58        21.86         2.14        66.41 
TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE 
       18.41        19.00        16.70       130.88       112.44        16.14 
TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 
       17.62        15.62         1.81        10.59         7.79       123.85 
TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ 
       87.32         2.20        13.58         7.82         8.22        17.72 
TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX 
       50.27        21.30        23.21         9.67        20.81        10.55 
TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 
      140.81        48.00        17.98        64.18        41.56        76.60 
TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6S 
       67.36        15.68        41.06        15.02        13.58       166.03 
TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA74 
       12.36        10.49         8.65         7.53        13.64        43.50 
TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 
       12.03        10.62        43.59        15.35        38.83        24.66 
TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KE 
        0.10         0.49         2.24        16.70        17.39         0.56 
TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DU 
        0.66        14.56        13.97        12.99        14.33         0.92 
TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A97P TCGA-E7-A97Q 
        1.22        13.68        14.07        12.95        14.37         8.09 
TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 
       32.02        16.77         8.94        33.04         4.01        12.62 
TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM 
       22.52        27.98        60.66        24.30        23.41        17.98 
TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SS TCGA-FD-A43N 
       29.16         5.52        25.74        46.78        12.85        22.98 
TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS 
       27.35        14.96        20.91         3.62        26.73        53.88 
TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ 
       11.01        19.33         5.36         5.69         8.25        27.45 
TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S 
       18.08        58.92         2.70         7.10         6.28        13.35 
TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF 
       62.86        18.81         6.15        12.69        12.36         2.27 
TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 
        3.06         4.31         9.67        10.85        31.07         7.13 
TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FJ-A871 TCGA-FT-A3EE TCGA-G2-A2EC TCGA-G2-A2EF 
       10.65        17.23         8.94         3.25        22.88        61.94 
TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB 
       30.61        15.95        26.93        35.24        33.01         7.23 
TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3D TCGA-G2-AA3F 
       20.12        17.62        66.02         6.94        64.44        19.46 
TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD 
       21.40         2.24        15.81         4.50        15.91        14.07 
TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP 
       17.75        24.92         8.94        13.91         7.73         2.10 
TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42Q 
        3.12        20.98         2.20         7.36        10.92        11.31 
TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 
       11.31         7.63        27.09        20.05         5.62         4.73 
TCGA-GU-AATO TCGA-GU-AATP TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX 
       10.65        32.98         7.00        14.27        21.34        19.10 
TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E 
       19.82        20.28         8.48        10.59        27.35         8.58 
TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF 
       19.07        22.72         1.51        19.40        38.60         3.06 
TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB 
        9.01         8.22        25.02         3.45        21.24         2.76 
TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ 
        9.14        27.68         9.07        11.70         1.74         1.81 
TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-PQ-A6FI 
       15.42         6.38        11.80        15.32        15.58        12.23 
TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 TCGA-SY-A9G0 TCGA-UY-A78K 
       16.67        14.24         1.84         3.75        12.43        17.62 
TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A9PB TCGA-UY-A9PD 
       37.05        22.68        76.01        65.75        29.56        17.82 
TCGA-UY-A9PE TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI 
        4.54         1.87        17.88        48.62        64.80        79.66 
TCGA-XF-A9SJ TCGA-XF-A9SL TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY 
        3.22        66.41        12.76        11.90        23.64        21.04 
TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T5 
       28.24        26.27        18.90         2.24        16.27        66.64 
TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMG TCGA-XF-AAMH 
        2.10        13.74        92.98        10.82       110.60        11.31 
TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMW 
       54.90         7.63        71.57        91.73         2.96         8.32 
TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN2 
        6.77        98.99        44.32        56.48        30.94        61.45 
TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 
       86.30        27.06        75.39        18.81         3.88         9.63 
TCGA-YC-A9TC TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R2 
        0.66        11.97        13.64        18.64         7.36        21.11 
TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RC 
       24.13        30.28        27.19        21.86        28.41        74.56 
TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-A9RM 
       13.41         3.48        52.73        52.60        82.49        47.84 
TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4U TCGA-ZF-AA4V 
       20.22         2.89        34.06        19.69         8.61        59.38 
TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA56 
       63.02        38.73        35.41        57.90        19.40         8.52 
TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-ZF-AA5P 
       47.15        19.17         5.52        10.13 

  EPS8 MUTATED EPS8 WILD-TYPE 
          0.43           0.10 
  EPS8 MUTATED EPS8 WILD-TYPE 
         86.83         166.03 
  EPS8 MUTATED EPS8 WILD-TYPE 
         25.23          15.60 
[1] "0.4 - 86.8 (25.2)"  "0.1 - 166.0 (15.6)"
[1] "hr=" "1.5"
D50V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  EPS8 MUTATED         0        1         5        4
  EPS8 WILD-TYPE       4      116       117      124
D50V3, multiclass
           clus
vv          EPS8 MUTATED EPS8 WILD-TYPE
  STAGE I              0              4
  STAGE II             1            116
  STAGE III            5            117
  STAGE IV             4            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"
                vv
clus             T0+T1+T2  T3  T4
  EPS8 MUTATED          1   7   3
  EPS8 WILD-TYPE      113 172  49
D50V4, multiclass
          clus
vv         EPS8 MUTATED EPS8 WILD-TYPE
  T0+T1+T2            1            113
  T3                  7            172
  T4                  3             49
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  EPS8 MUTATED     6   2   3   0
  EPS8 WILD-TYPE 207  39  72   8
D50V5, multiclass
    clus
vv   EPS8 MUTATED EPS8 WILD-TYPE
  N0            6            207
  N1            2             39
  N2            3             72
  N3            0              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"
D50V6, binary
                cls
clus               0   1
  EPS8 MUTATED     3   0
  EPS8 WILD-TYPE 179  10
[1] "tbl2"
                cls
clus             [,1] [,2]
  EPS8 MUTATED      3    0
  EPS8 WILD-TYPE  179   10
   clus
vv  EPS8 MUTATED EPS8 WILD-TYPE
  0            3            179
  1            0             10
[1] 2 2
[1] FALSE
D50V7, binary
                cls
clus               0   1
  EPS8 MUTATED     2  10
  EPS8 WILD-TYPE  94 270
[1] "tbl2"
                cls
clus             [,1] [,2]
  EPS8 MUTATED      2   10
  EPS8 WILD-TYPE   94  270
        clus
vv       EPS8 MUTATED EPS8 WILD-TYPE
  FEMALE            2             94
  MALE             10            270
[1] 2 2
[1] FALSE
D50V8, continuous
D50V9, continuous
D50V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  EPS8 MUTATED       1                         0    11
  EPS8 WILD-TYPE    37                        21   290
D50V11, multiclass
                           clus
vv                          EPS8 MUTATED EPS8 WILD-TYPE
  ASIAN                                1             37
  BLACK OR AFRICAN AMERICAN            0             21
  WHITE                               11            290
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V12, binary
                cls
clus               0   1
  EPS8 MUTATED     0  12
  EPS8 WILD-TYPE   8 326
[1] "tbl2"
                cls
clus             [,1] [,2]
  EPS8 MUTATED      0   12
  EPS8 WILD-TYPE    8  326
                        clus
vv                       EPS8 MUTATED EPS8 WILD-TYPE
  HISPANIC OR LATINO                0              8
  NOT HISPANIC OR LATINO           12            326
[1] 2 2
[1] FALSE

Clustering(51) Variable = EPHA2 MUTATION ANALYSIS
D51V1, survival
                 sevent
clus2               0   1
  EPHA2 MUTATED     9   7
  EPHA2 WILD-TYPE 210 144
  EPHA2 MUTATED EPHA2 WILD-TYPE 
             16             354 
  EPHA2 MUTATED EPHA2 WILD-TYPE 
              7             144 
$`EPHA2 MUTATED`
TCGA-4Z-AA7Y TCGA-BT-A2LB TCGA-BT-A42B TCGA-DK-A1A7 TCGA-DK-A2I6 TCGA-DK-A3X1 
       49.12        16.18        17.56        18.41        87.32        48.00 
TCGA-DK-AA6L TCGA-E7-A7XN TCGA-FD-A3N5 TCGA-FD-A5BX TCGA-GC-A6I3 TCGA-GV-A3QH 
       38.24        14.07        22.52         5.69        13.91         8.48 
TCGA-H4-A2HQ TCGA-XF-A9T6 TCGA-XF-AAMH TCGA-XF-AAN5 
       19.40         2.10        11.31        75.39 

$`EPHA2 WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        91.63       103.50       105.70         8.35 
TCGA-4Z-AA7M TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7S 
       16.27        44.94        16.83        16.77        17.16        34.98 
TCGA-4Z-AA7W TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA84 
       27.62         0.62        41.75        51.16        66.54        15.12 
TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J 
       10.22        47.80        33.83        40.08         7.33         2.66 
TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N 
        6.74        12.39         6.58        13.15        19.04        32.84 
TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U 
       12.16        17.88        19.50         5.06        14.89        14.96 
TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LD TCGA-BT-A3PH 
        5.06         8.35         8.25        17.16        20.48         4.67 
TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42C TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ 
       12.82         9.96        28.70        24.26        28.41         8.98 
TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-C4-A0F6 TCGA-C4-A0F7 TCGA-CF-A1HR TCGA-CF-A1HS 
        1.94         2.93        23.01         2.04         0.46         0.43 
TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X 
        0.69        10.95        12.66        12.46        12.10        12.62 
TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A9FF TCGA-CF-A9FM 
       12.26        13.12        12.00        12.10        11.87        13.08 
TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL 
       12.92         4.90         7.20         5.46         5.19        16.31 
TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1AA 
        1.84        13.58        21.86         2.14        66.41        19.00 
TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG 
       16.70       130.88       112.44        16.14        17.62        15.62 
TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IK TCGA-DK-A3IL 
        1.81        10.59         7.79       123.85         2.20        13.58 
TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU 
        7.82         8.22        17.72        50.27        21.30        23.21 
TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X2 TCGA-DK-A6AV 
        9.67        20.81        10.55       140.81        17.98        64.18 
TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 
       41.56        76.60        67.36        15.68        41.06        30.67 
TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6W 
       15.02        13.58       166.03        12.36        10.49         8.65 
TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A2PC 
        7.53        13.64        43.50        12.03        10.62        43.59 
TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ 
       15.35        38.83        24.66         0.10         0.49         2.24 
TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 
       16.70        17.39         0.56         0.66        14.56        13.97 
TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A85H 
       12.99        14.33         0.92         1.22        13.68        12.95 
TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 
       14.37         8.09        32.02        16.77         8.94        33.04 
TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL 
        4.01        12.62        27.98        60.66        24.30        23.41 
TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR 
       17.98        29.16         5.52        25.74        46.78        19.79 
TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X 
       12.85        22.98        27.35        14.96        20.91         3.62 
TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BY 
       26.73        53.88        11.01        19.33         5.36         8.25 
TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P 
       27.45        18.08        58.92         2.70         7.10         6.28 
TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE 
       13.35        62.86        18.81         6.15        12.69        12.36 
TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z7 
        2.27         3.06         4.31         9.67        10.85        31.07 
TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FJ-A871 TCGA-FT-A3EE TCGA-FT-A61P 
        7.13        10.65        17.23         8.94         3.25         6.48 
TCGA-G2-A2EC TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO 
       22.88        61.94        30.61        15.95        26.93        35.24 
TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3C 
       33.01         7.23        20.12        17.62        66.02         6.94 
TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB 
       64.44        19.46        21.40         2.24        15.81         4.50 
TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GD-A2C5 
       15.91        14.07        17.75        24.92         8.94         7.73 
TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42P 
        2.10         3.12        20.98         2.20         7.36        10.92 
TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 
       11.31        11.31         7.63        27.09        20.05         5.62 
TCGA-GU-A767 TCGA-GU-AATO TCGA-GU-AATP TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW 
        4.73        10.65        32.98         7.00        14.27        21.34 
TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E 
       19.10        19.82        20.28        10.59        27.35         8.58 
TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND 
       19.07        22.72         1.51        38.60         3.06         9.01 
TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC 
        8.22        25.02         3.45        21.24         2.76         9.14 
TCGA-K4-A54R TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB 
       27.68         9.07        11.70         1.74         1.81        15.42 
TCGA-K4-A83P TCGA-K4-AAQO TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI 
        6.38        11.80        15.32        15.58        13.48        12.23 
TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 TCGA-SY-A9G0 TCGA-SY-A9G5 
       16.67        14.24         1.84         3.75        12.43        31.56 
TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78N TCGA-UY-A78O TCGA-UY-A8OB 
       17.62        37.05        22.68        86.83        76.01        65.75 
TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HH 
       35.24        29.56        17.82         4.54         1.64         1.87 
TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SL 
       17.88        48.62        64.80        79.66         3.22        66.41 
TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T0 
       12.76        11.90        23.64        21.04        28.24        26.27 
TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T8 TCGA-XF-AAME 
       18.90         2.24        16.27        66.64        13.74        92.98 
TCGA-XF-AAMF TCGA-XF-AAMG TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR 
       10.82       110.60        54.90         7.63        71.57        91.73 
TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN0 
        2.96         8.32         6.77        98.99        44.32        56.48 
TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN7 TCGA-XF-AAN8 
       30.94        61.45        86.30        27.06        18.81         3.88 
TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R0 TCGA-ZF-A9R1 
        9.63         0.66        11.97        13.64        18.64         7.36 
TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 
       21.11        24.13        30.28        27.19        21.86        28.41 
TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RL 
       74.56        13.41         3.48        52.73        52.60        82.49 
TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4U 
       47.84        20.22         2.89        34.06        19.69         8.61 
TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA53 
       59.38        60.16        63.02        38.73        35.41        57.90 
TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-ZF-AA5P 
       19.40         8.52        47.15        19.17         5.52        10.13 

  EPHA2 MUTATED EPHA2 WILD-TYPE 
            2.1             0.1 
  EPHA2 MUTATED EPHA2 WILD-TYPE 
          87.32          166.03 
  EPHA2 MUTATED EPHA2 WILD-TYPE 
         17.985          15.500 
[1] "2.1 - 87.3 (18.0)"  "0.1 - 166.0 (15.5)"
[1] "hr=" "1.1"
D51V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  EPHA2 MUTATED         0        3         5        7
  EPHA2 WILD-TYPE       4      114       117      121
D51V3, multiclass
           clus
vv          EPHA2 MUTATED EPHA2 WILD-TYPE
  STAGE I               0               4
  STAGE II              3             114
  STAGE III             5             117
  STAGE IV              7             121
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1+T2  T3  T4
  EPHA2 MUTATED          3  11   0
  EPHA2 WILD-TYPE      111 168  52
D51V4, multiclass
          clus
vv         EPHA2 MUTATED EPHA2 WILD-TYPE
  T0+T1+T2             3             111
  T3                  11             168
  T4                   0              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"
                 vv
clus               N0  N1  N2  N3
  EPHA2 MUTATED     7   6   1   0
  EPHA2 WILD-TYPE 206  35  74   8
D51V5, multiclass
    clus
vv   EPHA2 MUTATED EPHA2 WILD-TYPE
  N0             7             206
  N1             6              35
  N2             1              74
  N3             0               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"
D51V6, binary
                 cls
clus                0   1
  EPHA2 MUTATED     6   1
  EPHA2 WILD-TYPE 176   9
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EPHA2 MUTATED      6    1
  EPHA2 WILD-TYPE  176    9
   clus
vv  EPHA2 MUTATED EPHA2 WILD-TYPE
  0             6             176
  1             1               9
[1] 2 2
[1] FALSE
D51V7, binary
                 cls
clus                0   1
  EPHA2 MUTATED     7   9
  EPHA2 WILD-TYPE  89 271
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EPHA2 MUTATED      7    9
  EPHA2 WILD-TYPE   89  271
        clus
vv       EPHA2 MUTATED EPHA2 WILD-TYPE
  FEMALE             7              89
  MALE               9             271
[1] 2 2
[1] FALSE
D51V8, continuous
D51V9, continuous
D51V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  EPHA2 MUTATED       1                         3    12
  EPHA2 WILD-TYPE    37                        18   289
D51V11, multiclass
                           clus
vv                          EPHA2 MUTATED EPHA2 WILD-TYPE
  ASIAN                                 1              37
  BLACK OR AFRICAN AMERICAN             3              18
  WHITE                                12             289
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V12, binary
                 cls
clus                0   1
  EPHA2 MUTATED     0  15
  EPHA2 WILD-TYPE   8 323
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EPHA2 MUTATED      0   15
  EPHA2 WILD-TYPE    8  323
                        clus
vv                       EPHA2 MUTATED EPHA2 WILD-TYPE
  HISPANIC OR LATINO                 0               8
  NOT HISPANIC OR LATINO            15             323
[1] 2 2
[1] FALSE

Clustering(52) Variable = OGDH MUTATION ANALYSIS
D52V1, survival
                sevent
clus2              0   1
  OGDH MUTATED    14   5
  OGDH WILD-TYPE 205 146
  OGDH MUTATED OGDH WILD-TYPE 
            19            351 
  OGDH MUTATED OGDH WILD-TYPE 
             5            146 
$`OGDH MUTATED`
TCGA-4Z-AA7W TCGA-BT-A0YX TCGA-BT-A42C TCGA-CU-A0YR TCGA-DK-A3IS TCGA-DK-AA6S 
       27.62        13.15        28.70         7.20        50.27       166.03 
TCGA-DK-AA6U TCGA-FD-A62P TCGA-GV-A40E TCGA-K4-A5RH TCGA-K4-A83P TCGA-MV-A51V 
       10.49         6.28         8.58         9.07         6.38        13.48 
TCGA-S5-A6DX TCGA-UY-A78N TCGA-UY-A9PA TCGA-XF-A9SG TCGA-XF-A9SY TCGA-XF-A9T3 
        1.84        86.83        35.24        48.62        21.04         2.24 
TCGA-ZF-A9RC 
       74.56 

$`OGDH WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        91.63       103.50       105.70         8.35 
TCGA-4Z-AA7M TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7S 
       16.27        44.94        16.83        16.77        17.16        34.98 
TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA84 
       49.12         0.62        41.75        51.16        66.54        15.12 
TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J 
       10.22        47.80        33.83        40.08         7.33         2.66 
TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O 
        6.74        12.39         6.58        19.04        32.84        12.16 
TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20V 
       17.88        19.50         5.06        14.89        14.96         5.06 
TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH 
        8.35         8.25        17.16        16.18        20.48         4.67 
TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ 
       12.82         9.96        17.56        24.26        28.41         8.98 
TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-C4-A0F6 TCGA-C4-A0F7 TCGA-CF-A1HR TCGA-CF-A1HS 
        1.94         2.93        23.01         2.04         0.46         0.43 
TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X 
        0.69        10.95        12.66        12.46        12.10        12.62 
TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A9FF TCGA-CF-A9FM 
       12.26        13.12        12.00        12.10        11.87        13.08 
TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 
       12.92         4.90         5.46         5.19        16.31         1.84 
TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA 
       13.58        21.86         2.14        66.41        18.41        19.00 
TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG 
       16.70       130.88       112.44        16.14        17.62        15.62 
TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK 
        1.81        10.59         7.79       123.85        87.32         2.20 
TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IT TCGA-DK-A3IU 
       13.58         7.82         8.22        17.72        21.30        23.21 
TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A3X2 
        9.67        20.81        10.55       140.81        48.00        17.98 
TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 
       64.18        41.56        76.60        67.36        15.68        41.06 
TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-DK-AA6W 
       30.67        38.24        15.02        13.58        12.36         8.65 
TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A2PC 
        7.53        13.64        43.50        12.03        10.62        43.59 
TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ 
       15.35        38.83        24.66         0.10         0.49         2.24 
TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 
       16.70        17.39         0.56         0.66        14.56        13.97 
TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A7XN 
       12.99        14.33         0.92         1.22        13.68        14.07 
TCGA-E7-A85H TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 
       12.95        14.37         8.09        32.02        16.77         8.94 
TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA 
       33.04         4.01        12.62        22.52        27.98        60.66 
TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP 
       24.30        23.41        17.98        29.16         5.52        25.74 
TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S 
       46.78        19.79        12.85        22.98        27.35        14.96 
TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU 
       20.91         3.62        26.73        53.88        11.01        19.33 
TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 
        5.36         5.69         8.25        27.45        18.08        58.92 
TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC 
        2.70         7.10        13.35        62.86        18.81         6.15 
TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI 
       12.69        12.36         2.27         3.06         4.31         9.67 
TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FJ-A871 
       10.85        31.07         7.13        10.65        17.23         8.94 
TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EC TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK 
        3.25         6.48        22.88        61.94        30.61        15.95 
TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY 
       26.93        35.24        33.01         7.23        20.12        17.62 
TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 
       66.02         6.94        64.44        19.46        21.40         2.24 
TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS 
       15.81         4.50        15.91        14.07        17.75        24.92 
TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS 
        8.94        13.91         7.73         2.10         3.12        20.98 
TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 
        2.20         7.36        10.92        11.31        11.31         7.63 
TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATO TCGA-GU-AATP 
       27.09        20.05         5.62         4.73        10.65        32.98 
TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF 
        7.00        14.27        21.34        19.10        19.82        20.28 
TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO 
        8.48        10.59        27.35        19.07        22.72         1.51 
TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS 
       19.40        38.60         3.06         9.01         8.22        25.02 
TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RI 
        3.45        21.24         2.76         9.14        27.68        11.70 
TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-AAQO TCGA-LC-A66R TCGA-LT-A5Z6 
        1.74         1.81        15.42        11.80        15.32        15.58 
TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-AA26 TCGA-SY-A9G0 TCGA-SY-A9G5 
       12.23        16.67        14.24         3.75        12.43        31.56 
TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A9PB 
       17.62        37.05        22.68        76.01        65.75        29.56 
TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SH 
       17.82         4.54         1.64         1.87        17.88        64.80 
TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SL TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SX 
       79.66         3.22        66.41        12.76        11.90        23.64 
TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 
       28.24        26.27        18.90        16.27        66.64         2.10 
TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMG TCGA-XF-AAMH TCGA-XF-AAMJ 
       13.74        92.98        10.82       110.60        11.31        54.90 
TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX 
        7.63        71.57        91.73         2.96         8.32         6.77 
TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 
       98.99        44.32        56.48        30.94        61.45        86.30 
TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YC-A9TC 
       27.06        75.39        18.81         3.88         9.63         0.66 
TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R3 
       11.97        13.64        18.64         7.36        21.11        24.13 
TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RD TCGA-ZF-A9RE 
       30.28        27.19        21.86        28.41        13.41         3.48 
TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N 
       52.73        52.60        82.49        47.84        20.22         2.89 
TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA4X 
       34.06        19.69         8.61        59.38        60.16        63.02 
TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 
       38.73        35.41        57.90        19.40         8.52        47.15 
TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-ZF-AA5P 
       19.17         5.52        10.13 

  OGDH MUTATED OGDH WILD-TYPE 
          1.84           0.10 
  OGDH MUTATED OGDH WILD-TYPE 
        166.03         140.81 
  OGDH MUTATED OGDH WILD-TYPE 
         13.48          15.68 
[1] "1.8 - 166.0 (13.5)" "0.1 - 140.8 (15.7)"
[1] "hr=" "1.8"
D52V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  OGDH MUTATED         1        6         6        6
  OGDH WILD-TYPE       3      111       116      122
D52V3, multiclass
           clus
vv          OGDH MUTATED OGDH WILD-TYPE
  STAGE I              1              3
  STAGE II             6            111
  STAGE III            6            116
  STAGE IV             6            122
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1+T2  T3  T4
  OGDH MUTATED          6   8   2
  OGDH WILD-TYPE      108 171  50
D52V4, multiclass
          clus
vv         OGDH MUTATED OGDH WILD-TYPE
  T0+T1+T2            6            108
  T3                  8            171
  T4                  2             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"
                vv
clus              N0  N1  N2  N3
  OGDH MUTATED    12   2   4   0
  OGDH WILD-TYPE 201  39  71   8
D52V5, multiclass
    clus
vv   OGDH MUTATED OGDH WILD-TYPE
  N0           12            201
  N1            2             39
  N2            4             71
  N3            0              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"
D52V6, binary
                cls
clus               0   1
  OGDH MUTATED     8   0
  OGDH WILD-TYPE 174  10
[1] "tbl2"
                cls
clus             [,1] [,2]
  OGDH MUTATED      8    0
  OGDH WILD-TYPE  174   10
   clus
vv  OGDH MUTATED OGDH WILD-TYPE
  0            8            174
  1            0             10
[1] 2 2
[1] FALSE
D52V7, binary
                cls
clus               0   1
  OGDH MUTATED     3  16
  OGDH WILD-TYPE  93 264
[1] "tbl2"
                cls
clus             [,1] [,2]
  OGDH MUTATED      3   16
  OGDH WILD-TYPE   93  264
        clus
vv       OGDH MUTATED OGDH WILD-TYPE
  FEMALE            3             93
  MALE             16            264
[1] 2 2
[1] FALSE
D52V8, continuous
D52V9, continuous
D52V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  OGDH MUTATED       0                         0    18
  OGDH WILD-TYPE    38                        21   283
D52V11, multiclass
                           clus
vv                          OGDH MUTATED OGDH WILD-TYPE
  ASIAN                                0             38
  BLACK OR AFRICAN AMERICAN            0             21
  WHITE                               18            283
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V12, binary
                cls
clus               0   1
  OGDH MUTATED     1  17
  OGDH WILD-TYPE   7 321
[1] "tbl2"
                cls
clus             [,1] [,2]
  OGDH MUTATED      1   17
  OGDH WILD-TYPE    7  321
                        clus
vv                       OGDH MUTATED OGDH WILD-TYPE
  HISPANIC OR LATINO                1              7
  NOT HISPANIC OR LATINO           17            321
[1] 2 2
[1] FALSE

Clustering(53) Variable = SCARF2 MUTATION ANALYSIS
D53V1, survival
                  sevent
clus2                0   1
  SCARF2 MUTATED     5   2
  SCARF2 WILD-TYPE 214 149
  SCARF2 MUTATED SCARF2 WILD-TYPE 
               7              363 
  SCARF2 MUTATED SCARF2 WILD-TYPE 
               2              149 
$`SCARF2 MUTATED`
TCGA-4Z-AA83 TCGA-DK-A6B6 TCGA-DK-AA6P TCGA-GC-A3RD TCGA-GU-A767 TCGA-S5-A6DX 
       66.54        30.67        15.02        14.07         4.73         1.84 
TCGA-XF-AAN3 
       86.30 

$`SCARF2 WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        91.63       103.50       105.70         8.35 
TCGA-4Z-AA7M TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7S 
       16.27        44.94        16.83        16.77        17.16        34.98 
TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA84 
       27.62        49.12         0.62        41.75        51.16        15.12 
TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J 
       10.22        47.80        33.83        40.08         7.33         2.66 
TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N 
        6.74        12.39         6.58        13.15        19.04        32.84 
TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U 
       12.16        17.88        19.50         5.06        14.89        14.96 
TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A2LD 
        5.06         8.35         8.25        17.16        16.18        20.48 
TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E 
        4.67        12.82         9.96        17.56        28.70        24.26 
TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-C4-A0F6 TCGA-C4-A0F7 
       28.41         8.98         1.94         2.93        23.01         2.04 
TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V 
        0.46         0.43         0.69        10.95        12.66        12.46 
TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 
       12.10        12.62        12.26        13.12        12.00        12.10 
TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ 
       11.87        13.08        12.92         4.90         7.20         5.46 
TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 
        5.19        16.31         1.84        13.58        21.86         2.14 
TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD 
       66.41        18.41        19.00        16.70       130.88       112.44 
TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 
       16.14        17.62        15.62         1.81        10.59         7.79 
TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN 
      123.85        87.32         2.20        13.58         7.82         8.22 
TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW 
       17.72        50.27        21.30        23.21         9.67        20.81 
TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW 
       10.55       140.81        48.00        17.98        64.18        41.56 
TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-AA6L TCGA-DK-AA6Q 
       76.60        67.36        15.68        41.06        38.24        13.58 
TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA71 
      166.03        12.36        10.49         8.65         7.53        13.64 
TCGA-DK-AA74 TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E5-A4U1 
       43.50        12.03        10.62        43.59        15.35        38.83 
TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 
       24.66         0.10         0.49         2.24        16.70        17.39 
TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF 
        0.56         0.66        14.56        13.97        12.99        14.33 
TCGA-E7-A7DU TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A97P 
        0.92         1.22        13.68        14.07        12.95        14.37 
TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 
        8.09        32.02        16.77         8.94        33.04         4.01 
TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL 
       12.62        22.52        27.98        60.66        24.30        23.41 
TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR 
       17.98        29.16         5.52        25.74        46.78        19.79 
TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X 
       12.85        22.98        27.35        14.96        20.91         3.62 
TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX 
       26.73        53.88        11.01        19.33         5.36         5.69 
TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O 
        8.25        27.45        18.08        58.92         2.70         7.10 
TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD 
        6.28        13.35        62.86        18.81         6.15        12.69 
TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FD-A6TK 
       12.36         2.27         3.06         4.31         9.67        10.85 
TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FJ-A871 TCGA-FT-A3EE 
       31.07         7.13        10.65        17.23         8.94         3.25 
TCGA-FT-A61P TCGA-G2-A2EC TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL 
        6.48        22.88        61.94        30.61        15.95        26.93 
TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B 
       35.24        33.01         7.23        20.12        17.62        66.02 
TCGA-G2-AA3C TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO 
        6.94        64.44        19.46        21.40         2.24        15.81 
TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GC-A6I3 
        4.50        15.91        17.75        24.92         8.94        13.91 
TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GD-A76B 
        7.73         2.10         3.12        20.98         2.20         7.36 
TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A764 
       10.92        11.31        11.31         7.63        27.09        20.05 
TCGA-GU-A766 TCGA-GU-AATO TCGA-GU-AATP TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW 
        5.62        10.65        32.98         7.00        14.27        21.34 
TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK 
       19.10        19.82        20.28         8.48        10.59        27.35 
TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE 
        8.58        19.07        22.72         1.51        19.40        38.60 
TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV 
        3.06         9.01         8.22        25.02         3.45        21.24 
TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ 
        2.76         9.14        27.68         9.07        11.70         1.74 
TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO TCGA-LC-A66R TCGA-LT-A5Z6 
        1.81        15.42         6.38        11.80        15.32        15.58 
TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-AA26 TCGA-SY-A9G0 
       13.48        12.23        16.67        14.24         3.75        12.43 
TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78N TCGA-UY-A78O 
       31.56        17.62        37.05        22.68        86.83        76.01 
TCGA-UY-A8OB TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF 
       65.75        35.24        29.56        17.82         4.54         1.64 
TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SJ 
        1.87        17.88        48.62        64.80        79.66         3.22 
TCGA-XF-A9SL TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ 
       66.41        12.76        11.90        23.64        21.04        28.24 
TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 
       26.27        18.90         2.24        16.27        66.64         2.10 
TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMG TCGA-XF-AAMH TCGA-XF-AAMJ 
       13.74        92.98        10.82       110.60        11.31        54.90 
TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX 
        7.63        71.57        91.73         2.96         8.32         6.77 
TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN4 
       98.99        44.32        56.48        30.94        61.45        27.06 
TCGA-XF-AAN5 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L 
       75.39        18.81         3.88         9.63         0.66        11.97 
TCGA-YF-AA3M TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R4 
       13.64        18.64         7.36        21.11        24.13        30.28 
TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RE 
       27.19        21.86        28.41        74.56        13.41         3.48 
TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N 
       52.73        52.60        82.49        47.84        20.22         2.89 
TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA4X 
       34.06        19.69         8.61        59.38        60.16        63.02 
TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 
       38.73        35.41        57.90        19.40         8.52        47.15 
TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-ZF-AA5P 
       19.17         5.52        10.13 

  SCARF2 MUTATED SCARF2 WILD-TYPE 
            1.84             0.10 
  SCARF2 MUTATED SCARF2 WILD-TYPE 
           86.30           166.03 
  SCARF2 MUTATED SCARF2 WILD-TYPE 
           15.02            15.68 
[1] "1.8 - 86.3 (15.0)"  "0.1 - 166.0 (15.7)"
[1] "hr=" "1.7"
D53V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  SCARF2 MUTATED         0        3         1        3
  SCARF2 WILD-TYPE       4      114       121      125
D53V3, multiclass
           clus
vv          SCARF2 MUTATED SCARF2 WILD-TYPE
  STAGE I                0                4
  STAGE II               3              114
  STAGE III              1              121
  STAGE IV               3              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"
                  vv
clus               T0+T1+T2  T3  T4
  SCARF2 MUTATED          1   3   1
  SCARF2 WILD-TYPE      113 176  51
D53V4, multiclass
          clus
vv         SCARF2 MUTATED SCARF2 WILD-TYPE
  T0+T1+T2              1              113
  T3                    3              176
  T4                    1               51
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  SCARF2 MUTATED     3   0   3   0
  SCARF2 WILD-TYPE 210  41  72   8
D53V5, multiclass
    clus
vv   SCARF2 MUTATED SCARF2 WILD-TYPE
  N0              3              210
  N1              0               41
  N2              3               72
  N3              0                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"
D53V6, binary
                  cls
clus                 0   1
  SCARF2 MUTATED     3   0
  SCARF2 WILD-TYPE 179  10
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SCARF2 MUTATED      3    0
  SCARF2 WILD-TYPE  179   10
   clus
vv  SCARF2 MUTATED SCARF2 WILD-TYPE
  0              3              179
  1              0               10
[1] 2 2
[1] FALSE
D53V7, binary
                  cls
clus                 0   1
  SCARF2 MUTATED     2   5
  SCARF2 WILD-TYPE  94 275
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SCARF2 MUTATED      2    5
  SCARF2 WILD-TYPE   94  275
        clus
vv       SCARF2 MUTATED SCARF2 WILD-TYPE
  FEMALE              2               94
  MALE                5              275
[1] 2 2
[1] FALSE
D53V8, continuous
D53V9, continuous
D53V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SCARF2 MUTATED       0                         0     7
  SCARF2 WILD-TYPE    38                        21   294
D53V11, multiclass
                           clus
vv                          SCARF2 MUTATED SCARF2 WILD-TYPE
  ASIAN                                  0               38
  BLACK OR AFRICAN AMERICAN              0               21
  WHITE                                  7              294
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V12, binary
                  cls
clus                 0   1
  SCARF2 MUTATED     0   6
  SCARF2 WILD-TYPE   8 332
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SCARF2 MUTATED      0    6
  SCARF2 WILD-TYPE    8  332
                        clus
vv                       SCARF2 MUTATED SCARF2 WILD-TYPE
  HISPANIC OR LATINO                  0                8
  NOT HISPANIC OR LATINO              6              332
[1] 2 2
[1] FALSE

Clustering(54) Variable = SSH3 MUTATION ANALYSIS
D54V1, survival
                sevent
clus2              0   1
  SSH3 MUTATED    11   4
  SSH3 WILD-TYPE 208 147
  SSH3 MUTATED SSH3 WILD-TYPE 
            15            355 
  SSH3 MUTATED SSH3 WILD-TYPE 
             4            147 
$`SSH3 MUTATED`
TCGA-2F-A9KT TCGA-4Z-AA7O TCGA-4Z-AA7Y TCGA-C4-A0F6 TCGA-CU-A5W6 TCGA-DK-A1AG 
      105.70        16.83        49.12        23.01         1.84        15.62 
TCGA-DK-A2I6 TCGA-DK-A6AW TCGA-DK-AA77 TCGA-E7-A85H TCGA-FD-A3SS TCGA-S5-A6DX 
       87.32        41.56        10.62        12.95        12.85         1.84 
TCGA-XF-A9SH TCGA-ZF-A9R7 TCGA-ZF-A9RC 
       64.80        21.86        74.56 

$`SSH3 WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KW TCGA-4Z-AA7M 
       22.29        11.97        91.63       103.50         8.35        16.27 
TCGA-4Z-AA7N TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7W TCGA-4Z-AA80 
       44.94        16.77        17.16        34.98        27.62         0.62 
TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA84 TCGA-4Z-AA86 TCGA-4Z-AA87 
       41.75        51.16        66.54        15.12        10.22        47.80 
TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ 
       33.83        40.08         7.33         2.66         6.74        12.39 
TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P 
        6.58        13.15        19.04        32.84        12.16        17.88 
TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20W 
       19.50         5.06        14.89        14.96         5.06         8.35 
TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PJ 
        8.25        17.16        16.18        20.48         4.67        12.82 
TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ 
        9.96        17.56        28.70        24.26        28.41         8.98 
TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-C4-A0F7 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C 
        1.94         2.93         2.04         0.46         0.43         0.69 
TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y 
       10.95        12.66        12.46        12.10        12.62        12.26 
TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A0YN 
       13.12        12.00        12.10        11.87        13.08        12.92 
TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A72E 
        4.90         7.20         5.46         5.19        16.31        13.58 
TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB 
       21.86         2.14        66.41        18.41        19.00        16.70 
TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A2HX TCGA-DK-A2I1 
      130.88       112.44        16.14        17.62         1.81        10.59 
TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN 
        7.79       123.85         2.20        13.58         7.82         8.22 
TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW 
       17.72        50.27        21.30        23.21         9.67        20.81 
TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6B0 
       10.55       140.81        48.00        17.98        64.18        76.60 
TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6P 
       67.36        15.68        41.06        30.67        38.24        15.02 
TCGA-DK-AA6Q TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA6X 
       13.58       166.03        12.36        10.49         8.65         7.53 
TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA76 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E5-A4U1 
       13.64        43.50        12.03        43.59        15.35        38.83 
TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 
       24.66         0.10         0.49         2.24        16.70        17.39 
TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF 
        0.56         0.66        14.56        13.97        12.99        14.33 
TCGA-E7-A7DU TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A97P TCGA-E7-A97Q 
        0.92         1.22        13.68        14.07        14.37         8.09 
TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 
       32.02        16.77         8.94        33.04         4.01        12.62 
TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM 
       22.52        27.98        60.66        24.30        23.41        17.98 
TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A43N 
       29.16         5.52        25.74        46.78        19.79        22.98 
TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS 
       27.35        14.96        20.91         3.62        26.73        53.88 
TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ 
       11.01        19.33         5.36         5.69         8.25        27.45 
TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S 
       18.08        58.92         2.70         7.10         6.28        13.35 
TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF 
       62.86        18.81         6.15        12.69        12.36         2.27 
TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 
        3.06         4.31         9.67        10.85        31.07         7.13 
TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FJ-A871 TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EC 
       10.65        17.23         8.94         3.25         6.48        22.88 
TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES 
       61.94        30.61        15.95        26.93        35.24        33.01 
TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3D 
        7.23        20.12        17.62        66.02         6.94        64.44 
TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC 
       19.46        21.40         2.24        15.81         4.50        15.91 
TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 
       14.07        17.75        24.92         8.94        13.91         7.73 
TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42P 
        2.10         3.12        20.98         2.20         7.36        10.92 
TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 
       11.31        11.31         7.63        27.09        20.05         5.62 
TCGA-GU-A767 TCGA-GU-AATO TCGA-GU-AATP TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW 
        4.73        10.65        32.98         7.00        14.27        21.34 
TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK 
       19.10        19.82        20.28         8.48        10.59        27.35 
TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE 
        8.58        19.07        22.72         1.51        19.40        38.60 
TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV 
        3.06         9.01         8.22        25.02         3.45        21.24 
TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ 
        2.76         9.14        27.68         9.07        11.70         1.74 
TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO TCGA-LC-A66R TCGA-LT-A5Z6 
        1.81        15.42         6.38        11.80        15.32        15.58 
TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-AA26 TCGA-SY-A9G0 
       13.48        12.23        16.67        14.24         3.75        12.43 
TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78N TCGA-UY-A78O 
       31.56        17.62        37.05        22.68        86.83        76.01 
TCGA-UY-A8OB TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF 
       65.75        35.24        29.56        17.82         4.54         1.64 
TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SL 
        1.87        17.88        48.62        79.66         3.22        66.41 
TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T0 
       12.76        11.90        23.64        21.04        28.24        26.27 
TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 
       18.90         2.24        16.27        66.64         2.10        13.74 
TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMG TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML 
       92.98        10.82       110.60        11.31        54.90         7.63 
TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAMY 
       71.57        91.73         2.96         8.32         6.77        98.99 
TCGA-XF-AAMZ TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN4 
       44.32        56.48        30.94        61.45        86.30        27.06 
TCGA-XF-AAN5 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L 
       75.39        18.81         3.88         9.63         0.66        11.97 
TCGA-YF-AA3M TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R4 
       13.64        18.64         7.36        21.11        24.13        30.28 
TCGA-ZF-A9R5 TCGA-ZF-A9R9 TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RG 
       27.19        28.41        13.41         3.48        52.73        52.60 
TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4R TCGA-ZF-AA4T 
       82.49        47.84        20.22         2.89        34.06        19.69 
TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 
        8.61        59.38        60.16        63.02        38.73        35.41 
TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N 
       57.90        19.40         8.52        47.15        19.17         5.52 
TCGA-ZF-AA5P 
       10.13 

  SSH3 MUTATED SSH3 WILD-TYPE 
          1.84           0.10 
  SSH3 MUTATED SSH3 WILD-TYPE 
        105.70         166.03 
  SSH3 MUTATED SSH3 WILD-TYPE 
         21.86          15.42 
[1] "1.8 - 105.7 (21.9)" "0.1 - 166.0 (15.4)"
[1] "hr=" "2.1"
D54V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  SSH3 MUTATED         0        7         5        3
  SSH3 WILD-TYPE       4      110       117      125
D54V3, multiclass
           clus
vv          SSH3 MUTATED SSH3 WILD-TYPE
  STAGE I              0              4
  STAGE II             7            110
  STAGE III            5            117
  STAGE IV             3            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"
                vv
clus             T0+T1+T2  T3  T4
  SSH3 MUTATED          7   4   3
  SSH3 WILD-TYPE      107 175  49
D54V4, multiclass
          clus
vv         SSH3 MUTATED SSH3 WILD-TYPE
  T0+T1+T2            7            107
  T3                  4            175
  T4                  3             49
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  SSH3 MUTATED    11   1   1   1
  SSH3 WILD-TYPE 202  40  74   7
D54V5, multiclass
    clus
vv   SSH3 MUTATED SSH3 WILD-TYPE
  N0           11            202
  N1            1             40
  N2            1             74
  N3            1              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"
D54V6, binary
                cls
clus               0   1
  SSH3 MUTATED    12   0
  SSH3 WILD-TYPE 170  10
[1] "tbl2"
                cls
clus             [,1] [,2]
  SSH3 MUTATED     12    0
  SSH3 WILD-TYPE  170   10
   clus
vv  SSH3 MUTATED SSH3 WILD-TYPE
  0           12            170
  1            0             10
[1] 2 2
[1] FALSE
D54V7, binary
                cls
clus               0   1
  SSH3 MUTATED     3  12
  SSH3 WILD-TYPE  93 268
[1] "tbl2"
                cls
clus             [,1] [,2]
  SSH3 MUTATED      3   12
  SSH3 WILD-TYPE   93  268
        clus
vv       SSH3 MUTATED SSH3 WILD-TYPE
  FEMALE            3             93
  MALE             12            268
[1] 2 2
[1] FALSE
D54V8, continuous
[1] "Remove cluster labels:" "SSH3 MUTATED"          
clus
  SSH3 MUTATED SSH3 WILD-TYPE 
             2            118 
    TCGA-2F-A9KO     TCGA-2F-A9KP     TCGA-2F-A9KQ     TCGA-2F-A9KR 
"SSH3 WILD-TYPE" "SSH3 WILD-TYPE" "SSH3 WILD-TYPE" "SSH3 WILD-TYPE" 
    TCGA-2F-A9KW     TCGA-CF-A1HS     TCGA-CF-A27C     TCGA-CF-A3MF 
"SSH3 WILD-TYPE" "SSH3 WILD-TYPE" "SSH3 WILD-TYPE" "SSH3 WILD-TYPE" 
    TCGA-CF-A3MG     TCGA-CF-A3MH     TCGA-CF-A3MI     TCGA-CF-A47S 
"SSH3 WILD-TYPE" "SSH3 WILD-TYPE" "SSH3 WILD-TYPE" "SSH3 WILD-TYPE" 
    TCGA-CF-A47T     TCGA-CF-A47V     TCGA-CF-A47W     TCGA-CF-A47X 
"SSH3 WILD-TYPE" "SSH3 WILD-TYPE" "SSH3 WILD-TYPE" "SSH3 WILD-TYPE" 
    TCGA-CF-A47Y     TCGA-CF-A5U8     TCGA-CF-A5UA     TCGA-CF-A7I0 
"SSH3 WILD-TYPE" "SSH3 WILD-TYPE" "SSH3 WILD-TYPE" "SSH3 WILD-TYPE" 
    TCGA-DK-A2HX     TCGA-DK-A3IN     TCGA-DK-A3IV     TCGA-DK-A3WX 
"SSH3 WILD-TYPE" "SSH3 WILD-TYPE" "SSH3 WILD-TYPE" "SSH3 WILD-TYPE" 
    TCGA-DK-A3X2     TCGA-DK-A6B2     TCGA-DK-A6B5     TCGA-DK-A6B6 
"SSH3 WILD-TYPE" "SSH3 WILD-TYPE" "SSH3 WILD-TYPE" "SSH3 WILD-TYPE" 
    TCGA-DK-AA6P     TCGA-DK-AA6S     TCGA-DK-AA6U     TCGA-DK-AA6W 
"SSH3 WILD-TYPE" "SSH3 WILD-TYPE" "SSH3 WILD-TYPE" "SSH3 WILD-TYPE" 
    TCGA-DK-AA76     TCGA-E5-A2PC     TCGA-E5-A4TZ     TCGA-E5-A4U1 
"SSH3 WILD-TYPE" "SSH3 WILD-TYPE" "SSH3 WILD-TYPE" "SSH3 WILD-TYPE" 
    TCGA-E7-A519     TCGA-E7-A541     TCGA-E7-A7DU     TCGA-E7-A7DV 
"SSH3 WILD-TYPE" "SSH3 WILD-TYPE" "SSH3 WILD-TYPE" "SSH3 WILD-TYPE" 
    TCGA-FT-A61P     TCGA-G2-A2EC     TCGA-G2-A2EF     TCGA-G2-A2EJ 
"SSH3 WILD-TYPE" "SSH3 WILD-TYPE" "SSH3 WILD-TYPE" "SSH3 WILD-TYPE" 
    TCGA-G2-A2EK     TCGA-G2-A2EL     TCGA-G2-A2EO     TCGA-G2-A2ES 
"SSH3 WILD-TYPE" "SSH3 WILD-TYPE" "SSH3 WILD-TYPE" "SSH3 WILD-TYPE" 
    TCGA-G2-A3IB     TCGA-G2-A3IE     TCGA-G2-A3VY     TCGA-GC-A3BM 
"SSH3 WILD-TYPE" "SSH3 WILD-TYPE" "SSH3 WILD-TYPE" "SSH3 WILD-TYPE" 
    TCGA-GC-A3I6     TCGA-GC-A3OO     TCGA-GC-A3RC     TCGA-GC-A3RD 
"SSH3 WILD-TYPE" "SSH3 WILD-TYPE" "SSH3 WILD-TYPE" "SSH3 WILD-TYPE" 
    TCGA-GC-A3YS     TCGA-GC-A6I1     TCGA-GC-A6I3     TCGA-GD-A3OS 
"SSH3 WILD-TYPE" "SSH3 WILD-TYPE" "SSH3 WILD-TYPE" "SSH3 WILD-TYPE" 
    TCGA-GD-A6C6     TCGA-GV-A3JV     TCGA-GV-A3JW     TCGA-GV-A3JX 
"SSH3 WILD-TYPE" "SSH3 WILD-TYPE" "SSH3 WILD-TYPE" "SSH3 WILD-TYPE" 
    TCGA-GV-A3JZ     TCGA-GV-A3QF     TCGA-GV-A3QH     TCGA-GV-A3QI 
"SSH3 WILD-TYPE" "SSH3 WILD-TYPE" "SSH3 WILD-TYPE" "SSH3 WILD-TYPE" 
    TCGA-GV-A3QK     TCGA-GV-A40E     TCGA-GV-A40G     TCGA-GV-A6ZA 
"SSH3 WILD-TYPE" "SSH3 WILD-TYPE" "SSH3 WILD-TYPE" "SSH3 WILD-TYPE" 
    TCGA-SY-A9G0     TCGA-SY-A9G5     TCGA-UY-A78L     TCGA-UY-A78M 
"SSH3 WILD-TYPE" "SSH3 WILD-TYPE" "SSH3 WILD-TYPE" "SSH3 WILD-TYPE" 
    TCGA-UY-A78N     TCGA-XF-A8HH     TCGA-XF-A8HI     TCGA-XF-A9SG 
"SSH3 WILD-TYPE" "SSH3 WILD-TYPE" "SSH3 WILD-TYPE" "SSH3 WILD-TYPE" 
    TCGA-XF-A9SI     TCGA-XF-A9SJ     TCGA-XF-A9SL     TCGA-XF-A9SV 
"SSH3 WILD-TYPE" "SSH3 WILD-TYPE" "SSH3 WILD-TYPE" "SSH3 WILD-TYPE" 
    TCGA-XF-A9SW     TCGA-XF-A9SX     TCGA-XF-A9SY     TCGA-XF-A9SZ 
"SSH3 WILD-TYPE" "SSH3 WILD-TYPE" "SSH3 WILD-TYPE" "SSH3 WILD-TYPE" 
    TCGA-XF-A9T0     TCGA-XF-A9T2     TCGA-XF-A9T3     TCGA-XF-A9T4 
"SSH3 WILD-TYPE" "SSH3 WILD-TYPE" "SSH3 WILD-TYPE" "SSH3 WILD-TYPE" 
    TCGA-XF-A9T5     TCGA-XF-A9T6     TCGA-XF-A9T8     TCGA-XF-AAME 
"SSH3 WILD-TYPE" "SSH3 WILD-TYPE" "SSH3 WILD-TYPE" "SSH3 WILD-TYPE" 
    TCGA-XF-AAMF     TCGA-XF-AAMG     TCGA-XF-AAMH     TCGA-XF-AAMJ 
"SSH3 WILD-TYPE" "SSH3 WILD-TYPE" "SSH3 WILD-TYPE" "SSH3 WILD-TYPE" 
    TCGA-XF-AAML     TCGA-XF-AAMQ     TCGA-XF-AAMR     TCGA-XF-AAMT 
"SSH3 WILD-TYPE" "SSH3 WILD-TYPE" "SSH3 WILD-TYPE" "SSH3 WILD-TYPE" 
    TCGA-XF-AAMW     TCGA-XF-AAMX     TCGA-XF-AAMY     TCGA-XF-AAMZ 
"SSH3 WILD-TYPE" "SSH3 WILD-TYPE" "SSH3 WILD-TYPE" "SSH3 WILD-TYPE" 
    TCGA-XF-AAN0     TCGA-XF-AAN1     TCGA-XF-AAN2     TCGA-XF-AAN3 
"SSH3 WILD-TYPE" "SSH3 WILD-TYPE" "SSH3 WILD-TYPE" "SSH3 WILD-TYPE" 
    TCGA-XF-AAN4     TCGA-XF-AAN5     TCGA-XF-AAN7     TCGA-XF-AAN8 
"SSH3 WILD-TYPE" "SSH3 WILD-TYPE" "SSH3 WILD-TYPE" "SSH3 WILD-TYPE" 
    TCGA-YF-AA3L     TCGA-YF-AA3M 
"SSH3 WILD-TYPE" "SSH3 WILD-TYPE" 
D54V9, continuous
D54V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SSH3 MUTATED       2                         1    11
  SSH3 WILD-TYPE    36                        20   290
D54V11, multiclass
                           clus
vv                          SSH3 MUTATED SSH3 WILD-TYPE
  ASIAN                                2             36
  BLACK OR AFRICAN AMERICAN            1             20
  WHITE                               11            290
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V12, binary
                cls
clus               0   1
  SSH3 MUTATED     0  12
  SSH3 WILD-TYPE   8 326
[1] "tbl2"
                cls
clus             [,1] [,2]
  SSH3 MUTATED      0   12
  SSH3 WILD-TYPE    8  326
                        clus
vv                       SSH3 MUTATED SSH3 WILD-TYPE
  HISPANIC OR LATINO                0              8
  NOT HISPANIC OR LATINO           12            326
[1] 2 2
[1] FALSE

Clustering(55) Variable = HLA-A MUTATION ANALYSIS
D55V1, survival
                 sevent
clus2               0   1
  HLA-A MUTATED     2   3
  HLA-A WILD-TYPE 217 148
  HLA-A MUTATED HLA-A WILD-TYPE 
              5             365 
  HLA-A MUTATED HLA-A WILD-TYPE 
              3             148 
$`HLA-A MUTATED`
TCGA-BL-A13J TCGA-CU-A0YO TCGA-DK-A3WW TCGA-SY-A9G5 TCGA-XF-AAN1 
        2.66         4.90        20.81        31.56        30.94 

$`HLA-A WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        91.63       103.50       105.70         8.35 
TCGA-4Z-AA7M TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7S 
       16.27        44.94        16.83        16.77        17.16        34.98 
TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 
       27.62        49.12         0.62        41.75        51.16        66.54 
TCGA-4Z-AA84 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BL-A13I 
       15.12        10.22        47.80        33.83        40.08         7.33 
TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N 
        6.74        12.39         6.58        13.15        19.04        32.84 
TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U 
       12.16        17.88        19.50         5.06        14.89        14.96 
TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A2LD 
        5.06         8.35         8.25        17.16        16.18        20.48 
TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E 
        4.67        12.82         9.96        17.56        28.70        24.26 
TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-C4-A0F6 TCGA-C4-A0F7 
       28.41         8.98         1.94         2.93        23.01         2.04 
TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V 
        0.46         0.43         0.69        10.95        12.66        12.46 
TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 
       12.10        12.62        12.26        13.12        12.00        12.10 
TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3QU 
       11.87        13.08        12.92         7.20         5.46         5.19 
TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 
       16.31         1.84        13.58        21.86         2.14        66.41 
TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE 
       18.41        19.00        16.70       130.88       112.44        16.14 
TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 
       17.62        15.62         1.81        10.59         7.79       123.85 
TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ 
       87.32         2.20        13.58         7.82         8.22        17.72 
TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WX TCGA-DK-A3WY 
       50.27        21.30        23.21         9.67        10.55       140.81 
TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 
       48.00        17.98        64.18        41.56        76.60        67.36 
TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6P TCGA-DK-AA6Q 
       15.68        41.06        30.67        38.24        15.02        13.58 
TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA71 
      166.03        12.36        10.49         8.65         7.53        13.64 
TCGA-DK-AA74 TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E5-A4U1 
       43.50        12.03        10.62        43.59        15.35        38.83 
TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 
       24.66         0.10         0.49         2.24        16.70        17.39 
TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF 
        0.56         0.66        14.56        13.97        12.99        14.33 
TCGA-E7-A7DU TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A97P 
        0.92         1.22        13.68        14.07        12.95        14.37 
TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 
        8.09        32.02        16.77         8.94        33.04         4.01 
TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL 
       12.62        22.52        27.98        60.66        24.30        23.41 
TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR 
       17.98        29.16         5.52        25.74        46.78        19.79 
TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X 
       12.85        22.98        27.35        14.96        20.91         3.62 
TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX 
       26.73        53.88        11.01        19.33         5.36         5.69 
TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O 
        8.25        27.45        18.08        58.92         2.70         7.10 
TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD 
        6.28        13.35        62.86        18.81         6.15        12.69 
TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FD-A6TK 
       12.36         2.27         3.06         4.31         9.67        10.85 
TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FJ-A871 TCGA-FT-A3EE 
       31.07         7.13        10.65        17.23         8.94         3.25 
TCGA-FT-A61P TCGA-G2-A2EC TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL 
        6.48        22.88        61.94        30.61        15.95        26.93 
TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B 
       35.24        33.01         7.23        20.12        17.62        66.02 
TCGA-G2-AA3C TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO 
        6.94        64.44        19.46        21.40         2.24        15.81 
TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A6I1 
        4.50        15.91        14.07        17.75        24.92         8.94 
TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 
       13.91         7.73         2.10         3.12        20.98         2.20 
TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 
        7.36        10.92        11.31        11.31         7.63        27.09 
TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATO TCGA-GU-AATP TCGA-GU-AATQ 
       20.05         5.62         4.73        10.65        32.98         7.00 
TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH 
       14.27        21.34        19.10        19.82        20.28         8.48 
TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO 
       10.59        27.35         8.58        19.07        22.72         1.51 
TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS 
       19.40        38.60         3.06         9.01         8.22        25.02 
TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RH 
        3.45        21.24         2.76         9.14        27.68         9.07 
TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO 
       11.70         1.74         1.81        15.42         6.38        11.80 
TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X 
       15.32        15.58        13.48        12.23        16.67        14.24 
TCGA-S5-A6DX TCGA-S5-AA26 TCGA-SY-A9G0 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M 
        1.84         3.75        12.43        17.62        37.05        22.68 
TCGA-UY-A78N TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD 
       86.83        76.01        65.75        35.24        29.56        17.82 
TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH 
        4.54         1.64         1.87        17.88        48.62        64.80 
TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SL TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SX 
       79.66         3.22        66.41        12.76        11.90        23.64 
TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 
       21.04        28.24        26.27        18.90         2.24        16.27 
TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMG 
       66.64         2.10        13.74        92.98        10.82       110.60 
TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMT 
       11.31        54.90         7.63        71.57        91.73         2.96 
TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN0 TCGA-XF-AAN2 
        8.32         6.77        98.99        44.32        56.48        61.45 
TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 
       86.30        27.06        75.39        18.81         3.88         9.63 
TCGA-YC-A9TC TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R2 
        0.66        11.97        13.64        18.64         7.36        21.11 
TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RC 
       24.13        30.28        27.19        21.86        28.41        74.56 
TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-A9RM 
       13.41         3.48        52.73        52.60        82.49        47.84 
TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4U TCGA-ZF-AA4V 
       20.22         2.89        34.06        19.69         8.61        59.38 
TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA53 TCGA-ZF-AA54 
       60.16        63.02        38.73        35.41        57.90        19.40 
TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-ZF-AA5P 
        8.52        47.15        19.17         5.52        10.13 

  HLA-A MUTATED HLA-A WILD-TYPE 
           2.66            0.10 
  HLA-A MUTATED HLA-A WILD-TYPE 
          31.56          166.03 
  HLA-A MUTATED HLA-A WILD-TYPE 
          20.81           15.62 
[1] "2.7 - 31.6 (20.8)"  "0.1 - 166.0 (15.6)"
[1] "hr=" "1.6"
D55V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  HLA-A MUTATED         0        0         3        2
  HLA-A WILD-TYPE       4      117       119      126
D55V3, multiclass
           clus
vv          HLA-A MUTATED HLA-A WILD-TYPE
  STAGE I               0               4
  STAGE II              0             117
  STAGE III             3             119
  STAGE IV              2             126
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1+T2  T3  T4
  HLA-A MUTATED          0   2   3
  HLA-A WILD-TYPE      114 177  49
D55V4, multiclass
          clus
vv         HLA-A MUTATED HLA-A WILD-TYPE
  T0+T1+T2             0             114
  T3                   2             177
  T4                   3              49
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  HLA-A MUTATED     3   0   2   0
  HLA-A WILD-TYPE 210  41  73   8
D55V5, multiclass
    clus
vv   HLA-A MUTATED HLA-A WILD-TYPE
  N0             3             210
  N1             0              41
  N2             2              73
  N3             0               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"
D55V6, binary
                 cls
clus                0   1
  HLA-A MUTATED     4   0
  HLA-A WILD-TYPE 178  10
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HLA-A MUTATED      4    0
  HLA-A WILD-TYPE  178   10
   clus
vv  HLA-A MUTATED HLA-A WILD-TYPE
  0             4             178
  1             0              10
[1] 2 2
[1] FALSE
D55V7, binary
                 cls
clus                0   1
  HLA-A MUTATED     1   4
  HLA-A WILD-TYPE  95 276
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HLA-A MUTATED      1    4
  HLA-A WILD-TYPE   95  276
        clus
vv       HLA-A MUTATED HLA-A WILD-TYPE
  FEMALE             1              95
  MALE               4             276
[1] 2 2
[1] FALSE
D55V8, continuous
[1] "Remove cluster labels:" "HLA-A MUTATED"         
clus
  HLA-A MUTATED HLA-A WILD-TYPE 
              2             118 
     TCGA-2F-A9KO      TCGA-2F-A9KP      TCGA-2F-A9KQ      TCGA-2F-A9KR 
"HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" 
     TCGA-2F-A9KT      TCGA-2F-A9KW      TCGA-CF-A1HS      TCGA-CF-A27C 
"HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" 
     TCGA-CF-A3MF      TCGA-CF-A3MG      TCGA-CF-A3MH      TCGA-CF-A3MI 
"HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" 
     TCGA-CF-A47S      TCGA-CF-A47T      TCGA-CF-A47V      TCGA-CF-A47W 
"HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" 
     TCGA-CF-A47X      TCGA-CF-A47Y      TCGA-CF-A5U8      TCGA-CF-A5UA 
"HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" 
     TCGA-CF-A7I0      TCGA-DK-A2HX      TCGA-DK-A3IN      TCGA-DK-A3IV 
"HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" 
     TCGA-DK-A3WX      TCGA-DK-A3X2      TCGA-DK-A6B2      TCGA-DK-A6B5 
"HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" 
     TCGA-DK-A6B6      TCGA-DK-AA6P      TCGA-DK-AA6S      TCGA-DK-AA6U 
"HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" 
     TCGA-DK-AA6W      TCGA-DK-AA76      TCGA-E5-A2PC      TCGA-E5-A4TZ 
"HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" 
     TCGA-E5-A4U1      TCGA-E7-A519      TCGA-E7-A541      TCGA-E7-A7DU 
"HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" 
     TCGA-E7-A7DV      TCGA-FT-A61P      TCGA-G2-A2EC      TCGA-G2-A2EF 
"HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" 
     TCGA-G2-A2EJ      TCGA-G2-A2EK      TCGA-G2-A2EL      TCGA-G2-A2EO 
"HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" 
     TCGA-G2-A2ES      TCGA-G2-A3IB      TCGA-G2-A3IE      TCGA-G2-A3VY 
"HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" 
     TCGA-GC-A3BM      TCGA-GC-A3I6      TCGA-GC-A3OO      TCGA-GC-A3RC 
"HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" 
     TCGA-GC-A3RD      TCGA-GC-A3YS      TCGA-GC-A6I1      TCGA-GC-A6I3 
"HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" 
     TCGA-GD-A3OS      TCGA-GD-A6C6      TCGA-GV-A3JV      TCGA-GV-A3JW 
"HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" 
     TCGA-GV-A3JX      TCGA-GV-A3JZ      TCGA-GV-A3QF      TCGA-GV-A3QH 
"HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" 
     TCGA-GV-A3QI      TCGA-GV-A3QK      TCGA-GV-A40E      TCGA-GV-A40G 
"HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" 
     TCGA-GV-A6ZA      TCGA-SY-A9G0      TCGA-UY-A78L      TCGA-UY-A78M 
"HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" 
     TCGA-UY-A78N      TCGA-XF-A8HH      TCGA-XF-A8HI      TCGA-XF-A9SG 
"HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" 
     TCGA-XF-A9SH      TCGA-XF-A9SI      TCGA-XF-A9SJ      TCGA-XF-A9SL 
"HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" 
     TCGA-XF-A9SV      TCGA-XF-A9SW      TCGA-XF-A9SX      TCGA-XF-A9SY 
"HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" 
     TCGA-XF-A9SZ      TCGA-XF-A9T0      TCGA-XF-A9T2      TCGA-XF-A9T3 
"HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" 
     TCGA-XF-A9T4      TCGA-XF-A9T5      TCGA-XF-A9T6      TCGA-XF-A9T8 
"HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" 
     TCGA-XF-AAME      TCGA-XF-AAMF      TCGA-XF-AAMG      TCGA-XF-AAMH 
"HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" 
     TCGA-XF-AAMJ      TCGA-XF-AAML      TCGA-XF-AAMQ      TCGA-XF-AAMR 
"HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" 
     TCGA-XF-AAMT      TCGA-XF-AAMW      TCGA-XF-AAMX      TCGA-XF-AAMY 
"HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" 
     TCGA-XF-AAMZ      TCGA-XF-AAN0      TCGA-XF-AAN2      TCGA-XF-AAN3 
"HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" 
     TCGA-XF-AAN4      TCGA-XF-AAN5      TCGA-XF-AAN7      TCGA-XF-AAN8 
"HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" 
     TCGA-YF-AA3L      TCGA-YF-AA3M 
"HLA-A WILD-TYPE" "HLA-A WILD-TYPE" 
D55V9, continuous
[1] "Remove cluster labels:" "HLA-A MUTATED"         
clus
  HLA-A MUTATED HLA-A WILD-TYPE 
              2             203 
     TCGA-2F-A9KO      TCGA-2F-A9KP      TCGA-2F-A9KR      TCGA-4Z-AA7M 
"HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" 
     TCGA-4Z-AA89      TCGA-BL-A0C8      TCGA-BL-A13I      TCGA-BL-A3JM 
"HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" 
     TCGA-BL-A5ZZ      TCGA-BT-A20J      TCGA-BT-A20N      TCGA-BT-A2LA 
"HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" 
     TCGA-BT-A42B      TCGA-BT-A42C      TCGA-BT-A42E      TCGA-C4-A0EZ 
"HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" 
     TCGA-C4-A0F0      TCGA-C4-A0F1      TCGA-C4-A0F6      TCGA-CF-A3MH 
"HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" 
     TCGA-CF-A3MI      TCGA-CF-A47W      TCGA-CF-A47X      TCGA-CF-A5UA 
"HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" 
     TCGA-CF-A9FH      TCGA-CU-A0YN      TCGA-CU-A0YR      TCGA-CU-A3KJ 
"HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" 
     TCGA-CU-A3QU      TCGA-CU-A3YL      TCGA-CU-A5W6      TCGA-CU-A72E 
"HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" 
     TCGA-DK-A1A3      TCGA-DK-A1A5      TCGA-DK-A1A6      TCGA-DK-A1AA 
"HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" 
     TCGA-DK-A1AC      TCGA-DK-A1AE      TCGA-DK-A2HX      TCGA-DK-A2I6 
"HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" 
     TCGA-DK-A3IL      TCGA-DK-A3IM      TCGA-DK-A3IN      TCGA-DK-A3IQ 
"HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" 
     TCGA-DK-A3IU      TCGA-DK-A3IV      TCGA-DK-A3WX      TCGA-DK-A3X1 
"HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" 
     TCGA-DK-A3X2      TCGA-DK-A6AV      TCGA-DK-A6AW      TCGA-DK-A6B0 
"HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" 
     TCGA-DK-A6B2      TCGA-DK-A6B6      TCGA-DK-AA6L      TCGA-DK-AA6P 
"HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" 
     TCGA-DK-AA6T      TCGA-DK-AA6U      TCGA-DK-AA74      TCGA-DK-AA76 
"HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" 
     TCGA-E5-A4TZ      TCGA-E7-A4XJ      TCGA-E7-A519      TCGA-E7-A5KF 
"HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" 
     TCGA-E7-A678      TCGA-E7-A6ME      TCGA-E7-A6MF      TCGA-E7-A7PW 
"HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" 
     TCGA-E7-A7XN      TCGA-E7-A85H      TCGA-E7-A97Q      TCGA-FD-A3B3 
"HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" 
     TCGA-FD-A3B4      TCGA-FD-A3B5      TCGA-FD-A3B6      TCGA-FD-A3B7 
"HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" 
     TCGA-FD-A3B8      TCGA-FD-A3N5      TCGA-FD-A3N6      TCGA-FD-A3NA 
"HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" 
     TCGA-FD-A3SJ      TCGA-FD-A3SM      TCGA-FD-A3SN      TCGA-FD-A3SO 
"HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" 
     TCGA-FD-A3SP      TCGA-FD-A3SQ      TCGA-FD-A3SR      TCGA-FD-A3SS 
"HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" 
     TCGA-FD-A43N      TCGA-FD-A43P      TCGA-FD-A43S      TCGA-FD-A43U 
"HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" 
     TCGA-FD-A43X      TCGA-FD-A5BT      TCGA-FD-A5BU      TCGA-FD-A5BV 
"HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" 
     TCGA-FD-A5BX      TCGA-FD-A5C0      TCGA-FD-A62N      TCGA-FD-A6TB 
"HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" 
     TCGA-FD-A6TC      TCGA-FD-A6TE      TCGA-FD-A6TG      TCGA-FD-A6TH 
"HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" 
     TCGA-FD-A6TK      TCGA-FJ-A3Z9      TCGA-FJ-A3ZE      TCGA-FJ-A3ZF 
"HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" 
     TCGA-FJ-A871      TCGA-FT-A61P      TCGA-G2-A2EF      TCGA-G2-A2EJ 
"HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" 
     TCGA-G2-A2EL      TCGA-G2-A2ES      TCGA-G2-A3IE      TCGA-G2-AA3B 
"HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" 
     TCGA-G2-AA3C      TCGA-G2-AA3D      TCGA-G2-AA3F      TCGA-GC-A3BM 
"HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" 
     TCGA-GC-A3RB      TCGA-GC-A3WC      TCGA-GC-A3YS      TCGA-GD-A2C5 
"HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" 
     TCGA-GD-A3OQ      TCGA-GD-A3OS      TCGA-GD-A6C6      TCGA-GU-A42P 
"HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" 
     TCGA-GU-A42Q      TCGA-GU-A42R      TCGA-GU-A763      TCGA-GU-A764 
"HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" 
     TCGA-GU-AATO      TCGA-GU-AATP      TCGA-GU-AATQ      TCGA-GV-A3JV 
"HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" 
     TCGA-GV-A3JX      TCGA-GV-A3JZ      TCGA-GV-A3QF      TCGA-GV-A3QG 
"HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" 
     TCGA-GV-A3QH      TCGA-GV-A3QI      TCGA-GV-A3QK      TCGA-GV-A40E 
"HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" 
     TCGA-GV-A40G      TCGA-H4-A2HO      TCGA-H4-A2HQ      TCGA-HQ-A5ND 
"HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" 
     TCGA-HQ-A5NE      TCGA-K4-A3WS      TCGA-K4-A3WV      TCGA-K4-A5RH 
"HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" 
     TCGA-K4-A5RI      TCGA-K4-A83P      TCGA-K4-AAQO      TCGA-PQ-A6FI 
"HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" 
     TCGA-PQ-A6FN      TCGA-R3-A69X      TCGA-S5-A6DX      TCGA-SY-A9G0 
"HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" 
     TCGA-UY-A78N      TCGA-UY-A8OB      TCGA-UY-A9PB      TCGA-UY-A9PE 
"HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" 
     TCGA-UY-A9PF      TCGA-XF-A9SJ      TCGA-XF-A9SL      TCGA-XF-A9SV 
"HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" 
     TCGA-XF-A9SX      TCGA-XF-A9SY      TCGA-XF-A9SZ      TCGA-XF-A9T3 
"HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" 
     TCGA-XF-A9T8      TCGA-XF-AAMF      TCGA-XF-AAMH      TCGA-XF-AAMQ 
"HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" 
     TCGA-XF-AAMT      TCGA-XF-AAN0      TCGA-XF-AAN2      TCGA-XF-AAN4 
"HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" 
     TCGA-XF-AAN5      TCGA-XF-AAN7      TCGA-XF-AAN8      TCGA-YF-AA3L 
"HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" 
     TCGA-YF-AA3M      TCGA-ZF-A9R0      TCGA-ZF-A9R2      TCGA-ZF-A9R3 
"HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" 
     TCGA-ZF-A9R5      TCGA-ZF-A9R7      TCGA-ZF-A9R9      TCGA-ZF-A9RD 
"HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" 
     TCGA-ZF-A9RF      TCGA-ZF-A9RL      TCGA-ZF-A9RM      TCGA-ZF-AA4U 
"HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" 
     TCGA-ZF-AA4V      TCGA-ZF-AA51      TCGA-ZF-AA52      TCGA-ZF-AA58 
"HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" 
     TCGA-ZF-AA5H      TCGA-ZF-AA5N      TCGA-ZF-AA5P 
"HLA-A WILD-TYPE" "HLA-A WILD-TYPE" "HLA-A WILD-TYPE" 
D55V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  HLA-A MUTATED       0                         0     4
  HLA-A WILD-TYPE    38                        21   297
D55V11, multiclass
                           clus
vv                          HLA-A MUTATED HLA-A WILD-TYPE
  ASIAN                                 0              38
  BLACK OR AFRICAN AMERICAN             0              21
  WHITE                                 4             297
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V12, binary
                 cls
clus                0   1
  HLA-A MUTATED     0   5
  HLA-A WILD-TYPE   8 333
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HLA-A MUTATED      0    5
  HLA-A WILD-TYPE    8  333
                        clus
vv                       HLA-A MUTATED HLA-A WILD-TYPE
  HISPANIC OR LATINO                 0               8
  NOT HISPANIC OR LATINO             5             333
[1] 2 2
[1] FALSE

Clustering(56) Variable = PARD3 MUTATION ANALYSIS
D56V1, survival
                 sevent
clus2               0   1
  PARD3 MUTATED    14   7
  PARD3 WILD-TYPE 205 144
  PARD3 MUTATED PARD3 WILD-TYPE 
             21             349 
  PARD3 MUTATED PARD3 WILD-TYPE 
              7             144 
$`PARD3 MUTATED`
TCGA-CU-A3QU TCGA-DK-A2I4 TCGA-DK-A3IU TCGA-DK-A6AW TCGA-DK-A6B6 TCGA-E7-A541 
        5.19       123.85        23.21        41.56        30.67        17.39 
TCGA-FD-A3B6 TCGA-G2-AA3C TCGA-GU-A42Q TCGA-GU-A767 TCGA-GV-A3JZ TCGA-H4-A2HO 
       33.04         6.94        11.31         4.73        19.82         1.51 
TCGA-K4-A3WU TCGA-K4-A5RJ TCGA-S5-A6DX TCGA-SY-A9G5 TCGA-UY-A8OB TCGA-UY-A9PA 
        3.45         1.74         1.84        31.56        65.75        35.24 
TCGA-XF-A9T5 TCGA-XF-AAMG TCGA-ZF-A9R0 
       66.64       110.60        18.64 

$`PARD3 WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        91.63       103.50       105.70         8.35 
TCGA-4Z-AA7M TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7S 
       16.27        44.94        16.83        16.77        17.16        34.98 
TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 
       27.62        49.12         0.62        41.75        51.16        66.54 
TCGA-4Z-AA84 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BL-A13I 
       15.12        10.22        47.80        33.83        40.08         7.33 
TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J 
        2.66         6.74        12.39         6.58        13.15        19.04 
TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T 
       32.84        12.16        17.88        19.50         5.06        14.89 
TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB 
       14.96         5.06         8.35         8.25        17.16        16.18 
TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C 
       20.48         4.67        12.82         9.96        17.56        28.70 
TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-C4-A0F6 
       24.26        28.41         8.98         1.94         2.93        23.01 
TCGA-C4-A0F7 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T 
        2.04         0.46         0.43         0.69        10.95        12.66 
TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA 
       12.46        12.10        12.62        12.26        13.12        12.00 
TCGA-CF-A7I0 TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR 
       12.10        11.87        13.08        12.92         4.90         7.20 
TCGA-CU-A3KJ TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 
        5.46        16.31         1.84        13.58        21.86         2.14 
TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD 
       66.41        18.41        19.00        16.70       130.88       112.44 
TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 
       16.14        17.62        15.62         1.81        10.59         7.79 
TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ 
       87.32         2.20        13.58         7.82         8.22        17.72 
TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY 
       50.27        21.30         9.67        20.81        10.55       140.81 
TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 
       48.00        17.98        64.18        76.60        67.36        15.68 
TCGA-DK-A6B5 TCGA-DK-AA6L TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6S TCGA-DK-AA6T 
       41.06        38.24        15.02        13.58       166.03        12.36 
TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA76 
       10.49         8.65         7.53        13.64        43.50        12.03 
TCGA-DK-AA77 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 
       10.62        43.59        15.35        38.83        24.66         0.10 
TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 
        0.49         2.24        16.70         0.56         0.66        14.56 
TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7DV TCGA-E7-A7PW 
       13.97        12.99        14.33         0.92         1.22        13.68 
TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 
       14.07        12.95        14.37         8.09        32.02        16.77 
TCGA-FD-A3B5 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA 
        8.94         4.01        12.62        22.52        27.98        60.66 
TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP 
       24.30        23.41        17.98        29.16         5.52        25.74 
TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S 
       46.78        19.79        12.85        22.98        27.35        14.96 
TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU 
       20.91         3.62        26.73        53.88        11.01        19.33 
TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 
        5.36         5.69         8.25        27.45        18.08        58.92 
TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB 
        2.70         7.10         6.28        13.35        62.86        18.81 
TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH 
        6.15        12.69        12.36         2.27         3.06         4.31 
TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF 
        9.67        10.85        31.07         7.13        10.65        17.23 
TCGA-FJ-A871 TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EC TCGA-G2-A2EF TCGA-G2-A2EJ 
        8.94         3.25         6.48        22.88        61.94        30.61 
TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE 
       15.95        26.93        35.24        33.01         7.23        20.12 
TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 
       17.62        66.02        64.44        19.46        21.40         2.24 
TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS 
       15.81         4.50        15.91        14.07        17.75        24.92 
TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS 
        8.94        13.91         7.73         2.10         3.12        20.98 
TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 
        2.20         7.36        10.92        11.31         7.63        27.09 
TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-AATO TCGA-GU-AATP TCGA-GU-AATQ TCGA-GV-A3JV 
       20.05         5.62        10.65        32.98         7.00        14.27 
TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK 
       21.34        19.10        20.28         8.48        10.59        27.35 
TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF 
        8.58        19.07        22.72        19.40        38.60         3.06 
TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC 
        9.01         8.22        25.02        21.24         2.76         9.14 
TCGA-K4-A54R TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P 
       27.68         9.07        11.70         1.81        15.42         6.38 
TCGA-K4-AAQO TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN 
       11.80        15.32        15.58        13.48        12.23        16.67 
TCGA-R3-A69X TCGA-S5-AA26 TCGA-SY-A9G0 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M 
       14.24         3.75        12.43        17.62        37.05        22.68 
TCGA-UY-A78N TCGA-UY-A78O TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF 
       86.83        76.01        29.56        17.82         4.54         1.64 
TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SJ 
        1.87        17.88        48.62        64.80        79.66         3.22 
TCGA-XF-A9SL TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ 
       66.41        12.76        11.90        23.64        21.04        28.24 
TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T6 TCGA-XF-A9T8 
       26.27        18.90         2.24        16.27         2.10        13.74 
TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ 
       92.98        10.82        11.31        54.90         7.63        71.57 
TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAMZ 
       91.73         2.96         8.32         6.77        98.99        44.32 
TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN5 
       56.48        30.94        61.45        86.30        27.06        75.39 
TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-YF-AA3M 
       18.81         3.88         9.63         0.66        11.97        13.64 
TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R7 
        7.36        21.11        24.13        30.28        27.19        21.86 
TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RG 
       28.41        74.56        13.41         3.48        52.73        52.60 
TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4R TCGA-ZF-AA4T 
       82.49        47.84        20.22         2.89        34.06        19.69 
TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 
        8.61        59.38        60.16        63.02        38.73        35.41 
TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N 
       57.90        19.40         8.52        47.15        19.17         5.52 
TCGA-ZF-AA5P 
       10.13 

  PARD3 MUTATED PARD3 WILD-TYPE 
           1.51            0.10 
  PARD3 MUTATED PARD3 WILD-TYPE 
         123.85          166.03 
  PARD3 MUTATED PARD3 WILD-TYPE 
          19.82           15.42 
[1] "1.5 - 123.8 (19.8)" "0.1 - 166.0 (15.4)"
[1] "hr=" "1.5"
D56V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  PARD3 MUTATED         0        6         8        7
  PARD3 WILD-TYPE       4      111       114      121
D56V3, multiclass
           clus
vv          PARD3 MUTATED PARD3 WILD-TYPE
  STAGE I               0               4
  STAGE II              6             111
  STAGE III             8             114
  STAGE IV              7             121
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1+T2  T3  T4
  PARD3 MUTATED          6   8   6
  PARD3 WILD-TYPE      108 171  46
D56V4, multiclass
          clus
vv         PARD3 MUTATED PARD3 WILD-TYPE
  T0+T1+T2             6             108
  T3                   8             171
  T4                   6              46
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  PARD3 MUTATED    12   4   2   1
  PARD3 WILD-TYPE 201  37  73   7
D56V5, multiclass
    clus
vv   PARD3 MUTATED PARD3 WILD-TYPE
  N0            12             201
  N1             4              37
  N2             2              73
  N3             1               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"
D56V6, binary
                 cls
clus                0   1
  PARD3 MUTATED     8   0
  PARD3 WILD-TYPE 174  10
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PARD3 MUTATED      8    0
  PARD3 WILD-TYPE  174   10
   clus
vv  PARD3 MUTATED PARD3 WILD-TYPE
  0             8             174
  1             0              10
[1] 2 2
[1] FALSE
D56V7, binary
                 cls
clus                0   1
  PARD3 MUTATED     1  20
  PARD3 WILD-TYPE  95 260
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PARD3 MUTATED      1   20
  PARD3 WILD-TYPE   95  260
        clus
vv       PARD3 MUTATED PARD3 WILD-TYPE
  FEMALE             1              95
  MALE              20             260
[1] 2 2
[1] FALSE
D56V8, continuous
D56V9, continuous
D56V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PARD3 MUTATED       0                         0    21
  PARD3 WILD-TYPE    38                        21   280
D56V11, multiclass
                           clus
vv                          PARD3 MUTATED PARD3 WILD-TYPE
  ASIAN                                 0              38
  BLACK OR AFRICAN AMERICAN             0              21
  WHITE                                21             280
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V12, binary
                 cls
clus                0   1
  PARD3 MUTATED     2  19
  PARD3 WILD-TYPE   6 319
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PARD3 MUTATED      2   19
  PARD3 WILD-TYPE    6  319
                        clus
vv                       PARD3 MUTATED PARD3 WILD-TYPE
  HISPANIC OR LATINO                 2               6
  NOT HISPANIC OR LATINO            19             319
[1] 2 2
[1] FALSE

Clustering(57) Variable = BAP1 MUTATION ANALYSIS
D57V1, survival
                sevent
clus2              0   1
  BAP1 MUTATED     9   5
  BAP1 WILD-TYPE 210 146
  BAP1 MUTATED BAP1 WILD-TYPE 
            14            356 
  BAP1 MUTATED BAP1 WILD-TYPE 
             5            146 
$`BAP1 MUTATED`
TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-CU-A0YR TCGA-DK-A1A5 TCGA-DK-A3X2 TCGA-DK-A6AV 
       47.80        33.83         7.20         2.14        17.98        64.18 
TCGA-FJ-A3Z7 TCGA-GC-A3RB TCGA-HQ-A2OE TCGA-K4-A54R TCGA-UY-A78K TCGA-UY-A78M 
       31.07         4.50        38.60        27.68        17.62        22.68 
TCGA-XF-A8HI TCGA-XF-A9T0 
       17.88        26.27 

$`BAP1 WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        91.63       103.50       105.70         8.35 
TCGA-4Z-AA7M TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7S 
       16.27        44.94        16.83        16.77        17.16        34.98 
TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 
       27.62        49.12         0.62        41.75        51.16        66.54 
TCGA-4Z-AA84 TCGA-4Z-AA86 TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM 
       15.12        10.22        40.08         7.33         2.66         6.74 
TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O 
       12.39         6.58        13.15        19.04        32.84        12.16 
TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20V 
       17.88        19.50         5.06        14.89        14.96         5.06 
TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH 
        8.35         8.25        17.16        16.18        20.48         4.67 
TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E TCGA-BT-A42F 
       12.82         9.96        17.56        28.70        24.26        28.41 
TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-C4-A0F6 TCGA-C4-A0F7 TCGA-CF-A1HR 
        8.98         1.94         2.93        23.01         2.04         0.46 
TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W 
        0.43         0.69        10.95        12.66        12.46        12.10 
TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A9FF 
       12.62        12.26        13.12        12.00        12.10        11.87 
TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL 
       13.08        12.92         4.90         5.46         5.19        16.31 
TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA 
        1.84        13.58        21.86        66.41        18.41        19.00 
TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG 
       16.70       130.88       112.44        16.14        17.62        15.62 
TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK 
        1.81        10.59         7.79       123.85        87.32         2.20 
TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT 
       13.58         7.82         8.22        17.72        50.27        21.30 
TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 
       23.21         9.67        20.81        10.55       140.81        48.00 
TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 
       41.56        76.60        67.36        15.68        41.06        30.67 
TCGA-DK-AA6L TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6U 
       38.24        15.02        13.58       166.03        12.36        10.49 
TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA76 TCGA-DK-AA77 
        8.65         7.53        13.64        43.50        12.03        10.62 
TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ 
       43.59        15.35        38.83        24.66         0.10         0.49 
TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 
        2.24        16.70        17.39         0.56         0.66        14.56 
TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7DV TCGA-E7-A7PW 
       13.97        12.99        14.33         0.92         1.22        13.68 
TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 
       14.07        12.95        14.37         8.09        32.02        16.77 
TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 
        8.94        33.04         4.01        12.62        22.52        27.98 
TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO 
       60.66        24.30        23.41        17.98        29.16         5.52 
TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P 
       25.74        46.78        19.79        12.85        22.98        27.35 
TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT 
       14.96        20.91         3.62        26.73        53.88        11.01 
TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 
       19.33         5.36         5.69         8.25        27.45        18.08 
TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA 
       58.92         2.70         7.10         6.28        13.35        62.86 
TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TG 
       18.81         6.15        12.69        12.36         2.27         3.06 
TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF 
        4.31         9.67        10.85         7.13        10.65        17.23 
TCGA-FJ-A871 TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EC TCGA-G2-A2EF TCGA-G2-A2EJ 
        8.94         3.25         6.48        22.88        61.94        30.61 
TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE 
       15.95        26.93        35.24        33.01         7.23        20.12 
TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3BM 
       17.62        66.02         6.94        64.44        19.46        21.40 
TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS 
        2.24        15.81        15.91        14.07        17.75        24.92 
TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS 
        8.94        13.91         7.73         2.10         3.12        20.98 
TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 
        2.20         7.36        10.92        11.31        11.31         7.63 
TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATO TCGA-GU-AATP 
       27.09        20.05         5.62         4.73        10.65        32.98 
TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF 
        7.00        14.27        21.34        19.10        19.82        20.28 
TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA 
        8.48        10.59        27.35         8.58        19.07        22.72 
TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS 
        1.51        19.40         3.06         9.01         8.22        25.02 
TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A5RH TCGA-K4-A5RI 
        3.45        21.24         2.76         9.14         9.07        11.70 
TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO TCGA-LC-A66R 
        1.74         1.81        15.42         6.38        11.80        15.32 
TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX 
       15.58        13.48        12.23        16.67        14.24         1.84 
TCGA-S5-AA26 TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78L TCGA-UY-A78N TCGA-UY-A78O 
        3.75        12.43        31.56        37.05        86.83        76.01 
TCGA-UY-A8OB TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF 
       65.75        35.24        29.56        17.82         4.54         1.64 
TCGA-XF-A8HH TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SL 
        1.87        48.62        64.80        79.66         3.22        66.41 
TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T2 
       12.76        11.90        23.64        21.04        28.24        18.90 
TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAME 
        2.24        16.27        66.64         2.10        13.74        92.98 
TCGA-XF-AAMF TCGA-XF-AAMG TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ 
       10.82       110.60        11.31        54.90         7.63        71.57 
TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAMZ 
       91.73         2.96         8.32         6.77        98.99        44.32 
TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN5 
       56.48        30.94        61.45        86.30        27.06        75.39 
TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-YF-AA3M 
       18.81         3.88         9.63         0.66        11.97        13.64 
TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R5 
       18.64         7.36        21.11        24.13        30.28        27.19 
TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RF 
       21.86        28.41        74.56        13.41         3.48        52.73 
TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4R 
       52.60        82.49        47.84        20.22         2.89        34.06 
TCGA-ZF-AA4T TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA51 
       19.69         8.61        59.38        60.16        63.02        38.73 
TCGA-ZF-AA52 TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H 
       35.41        57.90        19.40         8.52        47.15        19.17 
TCGA-ZF-AA5N TCGA-ZF-AA5P 
        5.52        10.13 

  BAP1 MUTATED BAP1 WILD-TYPE 
          2.14           0.10 
  BAP1 MUTATED BAP1 WILD-TYPE 
         64.18         166.03 
  BAP1 MUTATED BAP1 WILD-TYPE 
        24.475         15.335 
[1] "2.1 - 64.2 (24.5)"  "0.1 - 166.0 (15.3)"
[1] "hr=" "1.4"
D57V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  BAP1 MUTATED         0        3         3        7
  BAP1 WILD-TYPE       4      114       119      121
D57V3, multiclass
           clus
vv          BAP1 MUTATED BAP1 WILD-TYPE
  STAGE I              0              4
  STAGE II             3            114
  STAGE III            3            119
  STAGE IV             7            121
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1+T2  T3  T4
  BAP1 MUTATED          7   3   3
  BAP1 WILD-TYPE      107 176  49
D57V4, multiclass
          clus
vv         BAP1 MUTATED BAP1 WILD-TYPE
  T0+T1+T2            7            107
  T3                  3            176
  T4                  3             49
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  BAP1 MUTATED     7   0   7   0
  BAP1 WILD-TYPE 206  41  68   8
D57V5, multiclass
    clus
vv   BAP1 MUTATED BAP1 WILD-TYPE
  N0            7            206
  N1            0             41
  N2            7             68
  N3            0              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"
D57V6, binary
                cls
clus               0   1
  BAP1 MUTATED     7   0
  BAP1 WILD-TYPE 175  10
[1] "tbl2"
                cls
clus             [,1] [,2]
  BAP1 MUTATED      7    0
  BAP1 WILD-TYPE  175   10
   clus
vv  BAP1 MUTATED BAP1 WILD-TYPE
  0            7            175
  1            0             10
[1] 2 2
[1] FALSE
D57V7, binary
                cls
clus               0   1
  BAP1 MUTATED     3  11
  BAP1 WILD-TYPE  93 269
[1] "tbl2"
                cls
clus             [,1] [,2]
  BAP1 MUTATED      3   11
  BAP1 WILD-TYPE   93  269
        clus
vv       BAP1 MUTATED BAP1 WILD-TYPE
  FEMALE            3             93
  MALE             11            269
[1] 2 2
[1] FALSE
D57V8, continuous
D57V9, continuous
D57V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  BAP1 MUTATED       2                         1    10
  BAP1 WILD-TYPE    36                        20   291
D57V11, multiclass
                           clus
vv                          BAP1 MUTATED BAP1 WILD-TYPE
  ASIAN                                2             36
  BLACK OR AFRICAN AMERICAN            1             20
  WHITE                               10            291
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V12, binary
                cls
clus               0   1
  BAP1 MUTATED     0  11
  BAP1 WILD-TYPE   8 327
[1] "tbl2"
                cls
clus             [,1] [,2]
  BAP1 MUTATED      0   11
  BAP1 WILD-TYPE    8  327
                        clus
vv                       BAP1 MUTATED BAP1 WILD-TYPE
  HISPANIC OR LATINO                0              8
  NOT HISPANIC OR LATINO           11            327
[1] 2 2
[1] FALSE

Clustering(58) Variable = RIPK4 MUTATION ANALYSIS
D58V1, survival
                 sevent
clus2               0   1
  RIPK4 MUTATED    10   7
  RIPK4 WILD-TYPE 209 144
  RIPK4 MUTATED RIPK4 WILD-TYPE 
             17             353 
  RIPK4 MUTATED RIPK4 WILD-TYPE 
              7             144 
$`RIPK4 MUTATED`
TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-DK-A6B2 TCGA-E7-A4IJ TCGA-FD-A3SJ TCGA-FD-A5BV 
       49.12         0.62        15.68         0.49        24.30         5.36 
TCGA-FD-A6TG TCGA-FJ-A3Z7 TCGA-G2-A2EO TCGA-G2-A3VY TCGA-GC-A3BM TCGA-GU-A42Q 
        3.06        31.07        35.24        17.62        21.40        11.31 
TCGA-GV-A6ZA TCGA-UY-A78M TCGA-XF-A9T3 TCGA-YC-A8S6 TCGA-ZF-A9R0 
       22.72        22.68         2.24         9.63        18.64 

$`RIPK4 WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        91.63       103.50       105.70         8.35 
TCGA-4Z-AA7M TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7S 
       16.27        44.94        16.83        16.77        17.16        34.98 
TCGA-4Z-AA7W TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA84 TCGA-4Z-AA86 
       27.62        41.75        51.16        66.54        15.12        10.22 
TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM 
       47.80        33.83        40.08         7.33         2.66         6.74 
TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O 
       12.39         6.58        13.15        19.04        32.84        12.16 
TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20V 
       17.88        19.50         5.06        14.89        14.96         5.06 
TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH 
        8.35         8.25        17.16        16.18        20.48         4.67 
TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E TCGA-BT-A42F 
       12.82         9.96        17.56        28.70        24.26        28.41 
TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-C4-A0F6 TCGA-C4-A0F7 TCGA-CF-A1HR 
        8.98         1.94         2.93        23.01         2.04         0.46 
TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W 
        0.43         0.69        10.95        12.66        12.46        12.10 
TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A9FF 
       12.62        12.26        13.12        12.00        12.10        11.87 
TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3QU 
       13.08        12.92         4.90         7.20         5.46         5.19 
TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 
       16.31         1.84        13.58        21.86         2.14        66.41 
TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE 
       18.41        19.00        16.70       130.88       112.44        16.14 
TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 
       17.62        15.62         1.81        10.59         7.79       123.85 
TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ 
       87.32         2.20        13.58         7.82         8.22        17.72 
TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX 
       50.27        21.30        23.21         9.67        20.81        10.55 
TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 
      140.81        48.00        17.98        64.18        41.56        76.60 
TCGA-DK-A6B1 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6P TCGA-DK-AA6Q 
       67.36        41.06        30.67        38.24        15.02        13.58 
TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA71 
      166.03        12.36        10.49         8.65         7.53        13.64 
TCGA-DK-AA74 TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E5-A4U1 
       43.50        12.03        10.62        43.59        15.35        38.83 
TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KE 
       24.66         0.10         2.24        16.70        17.39         0.56 
TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DU 
        0.66        14.56        13.97        12.99        14.33         0.92 
TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A97P TCGA-E7-A97Q 
        1.22        13.68        14.07        12.95        14.37         8.09 
TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 
       32.02        16.77         8.94        33.04         4.01        12.62 
TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN 
       22.52        27.98        60.66        23.41        17.98        29.16 
TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N 
        5.52        25.74        46.78        19.79        12.85        22.98 
TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS 
       27.35        14.96        20.91         3.62        26.73        53.88 
TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 
       11.01        19.33         5.69         8.25        27.45        18.08 
TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA 
       58.92         2.70         7.10         6.28        13.35        62.86 
TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TH 
       18.81         6.15        12.69        12.36         2.27         4.31 
TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FJ-A871 
        9.67        10.85         7.13        10.65        17.23         8.94 
TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EC TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK 
        3.25         6.48        22.88        61.94        30.61        15.95 
TCGA-G2-A2EL TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3B TCGA-G2-AA3C 
       26.93        33.01         7.23        20.12        66.02         6.94 
TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC 
       64.44        19.46         2.24        15.81         4.50        15.91 
TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 
       14.07        17.75        24.92         8.94        13.91         7.73 
TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42P 
        2.10         3.12        20.98         2.20         7.36        10.92 
TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 
       11.31         7.63        27.09        20.05         5.62         4.73 
TCGA-GU-AATO TCGA-GU-AATP TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX 
       10.65        32.98         7.00        14.27        21.34        19.10 
TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E 
       19.82        20.28         8.48        10.59        27.35         8.58 
TCGA-GV-A40G TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND 
       19.07         1.51        19.40        38.60         3.06         9.01 
TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC 
        8.22        25.02         3.45        21.24         2.76         9.14 
TCGA-K4-A54R TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB 
       27.68         9.07        11.70         1.74         1.81        15.42 
TCGA-K4-A83P TCGA-K4-AAQO TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI 
        6.38        11.80        15.32        15.58        13.48        12.23 
TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 TCGA-SY-A9G0 TCGA-SY-A9G5 
       16.67        14.24         1.84         3.75        12.43        31.56 
TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78N TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A9PA 
       17.62        37.05        86.83        76.01        65.75        35.24 
TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HH TCGA-XF-A8HI 
       29.56        17.82         4.54         1.64         1.87        17.88 
TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SL TCGA-XF-A9SV 
       48.62        64.80        79.66         3.22        66.41        12.76 
TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 
       11.90        23.64        21.04        28.24        26.27        18.90 
TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMF 
       16.27        66.64         2.10        13.74        92.98        10.82 
TCGA-XF-AAMG TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR 
      110.60        11.31        54.90         7.63        71.57        91.73 
TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN0 
        2.96         8.32         6.77        98.99        44.32        56.48 
TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN7 
       30.94        61.45        86.30        27.06        75.39        18.81 
TCGA-XF-AAN8 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R1 TCGA-ZF-A9R2 
        3.88         0.66        11.97        13.64         7.36        21.11 
TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RC 
       24.13        30.28        27.19        21.86        28.41        74.56 
TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-A9RM 
       13.41         3.48        52.73        52.60        82.49        47.84 
TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4U TCGA-ZF-AA4V 
       20.22         2.89        34.06        19.69         8.61        59.38 
TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA53 TCGA-ZF-AA54 
       60.16        63.02        38.73        35.41        57.90        19.40 
TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-ZF-AA5P 
        8.52        47.15        19.17         5.52        10.13 

  RIPK4 MUTATED RIPK4 WILD-TYPE 
           0.49            0.10 
  RIPK4 MUTATED RIPK4 WILD-TYPE 
          49.12          166.03 
  RIPK4 MUTATED RIPK4 WILD-TYPE 
          17.62           15.58 
[1] "0.5 - 49.1 (17.6)"  "0.1 - 166.0 (15.6)"
[1] "hr=" "1.2"
D58V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  RIPK4 MUTATED         0        7         4        6
  RIPK4 WILD-TYPE       4      110       118      122
D58V3, multiclass
           clus
vv          RIPK4 MUTATED RIPK4 WILD-TYPE
  STAGE I               0               4
  STAGE II              7             110
  STAGE III             4             118
  STAGE IV              6             122
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1+T2  T3  T4
  RIPK4 MUTATED          8   7   1
  RIPK4 WILD-TYPE      106 172  51
D58V4, multiclass
          clus
vv         RIPK4 MUTATED RIPK4 WILD-TYPE
  T0+T1+T2             8             106
  T3                   7             172
  T4                   1              51
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  RIPK4 MUTATED     8   1   5   0
  RIPK4 WILD-TYPE 205  40  70   8
D58V5, multiclass
    clus
vv   RIPK4 MUTATED RIPK4 WILD-TYPE
  N0             8             205
  N1             1              40
  N2             5              70
  N3             0               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"
D58V6, binary
                 cls
clus                0   1
  RIPK4 MUTATED     8   0
  RIPK4 WILD-TYPE 174  10
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RIPK4 MUTATED      8    0
  RIPK4 WILD-TYPE  174   10
   clus
vv  RIPK4 MUTATED RIPK4 WILD-TYPE
  0             8             174
  1             0              10
[1] 2 2
[1] FALSE
D58V7, binary
                 cls
clus                0   1
  RIPK4 MUTATED     3  14
  RIPK4 WILD-TYPE  93 266
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RIPK4 MUTATED      3   14
  RIPK4 WILD-TYPE   93  266
        clus
vv       RIPK4 MUTATED RIPK4 WILD-TYPE
  FEMALE             3              93
  MALE              14             266
[1] 2 2
[1] FALSE
D58V8, continuous
D58V9, continuous
D58V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RIPK4 MUTATED       3                         0    14
  RIPK4 WILD-TYPE    35                        21   287
D58V11, multiclass
                           clus
vv                          RIPK4 MUTATED RIPK4 WILD-TYPE
  ASIAN                                 3              35
  BLACK OR AFRICAN AMERICAN             0              21
  WHITE                                14             287
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V12, binary
                 cls
clus                0   1
  RIPK4 MUTATED     0  15
  RIPK4 WILD-TYPE   8 323
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RIPK4 MUTATED      0   15
  RIPK4 WILD-TYPE    8  323
                        clus
vv                       RIPK4 MUTATED RIPK4 WILD-TYPE
  HISPANIC OR LATINO                 0               8
  NOT HISPANIC OR LATINO            15             323
[1] 2 2
[1] FALSE

Clustering(59) Variable = TMCO4 MUTATION ANALYSIS
D59V1, survival
                 sevent
clus2               0   1
  TMCO4 MUTATED     8   3
  TMCO4 WILD-TYPE 211 148
  TMCO4 MUTATED TMCO4 WILD-TYPE 
             11             359 
  TMCO4 MUTATED TMCO4 WILD-TYPE 
              3             148 
$`TMCO4 MUTATED`
TCGA-2F-A9KR TCGA-4Z-AA7O TCGA-E5-A4U1 TCGA-E7-A4IJ TCGA-E7-A5KF TCGA-E7-A7DU 
      103.50        16.83        38.83         0.49         0.66         0.92 
TCGA-H4-A2HQ TCGA-HQ-A5ND TCGA-MV-A51V TCGA-XF-AAML TCGA-XF-AAN0 
       19.40         9.01        13.48         7.63        56.48 

$`TMCO4 WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KT TCGA-2F-A9KW TCGA-4Z-AA7M 
       22.29        11.97        91.63       105.70         8.35        16.27 
TCGA-4Z-AA7N TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7W TCGA-4Z-AA7Y 
       44.94        16.77        17.16        34.98        27.62        49.12 
TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA84 TCGA-4Z-AA86 
        0.62        41.75        51.16        66.54        15.12        10.22 
TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM 
       47.80        33.83        40.08         7.33         2.66         6.74 
TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O 
       12.39         6.58        13.15        19.04        32.84        12.16 
TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20V 
       17.88        19.50         5.06        14.89        14.96         5.06 
TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH 
        8.35         8.25        17.16        16.18        20.48         4.67 
TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E TCGA-BT-A42F 
       12.82         9.96        17.56        28.70        24.26        28.41 
TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-C4-A0F6 TCGA-C4-A0F7 TCGA-CF-A1HR 
        8.98         1.94         2.93        23.01         2.04         0.46 
TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W 
        0.43         0.69        10.95        12.66        12.46        12.10 
TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A9FF 
       12.62        12.26        13.12        12.00        12.10        11.87 
TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3QU 
       13.08        12.92         4.90         7.20         5.46         5.19 
TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 
       16.31         1.84        13.58        21.86         2.14        66.41 
TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE 
       18.41        19.00        16.70       130.88       112.44        16.14 
TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 
       17.62        15.62         1.81        10.59         7.79       123.85 
TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ 
       87.32         2.20        13.58         7.82         8.22        17.72 
TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX 
       50.27        21.30        23.21         9.67        20.81        10.55 
TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 
      140.81        48.00        17.98        64.18        41.56        76.60 
TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6P 
       67.36        15.68        41.06        30.67        38.24        15.02 
TCGA-DK-AA6Q TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA6X 
       13.58       166.03        12.36        10.49         8.65         7.53 
TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A2PC TCGA-E5-A4TZ 
       13.64        43.50        12.03        10.62        43.59        15.35 
TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KE 
       24.66         0.10         2.24        16.70        17.39         0.56 
TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DV TCGA-E7-A7PW 
       14.56        13.97        12.99        14.33         1.22        13.68 
TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 
       14.07        12.95        14.37         8.09        32.02        16.77 
TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 
        8.94        33.04         4.01        12.62        22.52        27.98 
TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO 
       60.66        24.30        23.41        17.98        29.16         5.52 
TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P 
       25.74        46.78        19.79        12.85        22.98        27.35 
TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT 
       14.96        20.91         3.62        26.73        53.88        11.01 
TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 
       19.33         5.36         5.69         8.25        27.45        18.08 
TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA 
       58.92         2.70         7.10         6.28        13.35        62.86 
TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TG 
       18.81         6.15        12.69        12.36         2.27         3.06 
TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE 
        4.31         9.67        10.85        31.07         7.13        10.65 
TCGA-FJ-A3ZF TCGA-FJ-A871 TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EC TCGA-G2-A2EF 
       17.23         8.94         3.25         6.48        22.88        61.94 
TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB 
       30.61        15.95        26.93        35.24        33.01         7.23 
TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3D TCGA-G2-AA3F 
       20.12        17.62        66.02         6.94        64.44        19.46 
TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD 
       21.40         2.24        15.81         4.50        15.91        14.07 
TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP 
       17.75        24.92         8.94        13.91         7.73         2.10 
TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42Q 
        3.12        20.98         2.20         7.36        10.92        11.31 
TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 
       11.31         7.63        27.09        20.05         5.62         4.73 
TCGA-GU-AATO TCGA-GU-AATP TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX 
       10.65        32.98         7.00        14.27        21.34        19.10 
TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E 
       19.82        20.28         8.48        10.59        27.35         8.58 
TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5NE 
       19.07        22.72         1.51        38.60         3.06         8.22 
TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R 
       25.02         3.45        21.24         2.76         9.14        27.68 
TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P 
        9.07        11.70         1.74         1.81        15.42         6.38 
TCGA-K4-AAQO TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X 
       11.80        15.32        15.58        12.23        16.67        14.24 
TCGA-S5-A6DX TCGA-S5-AA26 TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L 
        1.84         3.75        12.43        31.56        17.62        37.05 
TCGA-UY-A78M TCGA-UY-A78N TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A9PA TCGA-UY-A9PB 
       22.68        86.83        76.01        65.75        35.24        29.56 
TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG 
       17.82         4.54         1.64         1.87        17.88        48.62 
TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SL TCGA-XF-A9SV TCGA-XF-A9SW 
       64.80        79.66         3.22        66.41        12.76        11.90 
TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 
       23.64        21.04        28.24        26.27        18.90         2.24 
TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMF 
       16.27        66.64         2.10        13.74        92.98        10.82 
TCGA-XF-AAMG TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMT 
      110.60        11.31        54.90        71.57        91.73         2.96 
TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN1 TCGA-XF-AAN2 
        8.32         6.77        98.99        44.32        30.94        61.45 
TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 
       86.30        27.06        75.39        18.81         3.88         9.63 
TCGA-YC-A9TC TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R2 
        0.66        11.97        13.64        18.64         7.36        21.11 
TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RC 
       24.13        30.28        27.19        21.86        28.41        74.56 
TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-A9RM 
       13.41         3.48        52.73        52.60        82.49        47.84 
TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4U TCGA-ZF-AA4V 
       20.22         2.89        34.06        19.69         8.61        59.38 
TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA53 TCGA-ZF-AA54 
       60.16        63.02        38.73        35.41        57.90        19.40 
TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-ZF-AA5P 
        8.52        47.15        19.17         5.52        10.13 

  TMCO4 MUTATED TMCO4 WILD-TYPE 
           0.49            0.10 
  TMCO4 MUTATED TMCO4 WILD-TYPE 
         103.50          166.03 
  TMCO4 MUTATED TMCO4 WILD-TYPE 
          13.48           15.68 
[1] "0.5 - 103.5 (13.5)" "0.1 - 166.0 (15.7)"
[1] "hr=" "1.4"
D59V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  TMCO4 MUTATED         0        5         3        3
  TMCO4 WILD-TYPE       4      112       119      125
D59V3, multiclass
           clus
vv          TMCO4 MUTATED TMCO4 WILD-TYPE
  STAGE I               0               4
  STAGE II              5             112
  STAGE III             3             119
  STAGE IV              3             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"
                 vv
clus              T0+T1+T2  T3  T4
  TMCO4 MUTATED          5   4   1
  TMCO4 WILD-TYPE      109 175  51
D59V4, multiclass
          clus
vv         TMCO4 MUTATED TMCO4 WILD-TYPE
  T0+T1+T2             5             109
  T3                   4             175
  T4                   1              51
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  TMCO4 MUTATED     7   1   1   0
  TMCO4 WILD-TYPE 206  40  74   8
D59V5, multiclass
    clus
vv   TMCO4 MUTATED TMCO4 WILD-TYPE
  N0             7             206
  N1             1              40
  N2             1              74
  N3             0               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"
D59V6, binary
                 cls
clus                0   1
  TMCO4 MUTATED     9   1
  TMCO4 WILD-TYPE 173   9
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TMCO4 MUTATED      9    1
  TMCO4 WILD-TYPE  173    9
   clus
vv  TMCO4 MUTATED TMCO4 WILD-TYPE
  0             9             173
  1             1               9
[1] 2 2
[1] FALSE
D59V7, binary
                 cls
clus                0   1
  TMCO4 MUTATED     2   9
  TMCO4 WILD-TYPE  94 271
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TMCO4 MUTATED      2    9
  TMCO4 WILD-TYPE   94  271
        clus
vv       TMCO4 MUTATED TMCO4 WILD-TYPE
  FEMALE             2              94
  MALE               9             271
[1] 2 2
[1] FALSE
D59V8, continuous
D59V9, continuous
D59V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TMCO4 MUTATED       2                         2     4
  TMCO4 WILD-TYPE    36                        19   297
D59V11, multiclass
                           clus
vv                          TMCO4 MUTATED TMCO4 WILD-TYPE
  ASIAN                                 2              36
  BLACK OR AFRICAN AMERICAN             2              19
  WHITE                                 4             297
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V12, binary
                 cls
clus                0   1
  TMCO4 MUTATED     0   8
  TMCO4 WILD-TYPE   8 330
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TMCO4 MUTATED      0    8
  TMCO4 WILD-TYPE    8  330
                        clus
vv                       TMCO4 MUTATED TMCO4 WILD-TYPE
  HISPANIC OR LATINO                 0               8
  NOT HISPANIC OR LATINO             8             330
[1] 2 2
[1] FALSE

Clustering(60) Variable = CDH1 MUTATION ANALYSIS
D60V1, survival
                sevent
clus2              0   1
  CDH1 MUTATED     8   5
  CDH1 WILD-TYPE 211 146
  CDH1 MUTATED CDH1 WILD-TYPE 
            13            357 
  CDH1 MUTATED CDH1 WILD-TYPE 
             5            146 
$`CDH1 MUTATED`
TCGA-C4-A0F0 TCGA-DK-A1AG TCGA-DK-A6AW TCGA-DK-AA6Q TCGA-G2-A3IE TCGA-G2-AA3D 
        1.94        15.62        41.56        13.58        20.12        64.44 
TCGA-GC-A3I6 TCGA-H4-A2HQ TCGA-HQ-A2OF TCGA-XF-A9SL TCGA-XF-A9SX TCGA-XF-A9T3 
        2.24        19.40         3.06        66.41        23.64         2.24 
TCGA-XF-AAN0 
       56.48 

$`CDH1 WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        91.63       103.50       105.70         8.35 
TCGA-4Z-AA7M TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7S 
       16.27        44.94        16.83        16.77        17.16        34.98 
TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 
       27.62        49.12         0.62        41.75        51.16        66.54 
TCGA-4Z-AA84 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BL-A13I 
       15.12        10.22        47.80        33.83        40.08         7.33 
TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J 
        2.66         6.74        12.39         6.58        13.15        19.04 
TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T 
       32.84        12.16        17.88        19.50         5.06        14.89 
TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB 
       14.96         5.06         8.35         8.25        17.16        16.18 
TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C 
       20.48         4.67        12.82         9.96        17.56        28.70 
TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F1 TCGA-C4-A0F6 TCGA-C4-A0F7 
       24.26        28.41         8.98         2.93        23.01         2.04 
TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V 
        0.46         0.43         0.69        10.95        12.66        12.46 
TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 
       12.10        12.62        12.26        13.12        12.00        12.10 
TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ 
       11.87        13.08        12.92         4.90         7.20         5.46 
TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 
        5.19        16.31         1.84        13.58        21.86         2.14 
TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD 
       66.41        18.41        19.00        16.70       130.88       112.44 
TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 
       16.14        17.62         1.81        10.59         7.79       123.85 
TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ 
       87.32         2.20        13.58         7.82         8.22        17.72 
TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX 
       50.27        21.30        23.21         9.67        20.81        10.55 
TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6B0 TCGA-DK-A6B1 
      140.81        48.00        17.98        64.18        76.60        67.36 
TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6P TCGA-DK-AA6S 
       15.68        41.06        30.67        38.24        15.02       166.03 
TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA74 
       12.36        10.49         8.65         7.53        13.64        43.50 
TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 
       12.03        10.62        43.59        15.35        38.83        24.66 
TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KE 
        0.10         0.49         2.24        16.70        17.39         0.56 
TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DU 
        0.66        14.56        13.97        12.99        14.33         0.92 
TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A97P TCGA-E7-A97Q 
        1.22        13.68        14.07        12.95        14.37         8.09 
TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 
       32.02        16.77         8.94        33.04         4.01        12.62 
TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM 
       22.52        27.98        60.66        24.30        23.41        17.98 
TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS 
       29.16         5.52        25.74        46.78        19.79        12.85 
TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BR 
       22.98        27.35        14.96        20.91         3.62        26.73 
TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY 
       53.88        11.01        19.33         5.36         5.69         8.25 
TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P 
       27.45        18.08        58.92         2.70         7.10         6.28 
TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE 
       13.35        62.86        18.81         6.15        12.69        12.36 
TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z7 
        2.27         3.06         4.31         9.67        10.85        31.07 
TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FJ-A871 TCGA-FT-A3EE TCGA-FT-A61P 
        7.13        10.65        17.23         8.94         3.25         6.48 
TCGA-G2-A2EC TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO 
       22.88        61.94        30.61        15.95        26.93        35.24 
TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3F 
       33.01         7.23        17.62        66.02         6.94        19.46 
TCGA-GC-A3BM TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC 
       21.40        15.81         4.50        15.91        14.07        17.75 
TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ 
       24.92         8.94        13.91         7.73         2.10         3.12 
TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R 
       20.98         2.20         7.36        10.92        11.31        11.31 
TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATO 
        7.63        27.09        20.05         5.62         4.73        10.65 
TCGA-GU-AATP TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ 
       32.98         7.00        14.27        21.34        19.10        19.82 
TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G 
       20.28         8.48        10.59        27.35         8.58        19.07 
TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-HQ-A2OE TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS 
       22.72         1.51        38.60         9.01         8.22        25.02 
TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RH 
        3.45        21.24         2.76         9.14        27.68         9.07 
TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO 
       11.70         1.74         1.81        15.42         6.38        11.80 
TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X 
       15.32        15.58        13.48        12.23        16.67        14.24 
TCGA-S5-A6DX TCGA-S5-AA26 TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L 
        1.84         3.75        12.43        31.56        17.62        37.05 
TCGA-UY-A78M TCGA-UY-A78N TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A9PA TCGA-UY-A9PB 
       22.68        86.83        76.01        65.75        35.24        29.56 
TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG 
       17.82         4.54         1.64         1.87        17.88        48.62 
TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SY 
       64.80        79.66         3.22        12.76        11.90        21.04 
TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 
       28.24        26.27        18.90        16.27        66.64         2.10 
TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMG TCGA-XF-AAMH TCGA-XF-AAMJ 
       13.74        92.98        10.82       110.60        11.31        54.90 
TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX 
        7.63        71.57        91.73         2.96         8.32         6.77 
TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN4 
       98.99        44.32        30.94        61.45        86.30        27.06 
TCGA-XF-AAN5 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L 
       75.39        18.81         3.88         9.63         0.66        11.97 
TCGA-YF-AA3M TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R4 
       13.64        18.64         7.36        21.11        24.13        30.28 
TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RE 
       27.19        21.86        28.41        74.56        13.41         3.48 
TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N 
       52.73        52.60        82.49        47.84        20.22         2.89 
TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA4X 
       34.06        19.69         8.61        59.38        60.16        63.02 
TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 
       38.73        35.41        57.90        19.40         8.52        47.15 
TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-ZF-AA5P 
       19.17         5.52        10.13 

  CDH1 MUTATED CDH1 WILD-TYPE 
          1.94           0.10 
  CDH1 MUTATED CDH1 WILD-TYPE 
         66.41         166.03 
  CDH1 MUTATED CDH1 WILD-TYPE 
         19.40          15.58 
[1] "1.9 - 66.4 (19.4)"  "0.1 - 166.0 (15.6)"
[1] "hr=" "1.2"
D60V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  CDH1 MUTATED         0        3         3        7
  CDH1 WILD-TYPE       4      114       119      121
D60V3, multiclass
           clus
vv          CDH1 MUTATED CDH1 WILD-TYPE
  STAGE I              0              4
  STAGE II             3            114
  STAGE III            3            119
  STAGE IV             7            121
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1+T2  T3  T4
  CDH1 MUTATED          2   8   1
  CDH1 WILD-TYPE      112 171  51
D60V4, multiclass
          clus
vv         CDH1 MUTATED CDH1 WILD-TYPE
  T0+T1+T2            2            112
  T3                  8            171
  T4                  1             51
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  CDH1 MUTATED     5   1   5   0
  CDH1 WILD-TYPE 208  40  70   8
D60V5, multiclass
    clus
vv   CDH1 MUTATED CDH1 WILD-TYPE
  N0            5            208
  N1            1             40
  N2            5             70
  N3            0              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"
D60V6, binary
                cls
clus               0   1
  CDH1 MUTATED     8   1
  CDH1 WILD-TYPE 174   9
[1] "tbl2"
                cls
clus             [,1] [,2]
  CDH1 MUTATED      8    1
  CDH1 WILD-TYPE  174    9
   clus
vv  CDH1 MUTATED CDH1 WILD-TYPE
  0            8            174
  1            1              9
[1] 2 2
[1] FALSE
D60V7, binary
                cls
clus               0   1
  CDH1 MUTATED     5   8
  CDH1 WILD-TYPE  91 272
[1] "tbl2"
                cls
clus             [,1] [,2]
  CDH1 MUTATED      5    8
  CDH1 WILD-TYPE   91  272
        clus
vv       CDH1 MUTATED CDH1 WILD-TYPE
  FEMALE            5             91
  MALE              8            272
[1] 2 2
[1] FALSE
D60V8, continuous
D60V9, continuous
D60V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CDH1 MUTATED       0                         1    10
  CDH1 WILD-TYPE    38                        20   291
D60V11, multiclass
                           clus
vv                          CDH1 MUTATED CDH1 WILD-TYPE
  ASIAN                                0             38
  BLACK OR AFRICAN AMERICAN            1             20
  WHITE                               10            291
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V12, binary
                cls
clus               0   1
  CDH1 MUTATED     0  11
  CDH1 WILD-TYPE   8 327
[1] "tbl2"
                cls
clus             [,1] [,2]
  CDH1 MUTATED      0   11
  CDH1 WILD-TYPE    8  327
                        clus
vv                       CDH1 MUTATED CDH1 WILD-TYPE
  HISPANIC OR LATINO                0              8
  NOT HISPANIC OR LATINO           11            327
[1] 2 2
[1] FALSE

Clustering(61) Variable = NRAS MUTATION ANALYSIS
D61V1, survival
                sevent
clus2              0   1
  NRAS MUTATED     5   2
  NRAS WILD-TYPE 214 149
  NRAS MUTATED NRAS WILD-TYPE 
             7            363 
  NRAS MUTATED NRAS WILD-TYPE 
             2            149 
$`NRAS MUTATED`
TCGA-4Z-AA82 TCGA-BT-A20W TCGA-FD-A43P TCGA-G2-A2EF TCGA-UY-A9PD TCGA-ZF-A9R5 
       51.16         8.35        27.35        61.94        17.82        27.19 
TCGA-ZF-A9RL 
       82.49 

$`NRAS WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        91.63       103.50       105.70         8.35 
TCGA-4Z-AA7M TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7S 
       16.27        44.94        16.83        16.77        17.16        34.98 
TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA83 TCGA-4Z-AA84 
       27.62        49.12         0.62        41.75        66.54        15.12 
TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J 
       10.22        47.80        33.83        40.08         7.33         2.66 
TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N 
        6.74        12.39         6.58        13.15        19.04        32.84 
TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U 
       12.16        17.88        19.50         5.06        14.89        14.96 
TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH 
        5.06         8.25        17.16        16.18        20.48         4.67 
TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E TCGA-BT-A42F 
       12.82         9.96        17.56        28.70        24.26        28.41 
TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-C4-A0F6 TCGA-C4-A0F7 TCGA-CF-A1HR 
        8.98         1.94         2.93        23.01         2.04         0.46 
TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W 
        0.43         0.69        10.95        12.66        12.46        12.10 
TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A9FF 
       12.62        12.26        13.12        12.00        12.10        11.87 
TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3QU 
       13.08        12.92         4.90         7.20         5.46         5.19 
TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 
       16.31         1.84        13.58        21.86         2.14        66.41 
TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE 
       18.41        19.00        16.70       130.88       112.44        16.14 
TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 
       17.62        15.62         1.81        10.59         7.79       123.85 
TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ 
       87.32         2.20        13.58         7.82         8.22        17.72 
TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX 
       50.27        21.30        23.21         9.67        20.81        10.55 
TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 
      140.81        48.00        17.98        64.18        41.56        76.60 
TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6P 
       67.36        15.68        41.06        30.67        38.24        15.02 
TCGA-DK-AA6Q TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA6X 
       13.58       166.03        12.36        10.49         8.65         7.53 
TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A2PC TCGA-E5-A4TZ 
       13.64        43.50        12.03        10.62        43.59        15.35 
TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 
       38.83        24.66         0.10         0.49         2.24        16.70 
TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME 
       17.39         0.56         0.66        14.56        13.97        12.99 
TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H 
       14.33         0.92         1.22        13.68        14.07        12.95 
TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 
       14.37         8.09        32.02        16.77         8.94        33.04 
TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ 
        4.01        12.62        22.52        27.98        60.66        24.30 
TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ 
       23.41        17.98        29.16         5.52        25.74        46.78 
TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X 
       19.79        12.85        22.98        14.96        20.91         3.62 
TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX 
       26.73        53.88        11.01        19.33         5.36         5.69 
TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O 
        8.25        27.45        18.08        58.92         2.70         7.10 
TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD 
        6.28        13.35        62.86        18.81         6.15        12.69 
TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FD-A6TK 
       12.36         2.27         3.06         4.31         9.67        10.85 
TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FJ-A871 TCGA-FT-A3EE 
       31.07         7.13        10.65        17.23         8.94         3.25 
TCGA-FT-A61P TCGA-G2-A2EC TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO 
        6.48        22.88        30.61        15.95        26.93        35.24 
TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3C 
       33.01         7.23        20.12        17.62        66.02         6.94 
TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB 
       64.44        19.46        21.40         2.24        15.81         4.50 
TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GC-A6I3 
       15.91        14.07        17.75        24.92         8.94        13.91 
TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GD-A76B 
        7.73         2.10         3.12        20.98         2.20         7.36 
TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A764 
       10.92        11.31        11.31         7.63        27.09        20.05 
TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATO TCGA-GU-AATP TCGA-GU-AATQ TCGA-GV-A3JV 
        5.62         4.73        10.65        32.98         7.00        14.27 
TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI 
       21.34        19.10        19.82        20.28         8.48        10.59 
TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-H4-A2HQ 
       27.35         8.58        19.07        22.72         1.51        19.40 
TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU 
       38.60         3.06         9.01         8.22        25.02         3.45 
TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RH TCGA-K4-A5RI 
       21.24         2.76         9.14        27.68         9.07        11.70 
TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO TCGA-LC-A66R 
        1.74         1.81        15.42         6.38        11.80        15.32 
TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX 
       15.58        13.48        12.23        16.67        14.24         1.84 
TCGA-S5-AA26 TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M 
        3.75        12.43        31.56        17.62        37.05        22.68 
TCGA-UY-A78N TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PE 
       86.83        76.01        65.75        35.24        29.56         4.54 
TCGA-UY-A9PF TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI 
        1.64         1.87        17.88        48.62        64.80        79.66 
TCGA-XF-A9SJ TCGA-XF-A9SL TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY 
        3.22        66.41        12.76        11.90        23.64        21.04 
TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T5 
       28.24        26.27        18.90         2.24        16.27        66.64 
TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMG TCGA-XF-AAMH 
        2.10        13.74        92.98        10.82       110.60        11.31 
TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMW 
       54.90         7.63        71.57        91.73         2.96         8.32 
TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN2 
        6.77        98.99        44.32        56.48        30.94        61.45 
TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 
       86.30        27.06        75.39        18.81         3.88         9.63 
TCGA-YC-A9TC TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R2 
        0.66        11.97        13.64        18.64         7.36        21.11 
TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RD 
       24.13        30.28        21.86        28.41        74.56        13.41 
TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N 
        3.48        52.73        52.60        47.84        20.22         2.89 
TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA4X 
       34.06        19.69         8.61        59.38        60.16        63.02 
TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 
       38.73        35.41        57.90        19.40         8.52        47.15 
TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-ZF-AA5P 
       19.17         5.52        10.13 

  NRAS MUTATED NRAS WILD-TYPE 
          8.35           0.10 
  NRAS MUTATED NRAS WILD-TYPE 
         82.49         166.03 
  NRAS MUTATED NRAS WILD-TYPE 
         27.35          15.42 
[1] "8.3 - 82.5 (27.4)"  "0.1 - 166.0 (15.4)"
[1] "hr=" "2.3"
D61V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  NRAS MUTATED         0        4         2        1
  NRAS WILD-TYPE       4      113       120      127
D61V3, multiclass
           clus
vv          NRAS MUTATED NRAS WILD-TYPE
  STAGE I              0              4
  STAGE II             4            113
  STAGE III            2            120
  STAGE IV             1            127
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1+T2  T3  T4
  NRAS MUTATED          3   2   0
  NRAS WILD-TYPE      111 177  52
D61V4, multiclass
          clus
vv         NRAS MUTATED NRAS WILD-TYPE
  T0+T1+T2            3            111
  T3                  2            177
  T4                  0             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"
                vv
clus              N0  N1  N2  N3
  NRAS MUTATED     5   1   0   0
  NRAS WILD-TYPE 208  40  75   8
D61V5, multiclass
    clus
vv   NRAS MUTATED NRAS WILD-TYPE
  N0            5            208
  N1            1             40
  N2            0             75
  N3            0              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"
D61V6, binary
                cls
clus               0   1
  NRAS MUTATED     4   0
  NRAS WILD-TYPE 178  10
[1] "tbl2"
                cls
clus             [,1] [,2]
  NRAS MUTATED      4    0
  NRAS WILD-TYPE  178   10
   clus
vv  NRAS MUTATED NRAS WILD-TYPE
  0            4            178
  1            0             10
[1] 2 2
[1] FALSE
D61V7, binary
                cls
clus               0   1
  NRAS MUTATED     0   7
  NRAS WILD-TYPE  96 273
[1] "tbl2"
                cls
clus             [,1] [,2]
  NRAS MUTATED      0    7
  NRAS WILD-TYPE   96  273
        clus
vv       NRAS MUTATED NRAS WILD-TYPE
  FEMALE            0             96
  MALE              7            273
[1] 2 2
[1] FALSE
D61V8, continuous
[1] "Remove cluster labels:" "NRAS MUTATED"          
clus
  NRAS MUTATED NRAS WILD-TYPE 
             1            119 
    TCGA-2F-A9KO     TCGA-2F-A9KP     TCGA-2F-A9KQ     TCGA-2F-A9KR 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-2F-A9KT     TCGA-2F-A9KW     TCGA-CF-A1HS     TCGA-CF-A27C 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-CF-A3MF     TCGA-CF-A3MG     TCGA-CF-A3MH     TCGA-CF-A3MI 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-CF-A47S     TCGA-CF-A47T     TCGA-CF-A47V     TCGA-CF-A47W 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-CF-A47X     TCGA-CF-A47Y     TCGA-CF-A5U8     TCGA-CF-A5UA 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-CF-A7I0     TCGA-DK-A2HX     TCGA-DK-A3IN     TCGA-DK-A3IV 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-DK-A3WX     TCGA-DK-A3X2     TCGA-DK-A6B2     TCGA-DK-A6B5 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-DK-A6B6     TCGA-DK-AA6P     TCGA-DK-AA6S     TCGA-DK-AA6U 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-DK-AA6W     TCGA-DK-AA76     TCGA-E5-A2PC     TCGA-E5-A4TZ 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-E5-A4U1     TCGA-E7-A519     TCGA-E7-A541     TCGA-E7-A7DU 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-E7-A7DV     TCGA-FT-A61P     TCGA-G2-A2EC     TCGA-G2-A2EJ 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-G2-A2EK     TCGA-G2-A2EL     TCGA-G2-A2EO     TCGA-G2-A2ES 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-G2-A3IB     TCGA-G2-A3IE     TCGA-G2-A3VY     TCGA-GC-A3BM 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-GC-A3I6     TCGA-GC-A3OO     TCGA-GC-A3RC     TCGA-GC-A3RD 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-GC-A3YS     TCGA-GC-A6I1     TCGA-GC-A6I3     TCGA-GD-A3OS 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-GD-A6C6     TCGA-GV-A3JV     TCGA-GV-A3JW     TCGA-GV-A3JX 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-GV-A3JZ     TCGA-GV-A3QF     TCGA-GV-A3QH     TCGA-GV-A3QI 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-GV-A3QK     TCGA-GV-A40E     TCGA-GV-A40G     TCGA-GV-A6ZA 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-SY-A9G0     TCGA-SY-A9G5     TCGA-UY-A78L     TCGA-UY-A78M 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-UY-A78N     TCGA-XF-A8HH     TCGA-XF-A8HI     TCGA-XF-A9SG 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-XF-A9SH     TCGA-XF-A9SI     TCGA-XF-A9SJ     TCGA-XF-A9SL 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-XF-A9SV     TCGA-XF-A9SW     TCGA-XF-A9SX     TCGA-XF-A9SY 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-XF-A9SZ     TCGA-XF-A9T0     TCGA-XF-A9T2     TCGA-XF-A9T3 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-XF-A9T4     TCGA-XF-A9T5     TCGA-XF-A9T6     TCGA-XF-A9T8 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-XF-AAME     TCGA-XF-AAMF     TCGA-XF-AAMG     TCGA-XF-AAMH 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-XF-AAMJ     TCGA-XF-AAML     TCGA-XF-AAMQ     TCGA-XF-AAMR 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-XF-AAMT     TCGA-XF-AAMW     TCGA-XF-AAMX     TCGA-XF-AAMY 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-XF-AAMZ     TCGA-XF-AAN0     TCGA-XF-AAN1     TCGA-XF-AAN2 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-XF-AAN3     TCGA-XF-AAN4     TCGA-XF-AAN5     TCGA-XF-AAN7 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-XF-AAN8     TCGA-YF-AA3L     TCGA-YF-AA3M 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
D61V9, continuous
D61V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  NRAS MUTATED       0                         2     5
  NRAS WILD-TYPE    38                        19   296
D61V11, multiclass
                           clus
vv                          NRAS MUTATED NRAS WILD-TYPE
  ASIAN                                0             38
  BLACK OR AFRICAN AMERICAN            2             19
  WHITE                                5            296
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V12, binary
                cls
clus               0   1
  NRAS MUTATED     0   6
  NRAS WILD-TYPE   8 332
[1] "tbl2"
                cls
clus             [,1] [,2]
  NRAS MUTATED      0    6
  NRAS WILD-TYPE    8  332
                        clus
vv                       NRAS MUTATED NRAS WILD-TYPE
  HISPANIC OR LATINO                0              8
  NOT HISPANIC OR LATINO            6            332
[1] 2 2
[1] FALSE

Clustering(62) Variable = ARID1B MUTATION ANALYSIS
D62V1, survival
                  sevent
clus2                0   1
  ARID1B MUTATED    14   7
  ARID1B WILD-TYPE 205 144
  ARID1B MUTATED ARID1B WILD-TYPE 
              21              349 
  ARID1B MUTATED ARID1B WILD-TYPE 
               7              144 
$`ARID1B MUTATED`
TCGA-2F-A9KO TCGA-4Z-AA80 TCGA-BL-A13I TCGA-BT-A3PH TCGA-CU-A0YR TCGA-DK-A1A3 
       22.29         0.62         7.33         4.67         7.20        21.86 
TCGA-DK-A3X1 TCGA-DK-A6AW TCGA-DK-AA74 TCGA-E7-A4IJ TCGA-E7-A541 TCGA-FD-A6TA 
       48.00        41.56        43.50         0.49        17.39        62.86 
TCGA-FD-A6TC TCGA-GU-AATO TCGA-GU-AATP TCGA-XF-AAML TCGA-ZF-A9R4 TCGA-ZF-A9R7 
        6.15        10.65        32.98         7.63        30.28        21.86 
TCGA-ZF-AA4V TCGA-ZF-AA51 TCGA-ZF-AA5N 
       59.38        38.73         5.52 

$`ARID1B WILD-TYPE`
TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW TCGA-4Z-AA7M 
       11.97        91.63       103.50       105.70         8.35        16.27 
TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7W 
       44.94        16.83        16.77        17.16        34.98        27.62 
TCGA-4Z-AA7Y TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA84 TCGA-4Z-AA86 
       49.12        41.75        51.16        66.54        15.12        10.22 
TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ 
       47.80        33.83        40.08         2.66         6.74        12.39 
TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P 
        6.58        13.15        19.04        32.84        12.16        17.88 
TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20W 
       19.50         5.06        14.89        14.96         5.06         8.35 
TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A3PK 
        8.25        17.16        16.18        20.48        12.82         9.96 
TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 
       17.56        28.70        24.26        28.41         8.98         1.94 
TCGA-C4-A0F1 TCGA-C4-A0F6 TCGA-C4-A0F7 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C 
        2.93        23.01         2.04         0.46         0.43         0.69 
TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y 
       10.95        12.66        12.46        12.10        12.62        12.26 
TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A0YN 
       13.12        12.00        12.10        11.87        13.08        12.92 
TCGA-CU-A0YO TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E 
        4.90         5.46         5.19        16.31         1.84        13.58 
TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC 
        2.14        66.41        18.41        19.00        16.70       130.88 
TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 
      112.44        16.14        17.62        15.62         1.81        10.59 
TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM 
        7.79       123.85        87.32         2.20        13.58         7.82 
TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV 
        8.22        17.72        50.27        21.30        23.21         9.67 
TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6B0 
       20.81        10.55       140.81        17.98        64.18        76.60 
TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6P 
       67.36        15.68        41.06        30.67        38.24        15.02 
TCGA-DK-AA6Q TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA6X 
       13.58       166.03        12.36        10.49         8.65         7.53 
TCGA-DK-AA71 TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E5-A4U1 
       13.64        12.03        10.62        43.59        15.35        38.83 
TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KE TCGA-E7-A5KF 
       24.66         0.10         2.24        16.70         0.56         0.66 
TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7DV 
       14.56        13.97        12.99        14.33         0.92         1.22 
TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B3 
       13.68        14.07        12.95        14.37         8.09        32.02 
TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 
       16.77         8.94        33.04         4.01        12.62        22.52 
TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN 
       27.98        60.66        24.30        23.41        17.98        29.16 
TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N 
        5.52        25.74        46.78        19.79        12.85        22.98 
TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS 
       27.35        14.96        20.91         3.62        26.73        53.88 
TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ 
       11.01        19.33         5.36         5.69         8.25        27.45 
TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S 
       18.08        58.92         2.70         7.10         6.28        13.35 
TCGA-FD-A6TB TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH 
       18.81        12.69        12.36         2.27         3.06         4.31 
TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF 
        9.67        10.85        31.07         7.13        10.65        17.23 
TCGA-FJ-A871 TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EC TCGA-G2-A2EF TCGA-G2-A2EJ 
        8.94         3.25         6.48        22.88        61.94        30.61 
TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE 
       15.95        26.93        35.24        33.01         7.23        20.12 
TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3BM 
       17.62        66.02         6.94        64.44        19.46        21.40 
TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC 
        2.24        15.81         4.50        15.91        14.07        17.75 
TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ 
       24.92         8.94        13.91         7.73         2.10         3.12 
TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R 
       20.98         2.20         7.36        10.92        11.31        11.31 
TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATQ 
        7.63        27.09        20.05         5.62         4.73         7.00 
TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH 
       14.27        21.34        19.10        19.82        20.28         8.48 
TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO 
       10.59        27.35         8.58        19.07        22.72         1.51 
TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS 
       19.40        38.60         3.06         9.01         8.22        25.02 
TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RH 
        3.45        21.24         2.76         9.14        27.68         9.07 
TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO 
       11.70         1.74         1.81        15.42         6.38        11.80 
TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X 
       15.32        15.58        13.48        12.23        16.67        14.24 
TCGA-S5-A6DX TCGA-S5-AA26 TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L 
        1.84         3.75        12.43        31.56        17.62        37.05 
TCGA-UY-A78M TCGA-UY-A78N TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A9PA TCGA-UY-A9PB 
       22.68        86.83        76.01        65.75        35.24        29.56 
TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG 
       17.82         4.54         1.64         1.87        17.88        48.62 
TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SL TCGA-XF-A9SV TCGA-XF-A9SW 
       64.80        79.66         3.22        66.41        12.76        11.90 
TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 
       23.64        21.04        28.24        26.27        18.90         2.24 
TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMF 
       16.27        66.64         2.10        13.74        92.98        10.82 
TCGA-XF-AAMG TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMT 
      110.60        11.31        54.90        71.57        91.73         2.96 
TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN0 TCGA-XF-AAN1 
        8.32         6.77        98.99        44.32        56.48        30.94 
TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN7 TCGA-XF-AAN8 
       61.45        86.30        27.06        75.39        18.81         3.88 
TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R0 TCGA-ZF-A9R1 
        9.63         0.66        11.97        13.64        18.64         7.36 
TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RD 
       21.11        24.13        27.19        28.41        74.56        13.41 
TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-A9RN 
        3.48        52.73        52.60        82.49        47.84        20.22 
TCGA-ZF-AA4N TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4U TCGA-ZF-AA4W TCGA-ZF-AA4X 
        2.89        34.06        19.69         8.61        60.16        63.02 
TCGA-ZF-AA52 TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H 
       35.41        57.90        19.40         8.52        47.15        19.17 
TCGA-ZF-AA5P 
       10.13 

  ARID1B MUTATED ARID1B WILD-TYPE 
            0.49             0.10 
  ARID1B MUTATED ARID1B WILD-TYPE 
           62.86           166.03 
  ARID1B MUTATED ARID1B WILD-TYPE 
           21.86            15.58 
[1] "0.5 - 62.9 (21.9)"  "0.1 - 166.0 (15.6)"
[1] "hr=" "1.3"
D62V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  ARID1B MUTATED         0        8         5        8
  ARID1B WILD-TYPE       4      109       117      120
D62V3, multiclass
           clus
vv          ARID1B MUTATED ARID1B WILD-TYPE
  STAGE I                0                4
  STAGE II               8              109
  STAGE III              5              117
  STAGE IV               8              120
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1+T2  T3  T4
  ARID1B MUTATED         10   8   2
  ARID1B WILD-TYPE      104 171  50
D62V4, multiclass
          clus
vv         ARID1B MUTATED ARID1B WILD-TYPE
  T0+T1+T2             10              104
  T3                    8              171
  T4                    2               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"
                  vv
clus                N0  N1  N2  N3
  ARID1B MUTATED     9   1   6   0
  ARID1B WILD-TYPE 204  40  69   8
D62V5, multiclass
    clus
vv   ARID1B MUTATED ARID1B WILD-TYPE
  N0              9              204
  N1              1               40
  N2              6               69
  N3              0                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"
D62V6, binary
                  cls
clus                 0   1
  ARID1B MUTATED    13   1
  ARID1B WILD-TYPE 169   9
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID1B MUTATED     13    1
  ARID1B WILD-TYPE  169    9
   clus
vv  ARID1B MUTATED ARID1B WILD-TYPE
  0             13              169
  1              1                9
[1] 2 2
[1] FALSE
D62V7, binary
                  cls
clus                 0   1
  ARID1B MUTATED     6  15
  ARID1B WILD-TYPE  90 265
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID1B MUTATED      6   15
  ARID1B WILD-TYPE   90  265
        clus
vv       ARID1B MUTATED ARID1B WILD-TYPE
  FEMALE              6               90
  MALE               15              265
[1] 2 2
[1] FALSE
D62V8, continuous
D62V9, continuous
D62V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ARID1B MUTATED       1                         0    20
  ARID1B WILD-TYPE    37                        21   281
D62V11, multiclass
                           clus
vv                          ARID1B MUTATED ARID1B WILD-TYPE
  ASIAN                                  1               37
  BLACK OR AFRICAN AMERICAN              0               21
  WHITE                                 20              281
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V12, binary
                  cls
clus                 0   1
  ARID1B MUTATED     0  20
  ARID1B WILD-TYPE   8 318
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID1B MUTATED      0   20
  ARID1B WILD-TYPE    8  318
                        clus
vv                       ARID1B MUTATED ARID1B WILD-TYPE
  HISPANIC OR LATINO                  0                8
  NOT HISPANIC OR LATINO             20              318
[1] 2 2
[1] FALSE

Clustering(63) Variable = ZNF511 MUTATION ANALYSIS
D63V1, survival
                  sevent
clus2                0   1
  ZNF511 MUTATED     6   2
  ZNF511 WILD-TYPE 213 149
  ZNF511 MUTATED ZNF511 WILD-TYPE 
               8              362 
  ZNF511 MUTATED ZNF511 WILD-TYPE 
               2              149 
$`ZNF511 MUTATED`
TCGA-2F-A9KQ TCGA-FD-A5BS TCGA-FD-A6TG TCGA-G2-A2EJ TCGA-GU-A767 TCGA-XF-A9SG 
       91.63        53.88         3.06        30.61         4.73        48.62 
TCGA-XF-A9T5 TCGA-XF-AAMG 
       66.64       110.60 

$`ZNF511 WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW TCGA-4Z-AA7M 
       22.29        11.97       103.50       105.70         8.35        16.27 
TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7W 
       44.94        16.83        16.77        17.16        34.98        27.62 
TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA84 
       49.12         0.62        41.75        51.16        66.54        15.12 
TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J 
       10.22        47.80        33.83        40.08         7.33         2.66 
TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N 
        6.74        12.39         6.58        13.15        19.04        32.84 
TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U 
       12.16        17.88        19.50         5.06        14.89        14.96 
TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A2LD 
        5.06         8.35         8.25        17.16        16.18        20.48 
TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E 
        4.67        12.82         9.96        17.56        28.70        24.26 
TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-C4-A0F6 TCGA-C4-A0F7 
       28.41         8.98         1.94         2.93        23.01         2.04 
TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V 
        0.46         0.43         0.69        10.95        12.66        12.46 
TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 
       12.10        12.62        12.26        13.12        12.00        12.10 
TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ 
       11.87        13.08        12.92         4.90         7.20         5.46 
TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 
        5.19        16.31         1.84        13.58        21.86         2.14 
TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD 
       66.41        18.41        19.00        16.70       130.88       112.44 
TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 
       16.14        17.62        15.62         1.81        10.59         7.79 
TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN 
      123.85        87.32         2.20        13.58         7.82         8.22 
TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW 
       17.72        50.27        21.30        23.21         9.67        20.81 
TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW 
       10.55       140.81        48.00        17.98        64.18        41.56 
TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L 
       76.60        67.36        15.68        41.06        30.67        38.24 
TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6W 
       15.02        13.58       166.03        12.36        10.49         8.65 
TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A2PC 
        7.53        13.64        43.50        12.03        10.62        43.59 
TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ 
       15.35        38.83        24.66         0.10         0.49         2.24 
TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 
       16.70        17.39         0.56         0.66        14.56        13.97 
TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A7XN 
       12.99        14.33         0.92         1.22        13.68        14.07 
TCGA-E7-A85H TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 
       12.95        14.37         8.09        32.02        16.77         8.94 
TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA 
       33.04         4.01        12.62        22.52        27.98        60.66 
TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP 
       24.30        23.41        17.98        29.16         5.52        25.74 
TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S 
       46.78        19.79        12.85        22.98        27.35        14.96 
TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV 
       20.91         3.62        26.73        11.01        19.33         5.36 
TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N 
        5.69         8.25        27.45        18.08        58.92         2.70 
TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC 
        7.10         6.28        13.35        62.86        18.81         6.15 
TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FD-A6TK 
       12.69        12.36         2.27         4.31         9.67        10.85 
TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FJ-A871 TCGA-FT-A3EE 
       31.07         7.13        10.65        17.23         8.94         3.25 
TCGA-FT-A61P TCGA-G2-A2EC TCGA-G2-A2EF TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO 
        6.48        22.88        61.94        15.95        26.93        35.24 
TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3C 
       33.01         7.23        20.12        17.62        66.02         6.94 
TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB 
       64.44        19.46        21.40         2.24        15.81         4.50 
TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GC-A6I3 
       15.91        14.07        17.75        24.92         8.94        13.91 
TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GD-A76B 
        7.73         2.10         3.12        20.98         2.20         7.36 
TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A764 
       10.92        11.31        11.31         7.63        27.09        20.05 
TCGA-GU-A766 TCGA-GU-AATO TCGA-GU-AATP TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW 
        5.62        10.65        32.98         7.00        14.27        21.34 
TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK 
       19.10        19.82        20.28         8.48        10.59        27.35 
TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE 
        8.58        19.07        22.72         1.51        19.40        38.60 
TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV 
        3.06         9.01         8.22        25.02         3.45        21.24 
TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ 
        2.76         9.14        27.68         9.07        11.70         1.74 
TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO TCGA-LC-A66R TCGA-LT-A5Z6 
        1.81        15.42         6.38        11.80        15.32        15.58 
TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 
       13.48        12.23        16.67        14.24         1.84         3.75 
TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78N 
       12.43        31.56        17.62        37.05        22.68        86.83 
TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE 
       76.01        65.75        35.24        29.56        17.82         4.54 
TCGA-UY-A9PF TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SJ 
        1.64         1.87        17.88        64.80        79.66         3.22 
TCGA-XF-A9SL TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ 
       66.41        12.76        11.90        23.64        21.04        28.24 
TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T6 TCGA-XF-A9T8 
       26.27        18.90         2.24        16.27         2.10        13.74 
TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ 
       92.98        10.82        11.31        54.90         7.63        71.57 
TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAMZ 
       91.73         2.96         8.32         6.77        98.99        44.32 
TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN5 
       56.48        30.94        61.45        86.30        27.06        75.39 
TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-YF-AA3M 
       18.81         3.88         9.63         0.66        11.97        13.64 
TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R5 
       18.64         7.36        21.11        24.13        30.28        27.19 
TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RF 
       21.86        28.41        74.56        13.41         3.48        52.73 
TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4R 
       52.60        82.49        47.84        20.22         2.89        34.06 
TCGA-ZF-AA4T TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA51 
       19.69         8.61        59.38        60.16        63.02        38.73 
TCGA-ZF-AA52 TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H 
       35.41        57.90        19.40         8.52        47.15        19.17 
TCGA-ZF-AA5N TCGA-ZF-AA5P 
        5.52        10.13 

  ZNF511 MUTATED ZNF511 WILD-TYPE 
            3.06             0.10 
  ZNF511 MUTATED ZNF511 WILD-TYPE 
          110.60           166.03 
  ZNF511 MUTATED ZNF511 WILD-TYPE 
           51.25            15.50 
[1] "3.1 - 110.6 (51.2)" "0.1 - 166.0 (15.5)"
[1] "hr=" "2.9"
D63V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  ZNF511 MUTATED         0        2         3        3
  ZNF511 WILD-TYPE       4      115       119      125
D63V3, multiclass
           clus
vv          ZNF511 MUTATED ZNF511 WILD-TYPE
  STAGE I                0                4
  STAGE II               2              115
  STAGE III              3              119
  STAGE IV               3              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"
                  vv
clus               T0+T1+T2  T3  T4
  ZNF511 MUTATED          1   5   1
  ZNF511 WILD-TYPE      113 174  51
D63V4, multiclass
          clus
vv         ZNF511 MUTATED ZNF511 WILD-TYPE
  T0+T1+T2              1              113
  T3                    5              174
  T4                    1               51
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  ZNF511 MUTATED     5   1   2   0
  ZNF511 WILD-TYPE 208  40  73   8
D63V5, multiclass
    clus
vv   ZNF511 MUTATED ZNF511 WILD-TYPE
  N0              5              208
  N1              1               40
  N2              2               73
  N3              0                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"
D63V6, binary
                  cls
clus                 0   1
  ZNF511 MUTATED     2   0
  ZNF511 WILD-TYPE 180  10
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF511 MUTATED      2    0
  ZNF511 WILD-TYPE  180   10
   clus
vv  ZNF511 MUTATED ZNF511 WILD-TYPE
  0              2              180
  1              0               10
[1] 2 2
[1] FALSE
D63V7, binary
                  cls
clus                 0   1
  ZNF511 MUTATED     2   6
  ZNF511 WILD-TYPE  94 274
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF511 MUTATED      2    6
  ZNF511 WILD-TYPE   94  274
        clus
vv       ZNF511 MUTATED ZNF511 WILD-TYPE
  FEMALE              2               94
  MALE                6              274
[1] 2 2
[1] FALSE
D63V8, continuous
D63V9, continuous
[1] "Remove cluster labels:" "ZNF511 MUTATED"        
clus
  ZNF511 MUTATED ZNF511 WILD-TYPE 
               2              203 
      TCGA-2F-A9KO       TCGA-2F-A9KP       TCGA-2F-A9KR       TCGA-4Z-AA7M 
"ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" 
      TCGA-4Z-AA89       TCGA-BL-A0C8       TCGA-BL-A13I       TCGA-BL-A13J 
"ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" 
      TCGA-BL-A3JM       TCGA-BL-A5ZZ       TCGA-BT-A20J       TCGA-BT-A20N 
"ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" 
      TCGA-BT-A2LA       TCGA-BT-A42B       TCGA-BT-A42C       TCGA-BT-A42E 
"ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" 
      TCGA-C4-A0EZ       TCGA-C4-A0F0       TCGA-C4-A0F1       TCGA-C4-A0F6 
"ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" 
      TCGA-CF-A3MH       TCGA-CF-A3MI       TCGA-CF-A47W       TCGA-CF-A47X 
"ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" 
      TCGA-CF-A5UA       TCGA-CF-A9FH       TCGA-CU-A0YN       TCGA-CU-A0YR 
"ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" 
      TCGA-CU-A3KJ       TCGA-CU-A3QU       TCGA-CU-A3YL       TCGA-CU-A5W6 
"ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" 
      TCGA-CU-A72E       TCGA-DK-A1A3       TCGA-DK-A1A5       TCGA-DK-A1A6 
"ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" 
      TCGA-DK-A1AA       TCGA-DK-A1AC       TCGA-DK-A1AE       TCGA-DK-A2HX 
"ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" 
      TCGA-DK-A2I6       TCGA-DK-A3IL       TCGA-DK-A3IM       TCGA-DK-A3IN 
"ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" 
      TCGA-DK-A3IQ       TCGA-DK-A3IU       TCGA-DK-A3IV       TCGA-DK-A3WX 
"ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" 
      TCGA-DK-A3X1       TCGA-DK-A3X2       TCGA-DK-A6AV       TCGA-DK-A6AW 
"ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" 
      TCGA-DK-A6B0       TCGA-DK-A6B2       TCGA-DK-A6B6       TCGA-DK-AA6L 
"ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" 
      TCGA-DK-AA6P       TCGA-DK-AA6T       TCGA-DK-AA6U       TCGA-DK-AA74 
"ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" 
      TCGA-DK-AA76       TCGA-E5-A4TZ       TCGA-E7-A4XJ       TCGA-E7-A519 
"ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" 
      TCGA-E7-A5KF       TCGA-E7-A678       TCGA-E7-A6ME       TCGA-E7-A6MF 
"ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" 
      TCGA-E7-A7PW       TCGA-E7-A7XN       TCGA-E7-A85H       TCGA-E7-A97Q 
"ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" 
      TCGA-FD-A3B3       TCGA-FD-A3B4       TCGA-FD-A3B5       TCGA-FD-A3B6 
"ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" 
      TCGA-FD-A3B7       TCGA-FD-A3B8       TCGA-FD-A3N5       TCGA-FD-A3N6 
"ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" 
      TCGA-FD-A3NA       TCGA-FD-A3SJ       TCGA-FD-A3SM       TCGA-FD-A3SN 
"ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" 
      TCGA-FD-A3SO       TCGA-FD-A3SP       TCGA-FD-A3SQ       TCGA-FD-A3SR 
"ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" 
      TCGA-FD-A3SS       TCGA-FD-A43N       TCGA-FD-A43P       TCGA-FD-A43S 
"ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" 
      TCGA-FD-A43U       TCGA-FD-A43X       TCGA-FD-A5BT       TCGA-FD-A5BU 
"ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" 
      TCGA-FD-A5BV       TCGA-FD-A5BX       TCGA-FD-A5C0       TCGA-FD-A62N 
"ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" 
      TCGA-FD-A6TB       TCGA-FD-A6TC       TCGA-FD-A6TE       TCGA-FD-A6TH 
"ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" 
      TCGA-FD-A6TK       TCGA-FJ-A3Z9       TCGA-FJ-A3ZE       TCGA-FJ-A3ZF 
"ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" 
      TCGA-FJ-A871       TCGA-FT-A61P       TCGA-G2-A2EF       TCGA-G2-A2EL 
"ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" 
      TCGA-G2-A2ES       TCGA-G2-A3IE       TCGA-G2-AA3B       TCGA-G2-AA3C 
"ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" 
      TCGA-G2-AA3D       TCGA-G2-AA3F       TCGA-GC-A3BM       TCGA-GC-A3RB 
"ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" 
      TCGA-GC-A3WC       TCGA-GC-A3YS       TCGA-GD-A2C5       TCGA-GD-A3OQ 
"ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" 
      TCGA-GD-A3OS       TCGA-GD-A6C6       TCGA-GU-A42P       TCGA-GU-A42Q 
"ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" 
      TCGA-GU-A42R       TCGA-GU-A763       TCGA-GU-A764       TCGA-GU-AATO 
"ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" 
      TCGA-GU-AATP       TCGA-GU-AATQ       TCGA-GV-A3JV       TCGA-GV-A3JX 
"ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" 
      TCGA-GV-A3JZ       TCGA-GV-A3QF       TCGA-GV-A3QG       TCGA-GV-A3QH 
"ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" 
      TCGA-GV-A3QI       TCGA-GV-A3QK       TCGA-GV-A40E       TCGA-GV-A40G 
"ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" 
      TCGA-H4-A2HO       TCGA-H4-A2HQ       TCGA-HQ-A5ND       TCGA-HQ-A5NE 
"ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" 
      TCGA-K4-A3WS       TCGA-K4-A3WV       TCGA-K4-A5RH       TCGA-K4-A5RI 
"ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" 
      TCGA-K4-A83P       TCGA-K4-AAQO       TCGA-PQ-A6FI       TCGA-PQ-A6FN 
"ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" 
      TCGA-R3-A69X       TCGA-S5-A6DX       TCGA-SY-A9G0       TCGA-UY-A78N 
"ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" 
      TCGA-UY-A8OB       TCGA-UY-A9PB       TCGA-UY-A9PE       TCGA-UY-A9PF 
"ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" 
      TCGA-XF-A9SJ       TCGA-XF-A9SL       TCGA-XF-A9SV       TCGA-XF-A9SX 
"ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" 
      TCGA-XF-A9SY       TCGA-XF-A9SZ       TCGA-XF-A9T3       TCGA-XF-A9T8 
"ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" 
      TCGA-XF-AAMF       TCGA-XF-AAMH       TCGA-XF-AAMQ       TCGA-XF-AAMT 
"ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" 
      TCGA-XF-AAN0       TCGA-XF-AAN1       TCGA-XF-AAN2       TCGA-XF-AAN4 
"ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" 
      TCGA-XF-AAN5       TCGA-XF-AAN7       TCGA-XF-AAN8       TCGA-YF-AA3L 
"ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" 
      TCGA-YF-AA3M       TCGA-ZF-A9R0       TCGA-ZF-A9R2       TCGA-ZF-A9R3 
"ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" 
      TCGA-ZF-A9R5       TCGA-ZF-A9R7       TCGA-ZF-A9R9       TCGA-ZF-A9RD 
"ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" 
      TCGA-ZF-A9RF       TCGA-ZF-A9RL       TCGA-ZF-A9RM       TCGA-ZF-AA4U 
"ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" 
      TCGA-ZF-AA4V       TCGA-ZF-AA51       TCGA-ZF-AA52       TCGA-ZF-AA58 
"ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" 
      TCGA-ZF-AA5H       TCGA-ZF-AA5N       TCGA-ZF-AA5P 
"ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" "ZNF511 WILD-TYPE" 
D63V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ZNF511 MUTATED       0                         0     7
  ZNF511 WILD-TYPE    38                        21   294
D63V11, multiclass
                           clus
vv                          ZNF511 MUTATED ZNF511 WILD-TYPE
  ASIAN                                  0               38
  BLACK OR AFRICAN AMERICAN              0               21
  WHITE                                  7              294
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V12, binary
                  cls
clus                 0   1
  ZNF511 MUTATED     2   6
  ZNF511 WILD-TYPE   6 332
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF511 MUTATED      2    6
  ZNF511 WILD-TYPE    6  332
                        clus
vv                       ZNF511 MUTATED ZNF511 WILD-TYPE
  HISPANIC OR LATINO                  2                6
  NOT HISPANIC OR LATINO              6              332
[1] 2 2
[1] FALSE

Clustering(64) Variable = TFG MUTATION ANALYSIS
D64V1, survival
               sevent
clus2             0   1
  TFG MUTATED     8   3
  TFG WILD-TYPE 211 148
  TFG MUTATED TFG WILD-TYPE 
           11           359 
  TFG MUTATED TFG WILD-TYPE 
            3           148 
$`TFG MUTATED`
TCGA-4Z-AA7Y TCGA-DK-A3IV TCGA-DK-A3X1 TCGA-DK-A6AW TCGA-DK-AA6U TCGA-DK-AA71 
       49.12         9.67        48.00        41.56        10.49        13.64 
TCGA-G2-A2EC TCGA-GU-A42R TCGA-MV-A51V TCGA-XF-AAMG TCGA-ZF-A9RN 
       22.88        11.31        13.48       110.60        20.22 

$`TFG WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        91.63       103.50       105.70         8.35 
TCGA-4Z-AA7M TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7S 
       16.27        44.94        16.83        16.77        17.16        34.98 
TCGA-4Z-AA7W TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA84 
       27.62         0.62        41.75        51.16        66.54        15.12 
TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J 
       10.22        47.80        33.83        40.08         7.33         2.66 
TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N 
        6.74        12.39         6.58        13.15        19.04        32.84 
TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U 
       12.16        17.88        19.50         5.06        14.89        14.96 
TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A2LD 
        5.06         8.35         8.25        17.16        16.18        20.48 
TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E 
        4.67        12.82         9.96        17.56        28.70        24.26 
TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-C4-A0F6 TCGA-C4-A0F7 
       28.41         8.98         1.94         2.93        23.01         2.04 
TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V 
        0.46         0.43         0.69        10.95        12.66        12.46 
TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 
       12.10        12.62        12.26        13.12        12.00        12.10 
TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ 
       11.87        13.08        12.92         4.90         7.20         5.46 
TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 
        5.19        16.31         1.84        13.58        21.86         2.14 
TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD 
       66.41        18.41        19.00        16.70       130.88       112.44 
TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 
       16.14        17.62        15.62         1.81        10.59         7.79 
TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN 
      123.85        87.32         2.20        13.58         7.82         8.22 
TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3WW TCGA-DK-A3WX 
       17.72        50.27        21.30        23.21        20.81        10.55 
TCGA-DK-A3WY TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 
      140.81        17.98        64.18        76.60        67.36        15.68 
TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6S 
       41.06        30.67        38.24        15.02        13.58       166.03 
TCGA-DK-AA6T TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA74 TCGA-DK-AA76 TCGA-DK-AA77 
       12.36         8.65         7.53        43.50        12.03        10.62 
TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ 
       43.59        15.35        38.83        24.66         0.10         0.49 
TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 
        2.24        16.70        17.39         0.56         0.66        14.56 
TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7DV TCGA-E7-A7PW 
       13.97        12.99        14.33         0.92         1.22        13.68 
TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 
       14.07        12.95        14.37         8.09        32.02        16.77 
TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 
        8.94        33.04         4.01        12.62        22.52        27.98 
TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO 
       60.66        24.30        23.41        17.98        29.16         5.52 
TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P 
       25.74        46.78        19.79        12.85        22.98        27.35 
TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT 
       14.96        20.91         3.62        26.73        53.88        11.01 
TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 
       19.33         5.36         5.69         8.25        27.45        18.08 
TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA 
       58.92         2.70         7.10         6.28        13.35        62.86 
TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TG 
       18.81         6.15        12.69        12.36         2.27         3.06 
TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE 
        4.31         9.67        10.85        31.07         7.13        10.65 
TCGA-FJ-A3ZF TCGA-FJ-A871 TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EJ 
       17.23         8.94         3.25         6.48        61.94        30.61 
TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE 
       15.95        26.93        35.24        33.01         7.23        20.12 
TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3BM 
       17.62        66.02         6.94        64.44        19.46        21.40 
TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC 
        2.24        15.81         4.50        15.91        14.07        17.75 
TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ 
       24.92         8.94        13.91         7.73         2.10         3.12 
TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A762 
       20.98         2.20         7.36        10.92        11.31         7.63 
TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATO TCGA-GU-AATP 
       27.09        20.05         5.62         4.73        10.65        32.98 
TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF 
        7.00        14.27        21.34        19.10        19.82        20.28 
TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA 
        8.48        10.59        27.35         8.58        19.07        22.72 
TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE 
        1.51        19.40        38.60         3.06         9.01         8.22 
TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R 
       25.02         3.45        21.24         2.76         9.14        27.68 
TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P 
        9.07        11.70         1.74         1.81        15.42         6.38 
TCGA-K4-AAQO TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X 
       11.80        15.32        15.58        12.23        16.67        14.24 
TCGA-S5-A6DX TCGA-S5-AA26 TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L 
        1.84         3.75        12.43        31.56        17.62        37.05 
TCGA-UY-A78M TCGA-UY-A78N TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A9PA TCGA-UY-A9PB 
       22.68        86.83        76.01        65.75        35.24        29.56 
TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG 
       17.82         4.54         1.64         1.87        17.88        48.62 
TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SL TCGA-XF-A9SV TCGA-XF-A9SW 
       64.80        79.66         3.22        66.41        12.76        11.90 
TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 
       23.64        21.04        28.24        26.27        18.90         2.24 
TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMF 
       16.27        66.64         2.10        13.74        92.98        10.82 
TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMT 
       11.31        54.90         7.63        71.57        91.73         2.96 
TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN0 TCGA-XF-AAN1 
        8.32         6.77        98.99        44.32        56.48        30.94 
TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN7 TCGA-XF-AAN8 
       61.45        86.30        27.06        75.39        18.81         3.88 
TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R0 TCGA-ZF-A9R1 
        9.63         0.66        11.97        13.64        18.64         7.36 
TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 
       21.11        24.13        30.28        27.19        21.86        28.41 
TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RL 
       74.56        13.41         3.48        52.73        52.60        82.49 
TCGA-ZF-A9RM TCGA-ZF-AA4N TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4U TCGA-ZF-AA4V 
       47.84         2.89        34.06        19.69         8.61        59.38 
TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA53 TCGA-ZF-AA54 
       60.16        63.02        38.73        35.41        57.90        19.40 
TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-ZF-AA5P 
        8.52        47.15        19.17         5.52        10.13 

  TFG MUTATED TFG WILD-TYPE 
         9.67          0.10 
  TFG MUTATED TFG WILD-TYPE 
       110.60        166.03 
  TFG MUTATED TFG WILD-TYPE 
        20.22         15.62 
[1] "9.7 - 110.6 (20.2)" "0.1 - 166.0 (15.6)"
[1] "hr=" "2"  
D64V2, continuous
               vv
clus            STAGE I STAGE II STAGE III STAGE IV
  TFG MUTATED         1        5         4        1
  TFG WILD-TYPE       3      112       118      127
D64V3, multiclass
           clus
vv          TFG MUTATED TFG WILD-TYPE
  STAGE I             1             3
  STAGE II            5           112
  STAGE III           4           118
  STAGE IV            1           127
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            T0+T1+T2  T3  T4
  TFG MUTATED          3   3   2
  TFG WILD-TYPE      111 176  50
D64V4, multiclass
          clus
vv         TFG MUTATED TFG WILD-TYPE
  T0+T1+T2           3           111
  T3                 3           176
  T4                 2            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"
               vv
clus             N0  N1  N2  N3
  TFG MUTATED     8   0   1   0
  TFG WILD-TYPE 205  41  74   8
D64V5, multiclass
    clus
vv   TFG MUTATED TFG WILD-TYPE
  N0           8           205
  N1           0            41
  N2           1            74
  N3           0             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"
D64V6, binary
               cls
clus              0   1
  TFG MUTATED     9   0
  TFG WILD-TYPE 173  10
[1] "tbl2"
               cls
clus            [,1] [,2]
  TFG MUTATED      9    0
  TFG WILD-TYPE  173   10
   clus
vv  TFG MUTATED TFG WILD-TYPE
  0           9           173
  1           0            10
[1] 2 2
[1] FALSE
D64V7, binary
               cls
clus              0   1
  TFG MUTATED     3   8
  TFG WILD-TYPE  93 272
[1] "tbl2"
               cls
clus            [,1] [,2]
  TFG MUTATED      3    8
  TFG WILD-TYPE   93  272
        clus
vv       TFG MUTATED TFG WILD-TYPE
  FEMALE           3            93
  MALE             8           272
[1] 2 2
[1] FALSE
D64V8, continuous
D64V9, continuous
D64V10, continuous
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TFG MUTATED       0                         1    10
  TFG WILD-TYPE    38                        20   291
D64V11, multiclass
                           clus
vv                          TFG MUTATED TFG WILD-TYPE
  ASIAN                               0            38
  BLACK OR AFRICAN AMERICAN           1            20
  WHITE                              10           291
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V12, binary
               cls
clus              0   1
  TFG MUTATED     1   9
  TFG WILD-TYPE   7 329
[1] "tbl2"
               cls
clus            [,1] [,2]
  TFG MUTATED      1    9
  TFG WILD-TYPE    7  329
                        clus
vv                       TFG MUTATED TFG WILD-TYPE
  HISPANIC OR LATINO               1             7
  NOT HISPANIC OR LATINO           9           329
[1] 2 2
[1] FALSE

Clustering(65) Variable = FUS MUTATION ANALYSIS
D65V1, survival
               sevent
clus2             0   1
  FUS MUTATED     4   4
  FUS WILD-TYPE 215 147
  FUS MUTATED FUS WILD-TYPE 
            8           362 
  FUS MUTATED FUS WILD-TYPE 
            4           147 
$`FUS MUTATED`
TCGA-BL-A3JM TCGA-BT-A0YX TCGA-BT-A42C TCGA-DK-A3IU TCGA-DK-A6B6 TCGA-E7-A7XN 
        6.74        13.15        28.70        23.21        30.67        14.07 
TCGA-XF-AAN0 TCGA-YF-AA3M 
       56.48        13.64 

$`FUS WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        91.63       103.50       105.70         8.35 
TCGA-4Z-AA7M TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7S 
       16.27        44.94        16.83        16.77        17.16        34.98 
TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 
       27.62        49.12         0.62        41.75        51.16        66.54 
TCGA-4Z-AA84 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BL-A13I 
       15.12        10.22        47.80        33.83        40.08         7.33 
TCGA-BL-A13J TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O 
        2.66        12.39         6.58        19.04        32.84        12.16 
TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20V 
       17.88        19.50         5.06        14.89        14.96         5.06 
TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH 
        8.35         8.25        17.16        16.18        20.48         4.67 
TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ 
       12.82         9.96        17.56        24.26        28.41         8.98 
TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-C4-A0F6 TCGA-C4-A0F7 TCGA-CF-A1HR TCGA-CF-A1HS 
        1.94         2.93        23.01         2.04         0.46         0.43 
TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X 
        0.69        10.95        12.66        12.46        12.10        12.62 
TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A9FF TCGA-CF-A9FM 
       12.26        13.12        12.00        12.10        11.87        13.08 
TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL 
       12.92         4.90         7.20         5.46         5.19        16.31 
TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 
        1.84        13.58        21.86         2.14        66.41        18.41 
TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF 
       19.00        16.70       130.88       112.44        16.14        17.62 
TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A2I6 
       15.62         1.81        10.59         7.79       123.85        87.32 
TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS 
        2.20        13.58         7.82         8.22        17.72        50.27 
TCGA-DK-A3IT TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 
       21.30         9.67        20.81        10.55       140.81        48.00 
TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 
       17.98        64.18        41.56        76.60        67.36        15.68 
TCGA-DK-A6B5 TCGA-DK-AA6L TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6S TCGA-DK-AA6T 
       41.06        38.24        15.02        13.58       166.03        12.36 
TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA76 
       10.49         8.65         7.53        13.64        43.50        12.03 
TCGA-DK-AA77 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 
       10.62        43.59        15.35        38.83        24.66         0.10 
TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF 
        0.49         2.24        16.70        17.39         0.56         0.66 
TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7DV 
       14.56        13.97        12.99        14.33         0.92         1.22 
TCGA-E7-A7PW TCGA-E7-A85H TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 
       13.68        12.95        14.37         8.09        32.02        16.77 
TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 
        8.94        33.04         4.01        12.62        22.52        27.98 
TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO 
       60.66        24.30        23.41        17.98        29.16         5.52 
TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P 
       25.74        46.78        19.79        12.85        22.98        27.35 
TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT 
       14.96        20.91         3.62        26.73        53.88        11.01 
TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 
       19.33         5.36         5.69         8.25        27.45        18.08 
TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA 
       58.92         2.70         7.10         6.28        13.35        62.86 
TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TG 
       18.81         6.15        12.69        12.36         2.27         3.06 
TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE 
        4.31         9.67        10.85        31.07         7.13        10.65 
TCGA-FJ-A3ZF TCGA-FJ-A871 TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EC TCGA-G2-A2EF 
       17.23         8.94         3.25         6.48        22.88        61.94 
TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB 
       30.61        15.95        26.93        35.24        33.01         7.23 
TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3D TCGA-G2-AA3F 
       20.12        17.62        66.02         6.94        64.44        19.46 
TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD 
       21.40         2.24        15.81         4.50        15.91        14.07 
TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP 
       17.75        24.92         8.94        13.91         7.73         2.10 
TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42Q 
        3.12        20.98         2.20         7.36        10.92        11.31 
TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 
       11.31         7.63        27.09        20.05         5.62         4.73 
TCGA-GU-AATO TCGA-GU-AATP TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX 
       10.65        32.98         7.00        14.27        21.34        19.10 
TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E 
       19.82        20.28         8.48        10.59        27.35         8.58 
TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF 
       19.07        22.72         1.51        19.40        38.60         3.06 
TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB 
        9.01         8.22        25.02         3.45        21.24         2.76 
TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ 
        9.14        27.68         9.07        11.70         1.74         1.81 
TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V 
       15.42         6.38        11.80        15.32        15.58        13.48 
TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 TCGA-SY-A9G0 
       12.23        16.67        14.24         1.84         3.75        12.43 
TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78N TCGA-UY-A78O 
       31.56        17.62        37.05        22.68        86.83        76.01 
TCGA-UY-A8OB TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF 
       65.75        35.24        29.56        17.82         4.54         1.64 
TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SJ 
        1.87        17.88        48.62        64.80        79.66         3.22 
TCGA-XF-A9SL TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ 
       66.41        12.76        11.90        23.64        21.04        28.24 
TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 
       26.27        18.90         2.24        16.27        66.64         2.10 
TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMG TCGA-XF-AAMH TCGA-XF-AAMJ 
       13.74        92.98        10.82       110.60        11.31        54.90 
TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX 
        7.63        71.57        91.73         2.96         8.32         6.77 
TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN4 
       98.99        44.32        30.94        61.45        86.30        27.06 
TCGA-XF-AAN5 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L 
       75.39        18.81         3.88         9.63         0.66        11.97 
TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R5 
       18.64         7.36        21.11        24.13        30.28        27.19 
TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RF 
       21.86        28.41        74.56        13.41         3.48        52.73 
TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4R 
       52.60        82.49        47.84        20.22         2.89        34.06 
TCGA-ZF-AA4T TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA51 
       19.69         8.61        59.38        60.16        63.02        38.73 
TCGA-ZF-AA52 TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H 
       35.41        57.90        19.40         8.52        47.15        19.17 
TCGA-ZF-AA5N TCGA-ZF-AA5P 
        5.52        10.13 

  FUS MUTATED FUS WILD-TYPE 
         6.74          0.10 
  FUS MUTATED FUS WILD-TYPE 
        56.48        166.03 
  FUS MUTATED FUS WILD-TYPE 
        18.64         15.65 
[1] "6.7 - 56.5 (18.6)"  "0.1 - 166.0 (15.6)"
[1] "hr=" "1.1"
D65V2, continuous
               vv
clus            STAGE I STAGE II STAGE III STAGE IV
  FUS MUTATED         0        4         3        1
  FUS WILD-TYPE       4      113       119      127
D65V3, multiclass
           clus
vv          FUS MUTATED FUS WILD-TYPE
  STAGE I             0             4
  STAGE II            4           113
  STAGE III           3           119
  STAGE IV            1           127
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            T0+T1+T2  T3  T4
  FUS MUTATED          2   3   1
  FUS WILD-TYPE      112 176  51
D65V4, multiclass
          clus
vv         FUS MUTATED FUS WILD-TYPE
  T0+T1+T2           2           112
  T3                 3           176
  T4                 1            51
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             N0  N1  N2  N3
  FUS MUTATED     5   0   1   0
  FUS WILD-TYPE 208  41  74   8
D65V5, multiclass
    clus
vv   FUS MUTATED FUS WILD-TYPE
  N0           5           208
  N1           0            41
  N2           1            74
  N3           0             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"
D65V6, binary
               cls
clus              0   1
  FUS MUTATED     6   0
  FUS WILD-TYPE 176  10
[1] "tbl2"
               cls
clus            [,1] [,2]
  FUS MUTATED      6    0
  FUS WILD-TYPE  176   10
   clus
vv  FUS MUTATED FUS WILD-TYPE
  0           6           176
  1           0            10
[1] 2 2
[1] FALSE
D65V7, binary
               cls
clus              0   1
  FUS MUTATED     1   7
  FUS WILD-TYPE  95 273
[1] "tbl2"
               cls
clus            [,1] [,2]
  FUS MUTATED      1    7
  FUS WILD-TYPE   95  273
        clus
vv       FUS MUTATED FUS WILD-TYPE
  FEMALE           1            95
  MALE             7           273
[1] 2 2
[1] FALSE
D65V8, continuous
D65V9, continuous
D65V10, continuous
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  FUS MUTATED       1                         0     6
  FUS WILD-TYPE    37                        21   295
D65V11, multiclass
                           clus
vv                          FUS MUTATED FUS WILD-TYPE
  ASIAN                               1            37
  BLACK OR AFRICAN AMERICAN           0            21
  WHITE                               6           295
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V12, binary
               cls
clus              0   1
  FUS MUTATED     1   7
  FUS WILD-TYPE   7 331
[1] "tbl2"
               cls
clus            [,1] [,2]
  FUS MUTATED      1    7
  FUS WILD-TYPE    7  331
                        clus
vv                       FUS MUTATED FUS WILD-TYPE
  HISPANIC OR LATINO               1             7
  NOT HISPANIC OR LATINO           7           331
[1] 2 2
[1] FALSE

Clustering(66) Variable = ASXL1 MUTATION ANALYSIS
D66V1, survival
                 sevent
clus2               0   1
  ASXL1 MUTATED    17   5
  ASXL1 WILD-TYPE 202 146
  ASXL1 MUTATED ASXL1 WILD-TYPE 
             22             348 
  ASXL1 MUTATED ASXL1 WILD-TYPE 
              5             146 
$`ASXL1 MUTATED`
TCGA-2F-A9KW TCGA-4Z-AA7M TCGA-4Z-AA84 TCGA-BT-A2LD TCGA-BT-A42C TCGA-CF-A27C 
        8.35        16.27        15.12        20.48        28.70         0.69 
TCGA-CU-A3QU TCGA-DK-A2I4 TCGA-DK-A3WW TCGA-DK-A3X1 TCGA-DK-A6AW TCGA-E5-A4U1 
        5.19       123.85        20.81        48.00        41.56        38.83 
TCGA-E7-A7XN TCGA-FD-A3SO TCGA-FJ-A3ZF TCGA-GC-A3RD TCGA-GU-A42P TCGA-GV-A6ZA 
       14.07         5.52        17.23        14.07        10.92        22.72 
TCGA-HQ-A5NE TCGA-SY-A9G5 TCGA-UY-A78K TCGA-ZF-A9R5 
        8.22        31.56        17.62        27.19 

$`ASXL1 WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-4Z-AA7N 
       22.29        11.97        91.63       103.50       105.70        44.94 
TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7W TCGA-4Z-AA7Y 
       16.83        16.77        17.16        34.98        27.62        49.12 
TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA86 TCGA-4Z-AA87 
        0.62        41.75        51.16        66.54        10.22        47.80 
TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ 
       33.83        40.08         7.33         2.66         6.74        12.39 
TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P 
        6.58        13.15        19.04        32.84        12.16        17.88 
TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20W 
       19.50         5.06        14.89        14.96         5.06         8.35 
TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK 
        8.25        17.16        16.18         4.67        12.82         9.96 
TCGA-BT-A42B TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F1 
       17.56        24.26        28.41         8.98         1.94         2.93 
TCGA-C4-A0F6 TCGA-C4-A0F7 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A47S TCGA-CF-A47T 
       23.01         2.04         0.46         0.43        10.95        12.66 
TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA 
       12.46        12.10        12.62        12.26        13.12        12.00 
TCGA-CF-A7I0 TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR 
       12.10        11.87        13.08        12.92         4.90         7.20 
TCGA-CU-A3KJ TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 
        5.46        16.31         1.84        13.58        21.86         2.14 
TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD 
       66.41        18.41        19.00        16.70       130.88       112.44 
TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 
       16.14        17.62        15.62         1.81        10.59         7.79 
TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ 
       87.32         2.20        13.58         7.82         8.22        17.72 
TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WX TCGA-DK-A3WY 
       50.27        21.30        23.21         9.67        10.55       140.81 
TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 
       17.98        64.18        76.60        67.36        15.68        41.06 
TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6S TCGA-DK-AA6T 
       30.67        38.24        15.02        13.58       166.03        12.36 
TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA76 
       10.49         8.65         7.53        13.64        43.50        12.03 
TCGA-DK-AA77 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ 
       10.62        43.59        15.35        24.66         0.10         0.49 
TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 
        2.24        16.70        17.39         0.56         0.66        14.56 
TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7DV TCGA-E7-A7PW 
       13.97        12.99        14.33         0.92         1.22        13.68 
TCGA-E7-A85H TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 
       12.95        14.37         8.09        32.02        16.77         8.94 
TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA 
       33.04         4.01        12.62        22.52        27.98        60.66 
TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SP TCGA-FD-A3SQ 
       24.30        23.41        17.98        29.16        25.74        46.78 
TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U 
       19.79        12.85        22.98        27.35        14.96        20.91 
TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV 
        3.62        26.73        53.88        11.01        19.33         5.36 
TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N 
        5.69         8.25        27.45        18.08        58.92         2.70 
TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC 
        7.10         6.28        13.35        62.86        18.81         6.15 
TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI 
       12.69        12.36         2.27         3.06         4.31         9.67 
TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A871 TCGA-FT-A3EE 
       10.85        31.07         7.13        10.65         8.94         3.25 
TCGA-FT-A61P TCGA-G2-A2EC TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL 
        6.48        22.88        61.94        30.61        15.95        26.93 
TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B 
       35.24        33.01         7.23        20.12        17.62        66.02 
TCGA-G2-AA3C TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO 
        6.94        64.44        19.46        21.40         2.24        15.81 
TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GC-A6I3 
        4.50        15.91        17.75        24.92         8.94        13.91 
TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GD-A76B 
        7.73         2.10         3.12        20.98         2.20         7.36 
TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 
       11.31        11.31         7.63        27.09        20.05         5.62 
TCGA-GU-A767 TCGA-GU-AATO TCGA-GU-AATP TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW 
        4.73        10.65        32.98         7.00        14.27        21.34 
TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK 
       19.10        19.82        20.28         8.48        10.59        27.35 
TCGA-GV-A40E TCGA-GV-A40G TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF 
        8.58        19.07         1.51        19.40        38.60         3.06 
TCGA-HQ-A5ND TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC 
        9.01        25.02         3.45        21.24         2.76         9.14 
TCGA-K4-A54R TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB 
       27.68         9.07        11.70         1.74         1.81        15.42 
TCGA-K4-A83P TCGA-K4-AAQO TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI 
        6.38        11.80        15.32        15.58        13.48        12.23 
TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 TCGA-SY-A9G0 TCGA-UY-A78L 
       16.67        14.24         1.84         3.75        12.43        37.05 
TCGA-UY-A78M TCGA-UY-A78N TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A9PA TCGA-UY-A9PB 
       22.68        86.83        76.01        65.75        35.24        29.56 
TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG 
       17.82         4.54         1.64         1.87        17.88        48.62 
TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SL TCGA-XF-A9SV TCGA-XF-A9SW 
       64.80        79.66         3.22        66.41        12.76        11.90 
TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 
       23.64        21.04        28.24        26.27        18.90         2.24 
TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMF 
       16.27        66.64         2.10        13.74        92.98        10.82 
TCGA-XF-AAMG TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR 
      110.60        11.31        54.90         7.63        71.57        91.73 
TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN0 
        2.96         8.32         6.77        98.99        44.32        56.48 
TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN7 
       30.94        61.45        86.30        27.06        75.39        18.81 
TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R0 
        3.88         9.63         0.66        11.97        13.64        18.64 
TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R7 TCGA-ZF-A9R9 
        7.36        21.11        24.13        30.28        21.86        28.41 
TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RL 
       74.56        13.41         3.48        52.73        52.60        82.49 
TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4U 
       47.84        20.22         2.89        34.06        19.69         8.61 
TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA53 
       59.38        60.16        63.02        38.73        35.41        57.90 
TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-ZF-AA5P 
       19.40         8.52        47.15        19.17         5.52        10.13 

  ASXL1 MUTATED ASXL1 WILD-TYPE 
           0.69            0.10 
  ASXL1 MUTATED ASXL1 WILD-TYPE 
         123.85          166.03 
  ASXL1 MUTATED ASXL1 WILD-TYPE 
         17.425          15.500 
[1] "0.7 - 123.8 (17.4)" "0.1 - 166.0 (15.5)"
[1] "hr=" "2"  
D66V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  ASXL1 MUTATED         0        4        11        6
  ASXL1 WILD-TYPE       4      113       111      122
D66V3, multiclass
           clus
vv          ASXL1 MUTATED ASXL1 WILD-TYPE
  STAGE I               0               4
  STAGE II              4             113
  STAGE III            11             111
  STAGE IV              6             122
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1+T2  T3  T4
  ASXL1 MUTATED          4  14   1
  ASXL1 WILD-TYPE      110 165  51
D66V4, multiclass
          clus
vv         ASXL1 MUTATED ASXL1 WILD-TYPE
  T0+T1+T2             4             110
  T3                  14             165
  T4                   1              51
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  ASXL1 MUTATED    16   4   2   0
  ASXL1 WILD-TYPE 197  37  73   8
D66V5, multiclass
    clus
vv   ASXL1 MUTATED ASXL1 WILD-TYPE
  N0            16             197
  N1             4              37
  N2             2              73
  N3             0               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"
D66V6, binary
                 cls
clus                0   1
  ASXL1 MUTATED    17   1
  ASXL1 WILD-TYPE 165   9
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ASXL1 MUTATED     17    1
  ASXL1 WILD-TYPE  165    9
   clus
vv  ASXL1 MUTATED ASXL1 WILD-TYPE
  0            17             165
  1             1               9
[1] 2 2
[1] FALSE
D66V7, binary
                 cls
clus                0   1
  ASXL1 MUTATED     4  18
  ASXL1 WILD-TYPE  92 262
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ASXL1 MUTATED      4   18
  ASXL1 WILD-TYPE   92  262
        clus
vv       ASXL1 MUTATED ASXL1 WILD-TYPE
  FEMALE             4              92
  MALE              18             262
[1] 2 2
[1] FALSE
D66V8, continuous
D66V9, continuous
D66V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ASXL1 MUTATED       2                         0    18
  ASXL1 WILD-TYPE    36                        21   283
D66V11, multiclass
                           clus
vv                          ASXL1 MUTATED ASXL1 WILD-TYPE
  ASIAN                                 2              36
  BLACK OR AFRICAN AMERICAN             0              21
  WHITE                                18             283
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V12, binary
                 cls
clus                0   1
  ASXL1 MUTATED     0  19
  ASXL1 WILD-TYPE   8 319
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ASXL1 MUTATED      0   19
  ASXL1 WILD-TYPE    8  319
                        clus
vv                       ASXL1 MUTATED ASXL1 WILD-TYPE
  HISPANIC OR LATINO                 0               8
  NOT HISPANIC OR LATINO            19             319
[1] 2 2
[1] FALSE

Clustering(67) Variable = CNOT3 MUTATION ANALYSIS
D67V1, survival
                 sevent
clus2               0   1
  CNOT3 MUTATED     4   7
  CNOT3 WILD-TYPE 215 144
  CNOT3 MUTATED CNOT3 WILD-TYPE 
             11             359 
  CNOT3 MUTATED CNOT3 WILD-TYPE 
              7             144 
$`CNOT3 MUTATED`
TCGA-4Z-AA81 TCGA-4Z-AA86 TCGA-BT-A0YX TCGA-C4-A0F6 TCGA-DK-A1AC TCGA-E7-A7XN 
       41.75        10.22        13.15        23.01       130.88        14.07 
TCGA-E7-A97P TCGA-FD-A3SM TCGA-FD-A3SO TCGA-GC-A3RC TCGA-S5-A6DX 
       14.37        17.98         5.52        15.91         1.84 

$`CNOT3 WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        91.63       103.50       105.70         8.35 
TCGA-4Z-AA7M TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7S 
       16.27        44.94        16.83        16.77        17.16        34.98 
TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA84 
       27.62        49.12         0.62        51.16        66.54        15.12 
TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM 
       47.80        33.83        40.08         7.33         2.66         6.74 
TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P 
       12.39         6.58        19.04        32.84        12.16        17.88 
TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20W 
       19.50         5.06        14.89        14.96         5.06         8.35 
TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PJ 
        8.25        17.16        16.18        20.48         4.67        12.82 
TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ 
        9.96        17.56        28.70        24.26        28.41         8.98 
TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-C4-A0F7 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C 
        1.94         2.93         2.04         0.46         0.43         0.69 
TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y 
       10.95        12.66        12.46        12.10        12.62        12.26 
TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A0YN 
       13.12        12.00        12.10        11.87        13.08        12.92 
TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 
        4.90         7.20         5.46         5.19        16.31         1.84 
TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA 
       13.58        21.86         2.14        66.41        18.41        19.00 
TCGA-DK-A1AB TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX 
       16.70       112.44        16.14        17.62        15.62         1.81 
TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL 
       10.59         7.79       123.85        87.32         2.20        13.58 
TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU 
        7.82         8.22        17.72        50.27        21.30        23.21 
TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A3X2 
        9.67        20.81        10.55       140.81        48.00        17.98 
TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 
       64.18        41.56        76.60        67.36        15.68        41.06 
TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6S TCGA-DK-AA6T 
       30.67        38.24        15.02        13.58       166.03        12.36 
TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA76 
       10.49         8.65         7.53        13.64        43.50        12.03 
TCGA-DK-AA77 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 
       10.62        43.59        15.35        38.83        24.66         0.10 
TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF 
        0.49         2.24        16.70        17.39         0.56         0.66 
TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7DV 
       14.56        13.97        12.99        14.33         0.92         1.22 
TCGA-E7-A7PW TCGA-E7-A85H TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 
       13.68        12.95         8.09        32.02        16.77         8.94 
TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA 
       33.04         4.01        12.62        22.52        27.98        60.66 
TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SN TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR 
       24.30        23.41        29.16        25.74        46.78        19.79 
TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X 
       12.85        22.98        27.35        14.96        20.91         3.62 
TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX 
       26.73        53.88        11.01        19.33         5.36         5.69 
TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O 
        8.25        27.45        18.08        58.92         2.70         7.10 
TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD 
        6.28        13.35        62.86        18.81         6.15        12.69 
TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FD-A6TK 
       12.36         2.27         3.06         4.31         9.67        10.85 
TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FJ-A871 TCGA-FT-A3EE 
       31.07         7.13        10.65        17.23         8.94         3.25 
TCGA-FT-A61P TCGA-G2-A2EC TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL 
        6.48        22.88        61.94        30.61        15.95        26.93 
TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B 
       35.24        33.01         7.23        20.12        17.62        66.02 
TCGA-G2-AA3C TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO 
        6.94        64.44        19.46        21.40         2.24        15.81 
TCGA-GC-A3RB TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GC-A6I3 
        4.50        14.07        17.75        24.92         8.94        13.91 
TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GD-A76B 
        7.73         2.10         3.12        20.98         2.20         7.36 
TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A764 
       10.92        11.31        11.31         7.63        27.09        20.05 
TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATO TCGA-GU-AATP TCGA-GU-AATQ TCGA-GV-A3JV 
        5.62         4.73        10.65        32.98         7.00        14.27 
TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI 
       21.34        19.10        19.82        20.28         8.48        10.59 
TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-H4-A2HQ 
       27.35         8.58        19.07        22.72         1.51        19.40 
TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU 
       38.60         3.06         9.01         8.22        25.02         3.45 
TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RH TCGA-K4-A5RI 
       21.24         2.76         9.14        27.68         9.07        11.70 
TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO TCGA-LC-A66R 
        1.74         1.81        15.42         6.38        11.80        15.32 
TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-AA26 
       15.58        13.48        12.23        16.67        14.24         3.75 
TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78N 
       12.43        31.56        17.62        37.05        22.68        86.83 
TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE 
       76.01        65.75        35.24        29.56        17.82         4.54 
TCGA-UY-A9PF TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI 
        1.64         1.87        17.88        48.62        64.80        79.66 
TCGA-XF-A9SJ TCGA-XF-A9SL TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY 
        3.22        66.41        12.76        11.90        23.64        21.04 
TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T5 
       28.24        26.27        18.90         2.24        16.27        66.64 
TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMG TCGA-XF-AAMH 
        2.10        13.74        92.98        10.82       110.60        11.31 
TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMW 
       54.90         7.63        71.57        91.73         2.96         8.32 
TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN2 
        6.77        98.99        44.32        56.48        30.94        61.45 
TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 
       86.30        27.06        75.39        18.81         3.88         9.63 
TCGA-YC-A9TC TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R2 
        0.66        11.97        13.64        18.64         7.36        21.11 
TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RC 
       24.13        30.28        27.19        21.86        28.41        74.56 
TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-A9RM 
       13.41         3.48        52.73        52.60        82.49        47.84 
TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4U TCGA-ZF-AA4V 
       20.22         2.89        34.06        19.69         8.61        59.38 
TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA53 TCGA-ZF-AA54 
       60.16        63.02        38.73        35.41        57.90        19.40 
TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-ZF-AA5P 
        8.52        47.15        19.17         5.52        10.13 

  CNOT3 MUTATED CNOT3 WILD-TYPE 
           1.84            0.10 
  CNOT3 MUTATED CNOT3 WILD-TYPE 
         130.88          166.03 
  CNOT3 MUTATED CNOT3 WILD-TYPE 
          14.37           15.68 
[1] "1.8 - 130.9 (14.4)" "0.1 - 166.0 (15.7)"
[1] "hr=" "1.6"
D67V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  CNOT3 MUTATED         0        3         4        4
  CNOT3 WILD-TYPE       4      114       118      124
D67V3, multiclass
           clus
vv          CNOT3 MUTATED CNOT3 WILD-TYPE
  STAGE I               0               4
  STAGE II              3             114
  STAGE III             4             118
  STAGE IV              4             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"
                 vv
clus              T0+T1+T2  T3  T4
  CNOT3 MUTATED          3   7   1
  CNOT3 WILD-TYPE      111 172  51
D67V4, multiclass
          clus
vv         CNOT3 MUTATED CNOT3 WILD-TYPE
  T0+T1+T2             3             111
  T3                   7             172
  T4                   1              51
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  CNOT3 MUTATED     6   2   2   0
  CNOT3 WILD-TYPE 207  39  73   8
D67V5, multiclass
    clus
vv   CNOT3 MUTATED CNOT3 WILD-TYPE
  N0             6             207
  N1             2              39
  N2             2              73
  N3             0               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"
D67V6, binary
                 cls
clus                0   1
  CNOT3 MUTATED     8   1
  CNOT3 WILD-TYPE 174   9
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CNOT3 MUTATED      8    1
  CNOT3 WILD-TYPE  174    9
   clus
vv  CNOT3 MUTATED CNOT3 WILD-TYPE
  0             8             174
  1             1               9
[1] 2 2
[1] FALSE
D67V7, binary
                 cls
clus                0   1
  CNOT3 MUTATED     2   9
  CNOT3 WILD-TYPE  94 271
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CNOT3 MUTATED      2    9
  CNOT3 WILD-TYPE   94  271
        clus
vv       CNOT3 MUTATED CNOT3 WILD-TYPE
  FEMALE             2              94
  MALE               9             271
[1] 2 2
[1] FALSE
D67V8, continuous
[1] "Remove cluster labels:" "CNOT3 MUTATED"         
clus
  CNOT3 MUTATED CNOT3 WILD-TYPE 
              1             119 
     TCGA-2F-A9KO      TCGA-2F-A9KP      TCGA-2F-A9KQ      TCGA-2F-A9KR 
"CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" 
     TCGA-2F-A9KT      TCGA-2F-A9KW      TCGA-CF-A1HS      TCGA-CF-A27C 
"CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" 
     TCGA-CF-A3MF      TCGA-CF-A3MG      TCGA-CF-A3MH      TCGA-CF-A3MI 
"CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" 
     TCGA-CF-A47S      TCGA-CF-A47T      TCGA-CF-A47V      TCGA-CF-A47W 
"CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" 
     TCGA-CF-A47X      TCGA-CF-A47Y      TCGA-CF-A5U8      TCGA-CF-A5UA 
"CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" 
     TCGA-CF-A7I0      TCGA-DK-A2HX      TCGA-DK-A3IN      TCGA-DK-A3IV 
"CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" 
     TCGA-DK-A3WX      TCGA-DK-A3X2      TCGA-DK-A6B2      TCGA-DK-A6B5 
"CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" 
     TCGA-DK-A6B6      TCGA-DK-AA6P      TCGA-DK-AA6S      TCGA-DK-AA6U 
"CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" 
     TCGA-DK-AA6W      TCGA-DK-AA76      TCGA-E5-A2PC      TCGA-E5-A4TZ 
"CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" 
     TCGA-E5-A4U1      TCGA-E7-A519      TCGA-E7-A541      TCGA-E7-A7DU 
"CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" 
     TCGA-E7-A7DV      TCGA-FT-A61P      TCGA-G2-A2EC      TCGA-G2-A2EF 
"CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" 
     TCGA-G2-A2EJ      TCGA-G2-A2EK      TCGA-G2-A2EL      TCGA-G2-A2EO 
"CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" 
     TCGA-G2-A2ES      TCGA-G2-A3IB      TCGA-G2-A3IE      TCGA-G2-A3VY 
"CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" 
     TCGA-GC-A3BM      TCGA-GC-A3I6      TCGA-GC-A3OO      TCGA-GC-A3RD 
"CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" 
     TCGA-GC-A3YS      TCGA-GC-A6I1      TCGA-GC-A6I3      TCGA-GD-A3OS 
"CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" 
     TCGA-GD-A6C6      TCGA-GV-A3JV      TCGA-GV-A3JW      TCGA-GV-A3JX 
"CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" 
     TCGA-GV-A3JZ      TCGA-GV-A3QF      TCGA-GV-A3QH      TCGA-GV-A3QI 
"CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" 
     TCGA-GV-A3QK      TCGA-GV-A40E      TCGA-GV-A40G      TCGA-GV-A6ZA 
"CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" 
     TCGA-SY-A9G0      TCGA-SY-A9G5      TCGA-UY-A78L      TCGA-UY-A78M 
"CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" 
     TCGA-UY-A78N      TCGA-XF-A8HH      TCGA-XF-A8HI      TCGA-XF-A9SG 
"CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" 
     TCGA-XF-A9SH      TCGA-XF-A9SI      TCGA-XF-A9SJ      TCGA-XF-A9SL 
"CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" 
     TCGA-XF-A9SV      TCGA-XF-A9SW      TCGA-XF-A9SX      TCGA-XF-A9SY 
"CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" 
     TCGA-XF-A9SZ      TCGA-XF-A9T0      TCGA-XF-A9T2      TCGA-XF-A9T3 
"CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" 
     TCGA-XF-A9T4      TCGA-XF-A9T5      TCGA-XF-A9T6      TCGA-XF-A9T8 
"CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" 
     TCGA-XF-AAME      TCGA-XF-AAMF      TCGA-XF-AAMG      TCGA-XF-AAMH 
"CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" 
     TCGA-XF-AAMJ      TCGA-XF-AAML      TCGA-XF-AAMQ      TCGA-XF-AAMR 
"CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" 
     TCGA-XF-AAMT      TCGA-XF-AAMW      TCGA-XF-AAMX      TCGA-XF-AAMY 
"CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" 
     TCGA-XF-AAMZ      TCGA-XF-AAN0      TCGA-XF-AAN1      TCGA-XF-AAN2 
"CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" 
     TCGA-XF-AAN3      TCGA-XF-AAN4      TCGA-XF-AAN5      TCGA-XF-AAN7 
"CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" 
     TCGA-XF-AAN8      TCGA-YF-AA3L      TCGA-YF-AA3M 
"CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" "CNOT3 WILD-TYPE" 
D67V9, continuous
D67V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CNOT3 MUTATED       2                         1     7
  CNOT3 WILD-TYPE    36                        20   294
D67V11, multiclass
                           clus
vv                          CNOT3 MUTATED CNOT3 WILD-TYPE
  ASIAN                                 2              36
  BLACK OR AFRICAN AMERICAN             1              20
  WHITE                                 7             294
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V12, binary
                 cls
clus                0   1
  CNOT3 MUTATED     0   7
  CNOT3 WILD-TYPE   8 331
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CNOT3 MUTATED      0    7
  CNOT3 WILD-TYPE    8  331
                        clus
vv                       CNOT3 MUTATED CNOT3 WILD-TYPE
  HISPANIC OR LATINO                 0               8
  NOT HISPANIC OR LATINO             7             331
[1] 2 2
[1] FALSE

Clustering(68) Variable = ARID2 MUTATION ANALYSIS
D68V1, survival
                 sevent
clus2               0   1
  ARID2 MUTATED    15   9
  ARID2 WILD-TYPE 204 142
  ARID2 MUTATED ARID2 WILD-TYPE 
             24             346 
  ARID2 MUTATED ARID2 WILD-TYPE 
              9             142 
$`ARID2 MUTATED`
TCGA-2F-A9KP TCGA-4Z-AA83 TCGA-4Z-AA84 TCGA-BT-A2LB TCGA-CF-A9FF TCGA-DK-A2I4 
       11.97        66.54        15.12        16.18        11.87       123.85 
TCGA-DK-A6AV TCGA-DK-AA76 TCGA-FD-A3N5 TCGA-FD-A3SJ TCGA-FD-A3SN TCGA-FD-A3SR 
       64.18        12.03        22.52        24.30        29.16        19.79 
TCGA-FD-A6TA TCGA-FD-A6TB TCGA-G2-A2EO TCGA-GC-A3WC TCGA-GD-A3OP TCGA-GV-A40G 
       62.86        18.81        35.24        17.75         2.10        19.07 
TCGA-K4-A3WS TCGA-K4-A4AC TCGA-SY-A9G5 TCGA-UY-A9PF TCGA-XF-A8HH TCGA-XF-A9SZ 
       25.02         9.14        31.56         1.64         1.87        28.24 

$`ARID2 WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW TCGA-4Z-AA7M 
       22.29        91.63       103.50       105.70         8.35        16.27 
TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7W 
       44.94        16.83        16.77        17.16        34.98        27.62 
TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA86 TCGA-4Z-AA87 
       49.12         0.62        41.75        51.16        10.22        47.80 
TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ 
       33.83        40.08         7.33         2.66         6.74        12.39 
TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P 
        6.58        13.15        19.04        32.84        12.16        17.88 
TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20W 
       19.50         5.06        14.89        14.96         5.06         8.35 
TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK 
        8.25        17.16        20.48         4.67        12.82         9.96 
TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 
       17.56        28.70        24.26        28.41         8.98         1.94 
TCGA-C4-A0F1 TCGA-C4-A0F6 TCGA-C4-A0F7 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C 
        2.93        23.01         2.04         0.46         0.43         0.69 
TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y 
       10.95        12.66        12.46        12.10        12.62        12.26 
TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YO 
       13.12        12.00        12.10        13.08        12.92         4.90 
TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E 
        7.20         5.46         5.19        16.31         1.84        13.58 
TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB 
       21.86         2.14        66.41        18.41        19.00        16.70 
TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX 
      130.88       112.44        16.14        17.62        15.62         1.81 
TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM 
       10.59         7.79        87.32         2.20        13.58         7.82 
TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV 
        8.22        17.72        50.27        21.30        23.21         9.67 
TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AW 
       20.81        10.55       140.81        48.00        17.98        41.56 
TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L 
       76.60        67.36        15.68        41.06        30.67        38.24 
TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6W 
       15.02        13.58       166.03        12.36        10.49         8.65 
TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA77 TCGA-E5-A2PC TCGA-E5-A4TZ 
        7.53        13.64        43.50        10.62        43.59        15.35 
TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 
       38.83        24.66         0.10         0.49         2.24        16.70 
TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME 
       17.39         0.56         0.66        14.56        13.97        12.99 
TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H 
       14.33         0.92         1.22        13.68        14.07        12.95 
TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 
       14.37         8.09        32.02        16.77         8.94        33.04 
TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SL TCGA-FD-A3SM 
        4.01        12.62        27.98        60.66        23.41        17.98 
TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P 
        5.52        25.74        46.78        12.85        22.98        27.35 
TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT 
       14.96        20.91         3.62        26.73        53.88        11.01 
TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 
       19.33         5.36         5.69         8.25        27.45        18.08 
TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TC 
       58.92         2.70         7.10         6.28        13.35         6.15 
TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI 
       12.69        12.36         2.27         3.06         4.31         9.67 
TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FJ-A871 
       10.85        31.07         7.13        10.65        17.23         8.94 
TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EC TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK 
        3.25         6.48        22.88        61.94        30.61        15.95 
TCGA-G2-A2EL TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B 
       26.93        33.01         7.23        20.12        17.62        66.02 
TCGA-G2-AA3C TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO 
        6.94        64.44        19.46        21.40         2.24        15.81 
TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GC-A6I3 
        4.50        15.91        14.07        24.92         8.94        13.91 
TCGA-GD-A2C5 TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42P 
        7.73         3.12        20.98         2.20         7.36        10.92 
TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 
       11.31        11.31         7.63        27.09        20.05         5.62 
TCGA-GU-A767 TCGA-GU-AATO TCGA-GU-AATP TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW 
        4.73        10.65        32.98         7.00        14.27        21.34 
TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK 
       19.10        19.82        20.28         8.48        10.59        27.35 
TCGA-GV-A40E TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF 
        8.58        22.72         1.51        19.40        38.60         3.06 
TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A54R 
        9.01         8.22         3.45        21.24         2.76        27.68 
TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P 
        9.07        11.70         1.74         1.81        15.42         6.38 
TCGA-K4-AAQO TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN 
       11.80        15.32        15.58        13.48        12.23        16.67 
TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 TCGA-SY-A9G0 TCGA-UY-A78K TCGA-UY-A78L 
       14.24         1.84         3.75        12.43        17.62        37.05 
TCGA-UY-A78M TCGA-UY-A78N TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A9PA TCGA-UY-A9PB 
       22.68        86.83        76.01        65.75        35.24        29.56 
TCGA-UY-A9PD TCGA-UY-A9PE TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI 
       17.82         4.54        17.88        48.62        64.80        79.66 
TCGA-XF-A9SJ TCGA-XF-A9SL TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY 
        3.22        66.41        12.76        11.90        23.64        21.04 
TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 
       26.27        18.90         2.24        16.27        66.64         2.10 
TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMG TCGA-XF-AAMH TCGA-XF-AAMJ 
       13.74        92.98        10.82       110.60        11.31        54.90 
TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX 
        7.63        71.57        91.73         2.96         8.32         6.77 
TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 
       98.99        44.32        56.48        30.94        61.45        86.30 
TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YC-A9TC 
       27.06        75.39        18.81         3.88         9.63         0.66 
TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R3 
       11.97        13.64        18.64         7.36        21.11        24.13 
TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RD 
       30.28        27.19        21.86        28.41        74.56        13.41 
TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-A9RN 
        3.48        52.73        52.60        82.49        47.84        20.22 
TCGA-ZF-AA4N TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W 
        2.89        34.06        19.69         8.61        59.38        60.16 
TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA56 
       63.02        38.73        35.41        57.90        19.40         8.52 
TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-ZF-AA5P 
       47.15        19.17         5.52        10.13 

  ARID2 MUTATED ARID2 WILD-TYPE 
           1.64            0.10 
  ARID2 MUTATED ARID2 WILD-TYPE 
         123.85          166.03 
  ARID2 MUTATED ARID2 WILD-TYPE 
         19.430          15.335 
[1] "1.6 - 123.8 (19.4)" "0.1 - 166.0 (15.3)"
[1] "hr=" "1.3"
D68V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  ARID2 MUTATED         0        8         8        9
  ARID2 WILD-TYPE       4      109       114      119
D68V3, multiclass
           clus
vv          ARID2 MUTATED ARID2 WILD-TYPE
  STAGE I               0               4
  STAGE II              8             109
  STAGE III             8             114
  STAGE IV              9             119
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1+T2  T3  T4
  ARID2 MUTATED          8  13   3
  ARID2 WILD-TYPE      106 166  49
D68V4, multiclass
          clus
vv         ARID2 MUTATED ARID2 WILD-TYPE
  T0+T1+T2             8             106
  T3                  13             166
  T4                   3              49
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  ARID2 MUTATED    16   0   9   0
  ARID2 WILD-TYPE 197  41  66   8
D68V5, multiclass
    clus
vv   ARID2 MUTATED ARID2 WILD-TYPE
  N0            16             197
  N1             0              41
  N2             9              66
  N3             0               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"
D68V6, binary
                 cls
clus                0   1
  ARID2 MUTATED    10   1
  ARID2 WILD-TYPE 172   9
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ARID2 MUTATED     10    1
  ARID2 WILD-TYPE  172    9
   clus
vv  ARID2 MUTATED ARID2 WILD-TYPE
  0            10             172
  1             1               9
[1] 2 2
[1] FALSE
D68V7, binary
                 cls
clus                0   1
  ARID2 MUTATED     6  19
  ARID2 WILD-TYPE  90 261
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ARID2 MUTATED      6   19
  ARID2 WILD-TYPE   90  261
        clus
vv       ARID2 MUTATED ARID2 WILD-TYPE
  FEMALE             6              90
  MALE              19             261
[1] 2 2
[1] FALSE
D68V8, continuous
D68V9, continuous
D68V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ARID2 MUTATED       3                         1    21
  ARID2 WILD-TYPE    35                        20   280
D68V11, multiclass
                           clus
vv                          ARID2 MUTATED ARID2 WILD-TYPE
  ASIAN                                 3              35
  BLACK OR AFRICAN AMERICAN             1              20
  WHITE                                21             280
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V12, binary
                 cls
clus                0   1
  ARID2 MUTATED     1  22
  ARID2 WILD-TYPE   7 316
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ARID2 MUTATED      1   22
  ARID2 WILD-TYPE    7  316
                        clus
vv                       ARID2 MUTATED ARID2 WILD-TYPE
  HISPANIC OR LATINO                 1               7
  NOT HISPANIC OR LATINO            22             316
[1] 2 2
[1] FALSE

Clustering(69) Variable = ZNF773 MUTATION ANALYSIS
D69V1, survival
                  sevent
clus2                0   1
  ZNF773 MUTATED     6   1
  ZNF773 WILD-TYPE 213 150
  ZNF773 MUTATED ZNF773 WILD-TYPE 
               7              363 
  ZNF773 MUTATED ZNF773 WILD-TYPE 
               1              150 
$`ZNF773 MUTATED`
TCGA-DK-A6AW TCGA-E7-A7DV TCGA-FJ-A3ZE TCGA-G2-AA3B TCGA-XF-A9SY TCGA-ZF-A9RG 
       41.56         1.22        10.65        66.02        21.04        52.60 
TCGA-ZF-AA51 
       38.73 

$`ZNF773 WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        91.63       103.50       105.70         8.35 
TCGA-4Z-AA7M TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7S 
       16.27        44.94        16.83        16.77        17.16        34.98 
TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 
       27.62        49.12         0.62        41.75        51.16        66.54 
TCGA-4Z-AA84 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BL-A13I 
       15.12        10.22        47.80        33.83        40.08         7.33 
TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J 
        2.66         6.74        12.39         6.58        13.15        19.04 
TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T 
       32.84        12.16        17.88        19.50         5.06        14.89 
TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB 
       14.96         5.06         8.35         8.25        17.16        16.18 
TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C 
       20.48         4.67        12.82         9.96        17.56        28.70 
TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-C4-A0F6 
       24.26        28.41         8.98         1.94         2.93        23.01 
TCGA-C4-A0F7 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T 
        2.04         0.46         0.43         0.69        10.95        12.66 
TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA 
       12.46        12.10        12.62        12.26        13.12        12.00 
TCGA-CF-A7I0 TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR 
       12.10        11.87        13.08        12.92         4.90         7.20 
TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 
        5.46         5.19        16.31         1.84        13.58        21.86 
TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC 
        2.14        66.41        18.41        19.00        16.70       130.88 
TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 
      112.44        16.14        17.62        15.62         1.81        10.59 
TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM 
        7.79       123.85        87.32         2.20        13.58         7.82 
TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV 
        8.22        17.72        50.27        21.30        23.21         9.67 
TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV 
       20.81        10.55       140.81        48.00        17.98        64.18 
TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L 
       76.60        67.36        15.68        41.06        30.67        38.24 
TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6W 
       15.02        13.58       166.03        12.36        10.49         8.65 
TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A2PC 
        7.53        13.64        43.50        12.03        10.62        43.59 
TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ 
       15.35        38.83        24.66         0.10         0.49         2.24 
TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 
       16.70        17.39         0.56         0.66        14.56        13.97 
TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H 
       12.99        14.33         0.92        13.68        14.07        12.95 
TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 
       14.37         8.09        32.02        16.77         8.94        33.04 
TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ 
        4.01        12.62        22.52        27.98        60.66        24.30 
TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ 
       23.41        17.98        29.16         5.52        25.74        46.78 
TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U 
       19.79        12.85        22.98        27.35        14.96        20.91 
TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV 
        3.62        26.73        53.88        11.01        19.33         5.36 
TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N 
        5.69         8.25        27.45        18.08        58.92         2.70 
TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC 
        7.10         6.28        13.35        62.86        18.81         6.15 
TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI 
       12.69        12.36         2.27         3.06         4.31         9.67 
TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZF TCGA-FJ-A871 TCGA-FT-A3EE 
       10.85        31.07         7.13        17.23         8.94         3.25 
TCGA-FT-A61P TCGA-G2-A2EC TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL 
        6.48        22.88        61.94        30.61        15.95        26.93 
TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3C 
       35.24        33.01         7.23        20.12        17.62         6.94 
TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB 
       64.44        19.46        21.40         2.24        15.81         4.50 
TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GC-A6I3 
       15.91        14.07        17.75        24.92         8.94        13.91 
TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GD-A76B 
        7.73         2.10         3.12        20.98         2.20         7.36 
TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A764 
       10.92        11.31        11.31         7.63        27.09        20.05 
TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATO TCGA-GU-AATP TCGA-GU-AATQ TCGA-GV-A3JV 
        5.62         4.73        10.65        32.98         7.00        14.27 
TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI 
       21.34        19.10        19.82        20.28         8.48        10.59 
TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-H4-A2HQ 
       27.35         8.58        19.07        22.72         1.51        19.40 
TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU 
       38.60         3.06         9.01         8.22        25.02         3.45 
TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RH TCGA-K4-A5RI 
       21.24         2.76         9.14        27.68         9.07        11.70 
TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO TCGA-LC-A66R 
        1.74         1.81        15.42         6.38        11.80        15.32 
TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX 
       15.58        13.48        12.23        16.67        14.24         1.84 
TCGA-S5-AA26 TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M 
        3.75        12.43        31.56        17.62        37.05        22.68 
TCGA-UY-A78N TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD 
       86.83        76.01        65.75        35.24        29.56        17.82 
TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH 
        4.54         1.64         1.87        17.88        48.62        64.80 
TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SL TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SX 
       79.66         3.22        66.41        12.76        11.90        23.64 
TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T5 
       28.24        26.27        18.90         2.24        16.27        66.64 
TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMG TCGA-XF-AAMH 
        2.10        13.74        92.98        10.82       110.60        11.31 
TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMW 
       54.90         7.63        71.57        91.73         2.96         8.32 
TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN2 
        6.77        98.99        44.32        56.48        30.94        61.45 
TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 
       86.30        27.06        75.39        18.81         3.88         9.63 
TCGA-YC-A9TC TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R2 
        0.66        11.97        13.64        18.64         7.36        21.11 
TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RC 
       24.13        30.28        27.19        21.86        28.41        74.56 
TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-A9RN 
       13.41         3.48        52.73        82.49        47.84        20.22 
TCGA-ZF-AA4N TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W 
        2.89        34.06        19.69         8.61        59.38        60.16 
TCGA-ZF-AA4X TCGA-ZF-AA52 TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 
       63.02        35.41        57.90        19.40         8.52        47.15 
TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-ZF-AA5P 
       19.17         5.52        10.13 

  ZNF773 MUTATED ZNF773 WILD-TYPE 
            1.22             0.10 
  ZNF773 MUTATED ZNF773 WILD-TYPE 
           66.02           166.03 
  ZNF773 MUTATED ZNF773 WILD-TYPE 
           38.73            15.58 
[1] "1.2 - 66.0 (38.7)"  "0.1 - 166.0 (15.6)"
[1] "hr=" "4.1"
D69V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  ZNF773 MUTATED         0        3         1        3
  ZNF773 WILD-TYPE       4      114       121      125
D69V3, multiclass
           clus
vv          ZNF773 MUTATED ZNF773 WILD-TYPE
  STAGE I                0                4
  STAGE II               3              114
  STAGE III              1              121
  STAGE IV               3              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"
                  vv
clus               T0+T1+T2  T3  T4
  ZNF773 MUTATED          3   2   1
  ZNF773 WILD-TYPE      111 177  51
D69V4, multiclass
          clus
vv         ZNF773 MUTATED ZNF773 WILD-TYPE
  T0+T1+T2              3              111
  T3                    2              177
  T4                    1               51
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  ZNF773 MUTATED     3   0   1   2
  ZNF773 WILD-TYPE 210  41  74   6
D69V5, multiclass
    clus
vv   ZNF773 MUTATED ZNF773 WILD-TYPE
  N0              3              210
  N1              0               41
  N2              1               74
  N3              2                6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V6, binary
                  cls
clus                 0   1
  ZNF773 MUTATED     3   1
  ZNF773 WILD-TYPE 179   9
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF773 MUTATED      3    1
  ZNF773 WILD-TYPE  179    9
   clus
vv  ZNF773 MUTATED ZNF773 WILD-TYPE
  0              3              179
  1              1                9
[1] 2 2
[1] FALSE
D69V7, binary
                  cls
clus                 0   1
  ZNF773 MUTATED     4   3
  ZNF773 WILD-TYPE  92 277
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF773 MUTATED      4    3
  ZNF773 WILD-TYPE   92  277
        clus
vv       ZNF773 MUTATED ZNF773 WILD-TYPE
  FEMALE              4               92
  MALE                3              277
[1] 2 2
[1] FALSE
D69V8, continuous
[1] "Remove cluster labels:" "ZNF773 MUTATED"        
clus
  ZNF773 MUTATED ZNF773 WILD-TYPE 
               2              118 
      TCGA-2F-A9KO       TCGA-2F-A9KP       TCGA-2F-A9KQ       TCGA-2F-A9KR 
"ZNF773 WILD-TYPE" "ZNF773 WILD-TYPE" "ZNF773 WILD-TYPE" "ZNF773 WILD-TYPE" 
      TCGA-2F-A9KT       TCGA-2F-A9KW       TCGA-CF-A1HS       TCGA-CF-A27C 
"ZNF773 WILD-TYPE" "ZNF773 WILD-TYPE" "ZNF773 WILD-TYPE" "ZNF773 WILD-TYPE" 
      TCGA-CF-A3MF       TCGA-CF-A3MG       TCGA-CF-A3MH       TCGA-CF-A3MI 
"ZNF773 WILD-TYPE" "ZNF773 WILD-TYPE" "ZNF773 WILD-TYPE" "ZNF773 WILD-TYPE" 
      TCGA-CF-A47S       TCGA-CF-A47T       TCGA-CF-A47V       TCGA-CF-A47W 
"ZNF773 WILD-TYPE" "ZNF773 WILD-TYPE" "ZNF773 WILD-TYPE" "ZNF773 WILD-TYPE" 
      TCGA-CF-A47X       TCGA-CF-A47Y       TCGA-CF-A5U8       TCGA-CF-A5UA 
"ZNF773 WILD-TYPE" "ZNF773 WILD-TYPE" "ZNF773 WILD-TYPE" "ZNF773 WILD-TYPE" 
      TCGA-CF-A7I0       TCGA-DK-A2HX       TCGA-DK-A3IN       TCGA-DK-A3IV 
"ZNF773 WILD-TYPE" "ZNF773 WILD-TYPE" "ZNF773 WILD-TYPE" "ZNF773 WILD-TYPE" 
      TCGA-DK-A3WX       TCGA-DK-A3X2       TCGA-DK-A6B2       TCGA-DK-A6B5 
"ZNF773 WILD-TYPE" "ZNF773 WILD-TYPE" "ZNF773 WILD-TYPE" "ZNF773 WILD-TYPE" 
      TCGA-DK-A6B6       TCGA-DK-AA6P       TCGA-DK-AA6S       TCGA-DK-AA6U 
"ZNF773 WILD-TYPE" "ZNF773 WILD-TYPE" "ZNF773 WILD-TYPE" "ZNF773 WILD-TYPE" 
      TCGA-DK-AA6W       TCGA-DK-AA76       TCGA-E5-A2PC       TCGA-E5-A4TZ 
"ZNF773 WILD-TYPE" "ZNF773 WILD-TYPE" "ZNF773 WILD-TYPE" "ZNF773 WILD-TYPE" 
      TCGA-E5-A4U1       TCGA-E7-A519       TCGA-E7-A541       TCGA-E7-A7DU 
"ZNF773 WILD-TYPE" "ZNF773 WILD-TYPE" "ZNF773 WILD-TYPE" "ZNF773 WILD-TYPE" 
      TCGA-FT-A61P       TCGA-G2-A2EC       TCGA-G2-A2EF       TCGA-G2-A2EJ 
"ZNF773 WILD-TYPE" "ZNF773 WILD-TYPE" "ZNF773 WILD-TYPE" "ZNF773 WILD-TYPE" 
      TCGA-G2-A2EK       TCGA-G2-A2EL       TCGA-G2-A2EO       TCGA-G2-A2ES 
"ZNF773 WILD-TYPE" "ZNF773 WILD-TYPE" "ZNF773 WILD-TYPE" "ZNF773 WILD-TYPE" 
      TCGA-G2-A3IB       TCGA-G2-A3IE       TCGA-G2-A3VY       TCGA-GC-A3BM 
"ZNF773 WILD-TYPE" "ZNF773 WILD-TYPE" "ZNF773 WILD-TYPE" "ZNF773 WILD-TYPE" 
      TCGA-GC-A3I6       TCGA-GC-A3OO       TCGA-GC-A3RC       TCGA-GC-A3RD 
"ZNF773 WILD-TYPE" "ZNF773 WILD-TYPE" "ZNF773 WILD-TYPE" "ZNF773 WILD-TYPE" 
      TCGA-GC-A3YS       TCGA-GC-A6I1       TCGA-GC-A6I3       TCGA-GD-A3OS 
"ZNF773 WILD-TYPE" "ZNF773 WILD-TYPE" "ZNF773 WILD-TYPE" "ZNF773 WILD-TYPE" 
      TCGA-GD-A6C6       TCGA-GV-A3JV       TCGA-GV-A3JW       TCGA-GV-A3JX 
"ZNF773 WILD-TYPE" "ZNF773 WILD-TYPE" "ZNF773 WILD-TYPE" "ZNF773 WILD-TYPE" 
      TCGA-GV-A3JZ       TCGA-GV-A3QF       TCGA-GV-A3QH       TCGA-GV-A3QI 
"ZNF773 WILD-TYPE" "ZNF773 WILD-TYPE" "ZNF773 WILD-TYPE" "ZNF773 WILD-TYPE" 
      TCGA-GV-A3QK       TCGA-GV-A40E       TCGA-GV-A40G       TCGA-GV-A6ZA 
"ZNF773 WILD-TYPE" "ZNF773 WILD-TYPE" "ZNF773 WILD-TYPE" "ZNF773 WILD-TYPE" 
      TCGA-SY-A9G0       TCGA-SY-A9G5       TCGA-UY-A78L       TCGA-UY-A78M 
"ZNF773 WILD-TYPE" "ZNF773 WILD-TYPE" "ZNF773 WILD-TYPE" "ZNF773 WILD-TYPE" 
      TCGA-UY-A78N       TCGA-XF-A8HH       TCGA-XF-A8HI       TCGA-XF-A9SG 
"ZNF773 WILD-TYPE" "ZNF773 WILD-TYPE" "ZNF773 WILD-TYPE" "ZNF773 WILD-TYPE" 
      TCGA-XF-A9SH       TCGA-XF-A9SI       TCGA-XF-A9SJ       TCGA-XF-A9SL 
"ZNF773 WILD-TYPE" "ZNF773 WILD-TYPE" "ZNF773 WILD-TYPE" "ZNF773 WILD-TYPE" 
      TCGA-XF-A9SV       TCGA-XF-A9SW       TCGA-XF-A9SX       TCGA-XF-A9SZ 
"ZNF773 WILD-TYPE" "ZNF773 WILD-TYPE" "ZNF773 WILD-TYPE" "ZNF773 WILD-TYPE" 
      TCGA-XF-A9T0       TCGA-XF-A9T2       TCGA-XF-A9T3       TCGA-XF-A9T4 
"ZNF773 WILD-TYPE" "ZNF773 WILD-TYPE" "ZNF773 WILD-TYPE" "ZNF773 WILD-TYPE" 
      TCGA-XF-A9T5       TCGA-XF-A9T6       TCGA-XF-A9T8       TCGA-XF-AAME 
"ZNF773 WILD-TYPE" "ZNF773 WILD-TYPE" "ZNF773 WILD-TYPE" "ZNF773 WILD-TYPE" 
      TCGA-XF-AAMF       TCGA-XF-AAMG       TCGA-XF-AAMH       TCGA-XF-AAMJ 
"ZNF773 WILD-TYPE" "ZNF773 WILD-TYPE" "ZNF773 WILD-TYPE" "ZNF773 WILD-TYPE" 
      TCGA-XF-AAML       TCGA-XF-AAMQ       TCGA-XF-AAMR       TCGA-XF-AAMT 
"ZNF773 WILD-TYPE" "ZNF773 WILD-TYPE" "ZNF773 WILD-TYPE" "ZNF773 WILD-TYPE" 
      TCGA-XF-AAMW       TCGA-XF-AAMX       TCGA-XF-AAMY       TCGA-XF-AAMZ 
"ZNF773 WILD-TYPE" "ZNF773 WILD-TYPE" "ZNF773 WILD-TYPE" "ZNF773 WILD-TYPE" 
      TCGA-XF-AAN0       TCGA-XF-AAN1       TCGA-XF-AAN2       TCGA-XF-AAN3 
"ZNF773 WILD-TYPE" "ZNF773 WILD-TYPE" "ZNF773 WILD-TYPE" "ZNF773 WILD-TYPE" 
      TCGA-XF-AAN4       TCGA-XF-AAN5       TCGA-XF-AAN7       TCGA-XF-AAN8 
"ZNF773 WILD-TYPE" "ZNF773 WILD-TYPE" "ZNF773 WILD-TYPE" "ZNF773 WILD-TYPE" 
      TCGA-YF-AA3L       TCGA-YF-AA3M 
"ZNF773 WILD-TYPE" "ZNF773 WILD-TYPE" 
D69V9, continuous
D69V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ZNF773 MUTATED       0                         0     7
  ZNF773 WILD-TYPE    38                        21   294
D69V11, multiclass
                           clus
vv                          ZNF773 MUTATED ZNF773 WILD-TYPE
  ASIAN                                  0               38
  BLACK OR AFRICAN AMERICAN              0               21
  WHITE                                  7              294
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V12, binary
                  cls
clus                 0   1
  ZNF773 MUTATED     0   7
  ZNF773 WILD-TYPE   8 331
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF773 MUTATED      0    7
  ZNF773 WILD-TYPE    8  331
                        clus
vv                       ZNF773 MUTATED ZNF773 WILD-TYPE
  HISPANIC OR LATINO                  0                8
  NOT HISPANIC OR LATINO              7              331
[1] 2 2
[1] FALSE

Clustering(70) Variable = DAZAP1 MUTATION ANALYSIS
D70V1, survival
                  sevent
clus2                0   1
  DAZAP1 MUTATED     5   1
  DAZAP1 WILD-TYPE 214 150
  DAZAP1 MUTATED DAZAP1 WILD-TYPE 
               6              364 
  DAZAP1 MUTATED DAZAP1 WILD-TYPE 
               1              150 
$`DAZAP1 MUTATED`
TCGA-DK-A3IS TCGA-DK-A6B6 TCGA-E5-A4U1 TCGA-FJ-A3Z9 TCGA-XF-A9SX TCGA-ZF-A9R4 
       50.27        30.67        38.83         7.13        23.64        30.28 

$`DAZAP1 WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        91.63       103.50       105.70         8.35 
TCGA-4Z-AA7M TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7S 
       16.27        44.94        16.83        16.77        17.16        34.98 
TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 
       27.62        49.12         0.62        41.75        51.16        66.54 
TCGA-4Z-AA84 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BL-A13I 
       15.12        10.22        47.80        33.83        40.08         7.33 
TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J 
        2.66         6.74        12.39         6.58        13.15        19.04 
TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T 
       32.84        12.16        17.88        19.50         5.06        14.89 
TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB 
       14.96         5.06         8.35         8.25        17.16        16.18 
TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C 
       20.48         4.67        12.82         9.96        17.56        28.70 
TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-C4-A0F6 
       24.26        28.41         8.98         1.94         2.93        23.01 
TCGA-C4-A0F7 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T 
        2.04         0.46         0.43         0.69        10.95        12.66 
TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA 
       12.46        12.10        12.62        12.26        13.12        12.00 
TCGA-CF-A7I0 TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR 
       12.10        11.87        13.08        12.92         4.90         7.20 
TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 
        5.46         5.19        16.31         1.84        13.58        21.86 
TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC 
        2.14        66.41        18.41        19.00        16.70       130.88 
TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 
      112.44        16.14        17.62        15.62         1.81        10.59 
TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM 
        7.79       123.85        87.32         2.20        13.58         7.82 
TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW 
        8.22        17.72        21.30        23.21         9.67        20.81 
TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW 
       10.55       140.81        48.00        17.98        64.18        41.56 
TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-AA6L TCGA-DK-AA6P 
       76.60        67.36        15.68        41.06        38.24        15.02 
TCGA-DK-AA6Q TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA6X 
       13.58       166.03        12.36        10.49         8.65         7.53 
TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A2PC TCGA-E5-A4TZ 
       13.64        43.50        12.03        10.62        43.59        15.35 
TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 
       24.66         0.10         0.49         2.24        16.70        17.39 
TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF 
        0.56         0.66        14.56        13.97        12.99        14.33 
TCGA-E7-A7DU TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A97P 
        0.92         1.22        13.68        14.07        12.95        14.37 
TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 
        8.09        32.02        16.77         8.94        33.04         4.01 
TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL 
       12.62        22.52        27.98        60.66        24.30        23.41 
TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR 
       17.98        29.16         5.52        25.74        46.78        19.79 
TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X 
       12.85        22.98        27.35        14.96        20.91         3.62 
TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX 
       26.73        53.88        11.01        19.33         5.36         5.69 
TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O 
        8.25        27.45        18.08        58.92         2.70         7.10 
TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD 
        6.28        13.35        62.86        18.81         6.15        12.69 
TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FD-A6TK 
       12.36         2.27         3.06         4.31         9.67        10.85 
TCGA-FJ-A3Z7 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FJ-A871 TCGA-FT-A3EE TCGA-FT-A61P 
       31.07        10.65        17.23         8.94         3.25         6.48 
TCGA-G2-A2EC TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO 
       22.88        61.94        30.61        15.95        26.93        35.24 
TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3C 
       33.01         7.23        20.12        17.62        66.02         6.94 
TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB 
       64.44        19.46        21.40         2.24        15.81         4.50 
TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GC-A6I3 
       15.91        14.07        17.75        24.92         8.94        13.91 
TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GD-A76B 
        7.73         2.10         3.12        20.98         2.20         7.36 
TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A764 
       10.92        11.31        11.31         7.63        27.09        20.05 
TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATO TCGA-GU-AATP TCGA-GU-AATQ TCGA-GV-A3JV 
        5.62         4.73        10.65        32.98         7.00        14.27 
TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI 
       21.34        19.10        19.82        20.28         8.48        10.59 
TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-H4-A2HQ 
       27.35         8.58        19.07        22.72         1.51        19.40 
TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU 
       38.60         3.06         9.01         8.22        25.02         3.45 
TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RH TCGA-K4-A5RI 
       21.24         2.76         9.14        27.68         9.07        11.70 
TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO TCGA-LC-A66R 
        1.74         1.81        15.42         6.38        11.80        15.32 
TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX 
       15.58        13.48        12.23        16.67        14.24         1.84 
TCGA-S5-AA26 TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M 
        3.75        12.43        31.56        17.62        37.05        22.68 
TCGA-UY-A78N TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD 
       86.83        76.01        65.75        35.24        29.56        17.82 
TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH 
        4.54         1.64         1.87        17.88        48.62        64.80 
TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SL TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SY 
       79.66         3.22        66.41        12.76        11.90        21.04 
TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T5 
       28.24        26.27        18.90         2.24        16.27        66.64 
TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMG TCGA-XF-AAMH 
        2.10        13.74        92.98        10.82       110.60        11.31 
TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMW 
       54.90         7.63        71.57        91.73         2.96         8.32 
TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN2 
        6.77        98.99        44.32        56.48        30.94        61.45 
TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 
       86.30        27.06        75.39        18.81         3.88         9.63 
TCGA-YC-A9TC TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R2 
        0.66        11.97        13.64        18.64         7.36        21.11 
TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RD 
       24.13        27.19        21.86        28.41        74.56        13.41 
TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-A9RN 
        3.48        52.73        52.60        82.49        47.84        20.22 
TCGA-ZF-AA4N TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W 
        2.89        34.06        19.69         8.61        59.38        60.16 
TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA56 
       63.02        38.73        35.41        57.90        19.40         8.52 
TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-ZF-AA5P 
       47.15        19.17         5.52        10.13 

  DAZAP1 MUTATED DAZAP1 WILD-TYPE 
            7.13             0.10 
  DAZAP1 MUTATED DAZAP1 WILD-TYPE 
           50.27           166.03 
  DAZAP1 MUTATED DAZAP1 WILD-TYPE 
          30.475           15.500 
[1] "7.1 - 50.3 (30.5)"  "0.1 - 166.0 (15.5)"
[1] "hr=" "3.5"
D70V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  DAZAP1 MUTATED         1        4         0        1
  DAZAP1 WILD-TYPE       3      113       122      127
D70V3, multiclass
           clus
vv          DAZAP1 MUTATED DAZAP1 WILD-TYPE
  STAGE I                1                3
  STAGE II               4              113
  STAGE III              0              122
  STAGE IV               1              127
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1+T2  T3  T4
  DAZAP1 MUTATED          4   1   0
  DAZAP1 WILD-TYPE      110 178  52
D70V4, multiclass
          clus
vv         DAZAP1 MUTATED DAZAP1 WILD-TYPE
  T0+T1+T2              4              110
  T3                    1              178
  T4                    0               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"
                  vv
clus                N0  N1  N2  N3
  DAZAP1 MUTATED     3   0   1   0
  DAZAP1 WILD-TYPE 210  41  74   8
D70V5, multiclass
    clus
vv   DAZAP1 MUTATED DAZAP1 WILD-TYPE
  N0              3              210
  N1              0               41
  N2              1               74
  N3              0                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"
D70V6, binary
                  cls
clus                 0   1
  DAZAP1 MUTATED     4   0
  DAZAP1 WILD-TYPE 178  10
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DAZAP1 MUTATED      4    0
  DAZAP1 WILD-TYPE  178   10
   clus
vv  DAZAP1 MUTATED DAZAP1 WILD-TYPE
  0              4              178
  1              0               10
[1] 2 2
[1] FALSE
D70V7, binary
                  cls
clus                 0   1
  DAZAP1 MUTATED     1   5
  DAZAP1 WILD-TYPE  95 275
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DAZAP1 MUTATED      1    5
  DAZAP1 WILD-TYPE   95  275
        clus
vv       DAZAP1 MUTATED DAZAP1 WILD-TYPE
  FEMALE              1               95
  MALE                5              275
[1] 2 2
[1] FALSE
D70V8, continuous
D70V9, continuous
D70V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DAZAP1 MUTATED       0                         0     5
  DAZAP1 WILD-TYPE    38                        21   296
D70V11, multiclass
                           clus
vv                          DAZAP1 MUTATED DAZAP1 WILD-TYPE
  ASIAN                                  0               38
  BLACK OR AFRICAN AMERICAN              0               21
  WHITE                                  5              296
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V12, binary
                  cls
clus                 0   1
  DAZAP1 MUTATED     0   6
  DAZAP1 WILD-TYPE   8 332
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DAZAP1 MUTATED      0    6
  DAZAP1 WILD-TYPE    8  332
                        clus
vv                       DAZAP1 MUTATED DAZAP1 WILD-TYPE
  HISPANIC OR LATINO                  0                8
  NOT HISPANIC OR LATINO              6              332
[1] 2 2
[1] FALSE

Clustering(71) Variable = ADC MUTATION ANALYSIS
D71V1, survival
               sevent
clus2             0   1
  ADC MUTATED     4   2
  ADC WILD-TYPE 215 149
  ADC MUTATED ADC WILD-TYPE 
            6           364 
  ADC MUTATED ADC WILD-TYPE 
            2           149 
$`ADC MUTATED`
TCGA-2F-A9KT TCGA-4Z-AA87 TCGA-DK-A6B2 TCGA-G2-A3IE TCGA-XF-A9SW TCGA-ZF-A9R7 
      105.70        47.80        15.68        20.12        11.90        21.86 

$`ADC WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KW TCGA-4Z-AA7M 
       22.29        11.97        91.63       103.50         8.35        16.27 
TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7W 
       44.94        16.83        16.77        17.16        34.98        27.62 
TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA84 
       49.12         0.62        41.75        51.16        66.54        15.12 
TCGA-4Z-AA86 TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM 
       10.22        33.83        40.08         7.33         2.66         6.74 
TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O 
       12.39         6.58        13.15        19.04        32.84        12.16 
TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20V 
       17.88        19.50         5.06        14.89        14.96         5.06 
TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH 
        8.35         8.25        17.16        16.18        20.48         4.67 
TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E TCGA-BT-A42F 
       12.82         9.96        17.56        28.70        24.26        28.41 
TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-C4-A0F6 TCGA-C4-A0F7 TCGA-CF-A1HR 
        8.98         1.94         2.93        23.01         2.04         0.46 
TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W 
        0.43         0.69        10.95        12.66        12.46        12.10 
TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A9FF 
       12.62        12.26        13.12        12.00        12.10        11.87 
TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3QU 
       13.08        12.92         4.90         7.20         5.46         5.19 
TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 
       16.31         1.84        13.58        21.86         2.14        66.41 
TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE 
       18.41        19.00        16.70       130.88       112.44        16.14 
TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 
       17.62        15.62         1.81        10.59         7.79       123.85 
TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ 
       87.32         2.20        13.58         7.82         8.22        17.72 
TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX 
       50.27        21.30        23.21         9.67        20.81        10.55 
TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 
      140.81        48.00        17.98        64.18        41.56        76.60 
TCGA-DK-A6B1 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6P TCGA-DK-AA6Q 
       67.36        41.06        30.67        38.24        15.02        13.58 
TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA71 
      166.03        12.36        10.49         8.65         7.53        13.64 
TCGA-DK-AA74 TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E5-A4U1 
       43.50        12.03        10.62        43.59        15.35        38.83 
TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 
       24.66         0.10         0.49         2.24        16.70        17.39 
TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF 
        0.56         0.66        14.56        13.97        12.99        14.33 
TCGA-E7-A7DU TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A97P 
        0.92         1.22        13.68        14.07        12.95        14.37 
TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 
        8.09        32.02        16.77         8.94        33.04         4.01 
TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL 
       12.62        22.52        27.98        60.66        24.30        23.41 
TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR 
       17.98        29.16         5.52        25.74        46.78        19.79 
TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X 
       12.85        22.98        27.35        14.96        20.91         3.62 
TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX 
       26.73        53.88        11.01        19.33         5.36         5.69 
TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O 
        8.25        27.45        18.08        58.92         2.70         7.10 
TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD 
        6.28        13.35        62.86        18.81         6.15        12.69 
TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FD-A6TK 
       12.36         2.27         3.06         4.31         9.67        10.85 
TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FJ-A871 TCGA-FT-A3EE 
       31.07         7.13        10.65        17.23         8.94         3.25 
TCGA-FT-A61P TCGA-G2-A2EC TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL 
        6.48        22.88        61.94        30.61        15.95        26.93 
TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3C 
       35.24        33.01         7.23        17.62        66.02         6.94 
TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB 
       64.44        19.46        21.40         2.24        15.81         4.50 
TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GC-A6I3 
       15.91        14.07        17.75        24.92         8.94        13.91 
TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GD-A76B 
        7.73         2.10         3.12        20.98         2.20         7.36 
TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A764 
       10.92        11.31        11.31         7.63        27.09        20.05 
TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATO TCGA-GU-AATP TCGA-GU-AATQ TCGA-GV-A3JV 
        5.62         4.73        10.65        32.98         7.00        14.27 
TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI 
       21.34        19.10        19.82        20.28         8.48        10.59 
TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-H4-A2HQ 
       27.35         8.58        19.07        22.72         1.51        19.40 
TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU 
       38.60         3.06         9.01         8.22        25.02         3.45 
TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RH TCGA-K4-A5RI 
       21.24         2.76         9.14        27.68         9.07        11.70 
TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO TCGA-LC-A66R 
        1.74         1.81        15.42         6.38        11.80        15.32 
TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX 
       15.58        13.48        12.23        16.67        14.24         1.84 
TCGA-S5-AA26 TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M 
        3.75        12.43        31.56        17.62        37.05        22.68 
TCGA-UY-A78N TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD 
       86.83        76.01        65.75        35.24        29.56        17.82 
TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH 
        4.54         1.64         1.87        17.88        48.62        64.80 
TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SL TCGA-XF-A9SV TCGA-XF-A9SX TCGA-XF-A9SY 
       79.66         3.22        66.41        12.76        23.64        21.04 
TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T5 
       28.24        26.27        18.90         2.24        16.27        66.64 
TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMG TCGA-XF-AAMH 
        2.10        13.74        92.98        10.82       110.60        11.31 
TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMW 
       54.90         7.63        71.57        91.73         2.96         8.32 
TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN2 
        6.77        98.99        44.32        56.48        30.94        61.45 
TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 
       86.30        27.06        75.39        18.81         3.88         9.63 
TCGA-YC-A9TC TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R2 
        0.66        11.97        13.64        18.64         7.36        21.11 
TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RD 
       24.13        30.28        27.19        28.41        74.56        13.41 
TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-A9RN 
        3.48        52.73        52.60        82.49        47.84        20.22 
TCGA-ZF-AA4N TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W 
        2.89        34.06        19.69         8.61        59.38        60.16 
TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA56 
       63.02        38.73        35.41        57.90        19.40         8.52 
TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-ZF-AA5P 
       47.15        19.17         5.52        10.13 

  ADC MUTATED ADC WILD-TYPE 
         11.9           0.1 
  ADC MUTATED ADC WILD-TYPE 
       105.70        166.03 
  ADC MUTATED ADC WILD-TYPE 
        20.99         15.50 
[1] "11.9 - 105.7 (21.0)" "0.1 - 166.0 (15.5)" 
[1] "hr=" "1.8"
D71V2, continuous
               vv
clus            STAGE I STAGE II STAGE III STAGE IV
  ADC MUTATED         0        3         1        2
  ADC WILD-TYPE       4      114       121      126
D71V3, multiclass
           clus
vv          ADC MUTATED ADC WILD-TYPE
  STAGE I             0             4
  STAGE II            3           114
  STAGE III           1           121
  STAGE IV            2           126
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            T0+T1+T2  T3  T4
  ADC MUTATED          1   2   1
  ADC WILD-TYPE      113 177  51
D71V4, multiclass
          clus
vv         ADC MUTATED ADC WILD-TYPE
  T0+T1+T2           1           113
  T3                 2           177
  T4                 1            51
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             N0  N1  N2  N3
  ADC MUTATED     2   1   1   0
  ADC WILD-TYPE 211  40  74   8
D71V5, multiclass
    clus
vv   ADC MUTATED ADC WILD-TYPE
  N0           2           211
  N1           1            40
  N2           1            74
  N3           0             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"
D71V6, binary
               cls
clus              0   1
  ADC MUTATED     4   0
  ADC WILD-TYPE 178  10
[1] "tbl2"
               cls
clus            [,1] [,2]
  ADC MUTATED      4    0
  ADC WILD-TYPE  178   10
   clus
vv  ADC MUTATED ADC WILD-TYPE
  0           4           178
  1           0            10
[1] 2 2
[1] FALSE
D71V7, binary
               cls
clus              0   1
  ADC MUTATED     1   5
  ADC WILD-TYPE  95 275
[1] "tbl2"
               cls
clus            [,1] [,2]
  ADC MUTATED      1    5
  ADC WILD-TYPE   95  275
        clus
vv       ADC MUTATED ADC WILD-TYPE
  FEMALE           1            95
  MALE             5           275
[1] 2 2
[1] FALSE
D71V8, continuous
D71V9, continuous
D71V10, continuous
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ADC MUTATED       0                         1     5
  ADC WILD-TYPE    38                        20   296
D71V11, multiclass
                           clus
vv                          ADC MUTATED ADC WILD-TYPE
  ASIAN                               0            38
  BLACK OR AFRICAN AMERICAN           1            20
  WHITE                               5           296
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V12, binary
               cls
clus              0   1
  ADC MUTATED     0   5
  ADC WILD-TYPE   8 333
[1] "tbl2"
               cls
clus            [,1] [,2]
  ADC MUTATED      0    5
  ADC WILD-TYPE    8  333
                        clus
vv                       ADC MUTATED ADC WILD-TYPE
  HISPANIC OR LATINO               0             8
  NOT HISPANIC OR LATINO           5           333
[1] 2 2
[1] FALSE

Clustering(72) Variable = FUT5 MUTATION ANALYSIS
D72V1, survival
                sevent
clus2              0   1
  FUT5 MUTATED     2   1
  FUT5 WILD-TYPE 217 150
  FUT5 MUTATED FUT5 WILD-TYPE 
             3            367 
  FUT5 MUTATED FUT5 WILD-TYPE 
             1            150 
$`FUT5 MUTATED`
TCGA-FJ-A3ZE TCGA-S5-AA26 TCGA-ZF-A9RC 
       10.65         3.75        74.56 

$`FUT5 WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        91.63       103.50       105.70         8.35 
TCGA-4Z-AA7M TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7S 
       16.27        44.94        16.83        16.77        17.16        34.98 
TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 
       27.62        49.12         0.62        41.75        51.16        66.54 
TCGA-4Z-AA84 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BL-A13I 
       15.12        10.22        47.80        33.83        40.08         7.33 
TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J 
        2.66         6.74        12.39         6.58        13.15        19.04 
TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T 
       32.84        12.16        17.88        19.50         5.06        14.89 
TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB 
       14.96         5.06         8.35         8.25        17.16        16.18 
TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C 
       20.48         4.67        12.82         9.96        17.56        28.70 
TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-C4-A0F6 
       24.26        28.41         8.98         1.94         2.93        23.01 
TCGA-C4-A0F7 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T 
        2.04         0.46         0.43         0.69        10.95        12.66 
TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA 
       12.46        12.10        12.62        12.26        13.12        12.00 
TCGA-CF-A7I0 TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR 
       12.10        11.87        13.08        12.92         4.90         7.20 
TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 
        5.46         5.19        16.31         1.84        13.58        21.86 
TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC 
        2.14        66.41        18.41        19.00        16.70       130.88 
TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 
      112.44        16.14        17.62        15.62         1.81        10.59 
TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM 
        7.79       123.85        87.32         2.20        13.58         7.82 
TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV 
        8.22        17.72        50.27        21.30        23.21         9.67 
TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV 
       20.81        10.55       140.81        48.00        17.98        64.18 
TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 
       41.56        76.60        67.36        15.68        41.06        30.67 
TCGA-DK-AA6L TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6U 
       38.24        15.02        13.58       166.03        12.36        10.49 
TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA76 TCGA-DK-AA77 
        8.65         7.53        13.64        43.50        12.03        10.62 
TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ 
       43.59        15.35        38.83        24.66         0.10         0.49 
TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 
        2.24        16.70        17.39         0.56         0.66        14.56 
TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7DV TCGA-E7-A7PW 
       13.97        12.99        14.33         0.92         1.22        13.68 
TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 
       14.07        12.95        14.37         8.09        32.02        16.77 
TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 
        8.94        33.04         4.01        12.62        22.52        27.98 
TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO 
       60.66        24.30        23.41        17.98        29.16         5.52 
TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P 
       25.74        46.78        19.79        12.85        22.98        27.35 
TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT 
       14.96        20.91         3.62        26.73        53.88        11.01 
TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 
       19.33         5.36         5.69         8.25        27.45        18.08 
TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA 
       58.92         2.70         7.10         6.28        13.35        62.86 
TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TG 
       18.81         6.15        12.69        12.36         2.27         3.06 
TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZF 
        4.31         9.67        10.85        31.07         7.13        17.23 
TCGA-FJ-A871 TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EC TCGA-G2-A2EF TCGA-G2-A2EJ 
        8.94         3.25         6.48        22.88        61.94        30.61 
TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE 
       15.95        26.93        35.24        33.01         7.23        20.12 
TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3BM 
       17.62        66.02         6.94        64.44        19.46        21.40 
TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC 
        2.24        15.81         4.50        15.91        14.07        17.75 
TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ 
       24.92         8.94        13.91         7.73         2.10         3.12 
TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R 
       20.98         2.20         7.36        10.92        11.31        11.31 
TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATO 
        7.63        27.09        20.05         5.62         4.73        10.65 
TCGA-GU-AATP TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ 
       32.98         7.00        14.27        21.34        19.10        19.82 
TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G 
       20.28         8.48        10.59        27.35         8.58        19.07 
TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND 
       22.72         1.51        19.40        38.60         3.06         9.01 
TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC 
        8.22        25.02         3.45        21.24         2.76         9.14 
TCGA-K4-A54R TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB 
       27.68         9.07        11.70         1.74         1.81        15.42 
TCGA-K4-A83P TCGA-K4-AAQO TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI 
        6.38        11.80        15.32        15.58        13.48        12.23 
TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78K 
       16.67        14.24         1.84        12.43        31.56        17.62 
TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78N TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A9PA 
       37.05        22.68        86.83        76.01        65.75        35.24 
TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HH TCGA-XF-A8HI 
       29.56        17.82         4.54         1.64         1.87        17.88 
TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SL TCGA-XF-A9SV 
       48.62        64.80        79.66         3.22        66.41        12.76 
TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 
       11.90        23.64        21.04        28.24        26.27        18.90 
TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAME 
        2.24        16.27        66.64         2.10        13.74        92.98 
TCGA-XF-AAMF TCGA-XF-AAMG TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ 
       10.82       110.60        11.31        54.90         7.63        71.57 
TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAMZ 
       91.73         2.96         8.32         6.77        98.99        44.32 
TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN5 
       56.48        30.94        61.45        86.30        27.06        75.39 
TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-YF-AA3M 
       18.81         3.88         9.63         0.66        11.97        13.64 
TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R5 
       18.64         7.36        21.11        24.13        30.28        27.19 
TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RG 
       21.86        28.41        13.41         3.48        52.73        52.60 
TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4R TCGA-ZF-AA4T 
       82.49        47.84        20.22         2.89        34.06        19.69 
TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 
        8.61        59.38        60.16        63.02        38.73        35.41 
TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N 
       57.90        19.40         8.52        47.15        19.17         5.52 
TCGA-ZF-AA5P 
       10.13 

  FUT5 MUTATED FUT5 WILD-TYPE 
          3.75           0.10 
  FUT5 MUTATED FUT5 WILD-TYPE 
         74.56         166.03 
  FUT5 MUTATED FUT5 WILD-TYPE 
         10.65          15.68 
[1] "3.8 - 74.6 (10.7)"  "0.1 - 166.0 (15.7)"
[1] "hr=" "1.3"
D72V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  FUT5 MUTATED         0        0         2        1
  FUT5 WILD-TYPE       4      117       120      127
D72V3, multiclass
           clus
vv          FUT5 MUTATED FUT5 WILD-TYPE
  STAGE I              0              4
  STAGE II             0            117
  STAGE III            2            120
  STAGE IV             1            127
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1+T2  T3  T4
  FUT5 MUTATED          0   2   0
  FUT5 WILD-TYPE      114 177  52
D72V4, multiclass
[1] "Remove cluster labels:" "FUT5 MUTATED"          
clus
  FUT5 MUTATED FUT5 WILD-TYPE 
             2            343 
    TCGA-2F-A9KO     TCGA-2F-A9KP     TCGA-2F-A9KQ     TCGA-2F-A9KR 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-2F-A9KT     TCGA-2F-A9KW     TCGA-4Z-AA7M     TCGA-4Z-AA7N 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-4Z-AA7O     TCGA-4Z-AA7Q     TCGA-4Z-AA7R     TCGA-4Z-AA7S 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-4Z-AA7W     TCGA-4Z-AA7Y     TCGA-4Z-AA80     TCGA-4Z-AA81 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-4Z-AA82     TCGA-4Z-AA83     TCGA-4Z-AA84     TCGA-4Z-AA86 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-4Z-AA87     TCGA-4Z-AA89     TCGA-BL-A0C8     TCGA-BL-A13I 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-BL-A13J     TCGA-BL-A3JM     TCGA-BL-A5ZZ     TCGA-BT-A0S7 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-BT-A0YX     TCGA-BT-A20J     TCGA-BT-A20N     TCGA-BT-A20O 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-BT-A20P     TCGA-BT-A20Q     TCGA-BT-A20R     TCGA-BT-A20T 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-BT-A20U     TCGA-BT-A20V     TCGA-BT-A20W     TCGA-BT-A20X 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-BT-A2LA     TCGA-BT-A2LB     TCGA-BT-A2LD     TCGA-BT-A3PH 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-BT-A3PJ     TCGA-BT-A3PK     TCGA-BT-A42B     TCGA-BT-A42E 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-BT-A42F     TCGA-C4-A0EZ     TCGA-C4-A0F0     TCGA-C4-A0F1 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-C4-A0F6     TCGA-C4-A0F7     TCGA-CF-A1HR     TCGA-CF-A1HS 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-CF-A27C     TCGA-CF-A3MF     TCGA-CF-A3MG     TCGA-CF-A3MH 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-CF-A3MI     TCGA-CF-A47S     TCGA-CF-A47T     TCGA-CF-A47V 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-CF-A47W     TCGA-CF-A47X     TCGA-CF-A47Y     TCGA-CF-A5U8 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-CF-A5UA     TCGA-CF-A7I0     TCGA-CF-A9FF     TCGA-CF-A9FH 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-CF-A9FM     TCGA-CU-A0YN     TCGA-CU-A0YO     TCGA-CU-A0YR 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-CU-A3KJ     TCGA-CU-A3QU     TCGA-CU-A3YL     TCGA-CU-A5W6 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-CU-A72E     TCGA-DK-A1A3     TCGA-DK-A1A5     TCGA-DK-A1A6 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-DK-A1A7     TCGA-DK-A1AA     TCGA-DK-A1AB     TCGA-DK-A1AC 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-DK-A1AD     TCGA-DK-A1AE     TCGA-DK-A1AF     TCGA-DK-A1AG 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-DK-A2HX     TCGA-DK-A2I1     TCGA-DK-A2I2     TCGA-DK-A2I4 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-DK-A2I6     TCGA-DK-A3IK     TCGA-DK-A3IL     TCGA-DK-A3IM 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-DK-A3IN     TCGA-DK-A3IQ     TCGA-DK-A3IS     TCGA-DK-A3IT 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-DK-A3IU     TCGA-DK-A3WW     TCGA-DK-A3WX     TCGA-DK-A3WY 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-DK-A3X1     TCGA-DK-A3X2     TCGA-DK-A6AV     TCGA-DK-A6AW 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-DK-A6B0     TCGA-DK-A6B1     TCGA-DK-A6B2     TCGA-DK-A6B5 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-DK-AA6L     TCGA-DK-AA6Q     TCGA-DK-AA6S     TCGA-DK-AA6W 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-DK-AA71     TCGA-DK-AA74     TCGA-DK-AA77     TCGA-E5-A2PC 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-E5-A4TZ     TCGA-E5-A4U1     TCGA-E7-A3X6     TCGA-E7-A4IJ 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-E7-A4XJ     TCGA-E7-A519     TCGA-E7-A541     TCGA-E7-A5KE 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-E7-A5KF     TCGA-E7-A677     TCGA-E7-A678     TCGA-E7-A6ME 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-E7-A6MF     TCGA-E7-A7DU     TCGA-E7-A7DV     TCGA-E7-A7PW 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-E7-A7XN     TCGA-E7-A85H     TCGA-E7-A97P     TCGA-E7-A97Q 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-FD-A3B3     TCGA-FD-A3B4     TCGA-FD-A3B5     TCGA-FD-A3B6 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-FD-A3B7     TCGA-FD-A3B8     TCGA-FD-A3N5     TCGA-FD-A3N6 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-FD-A3NA     TCGA-FD-A3SJ     TCGA-FD-A3SL     TCGA-FD-A3SM 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-FD-A3SN     TCGA-FD-A3SO     TCGA-FD-A3SP     TCGA-FD-A3SQ 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-FD-A3SR     TCGA-FD-A3SS     TCGA-FD-A43N     TCGA-FD-A43P 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-FD-A43S     TCGA-FD-A43U     TCGA-FD-A43X     TCGA-FD-A5BR 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-FD-A5BS     TCGA-FD-A5BT     TCGA-FD-A5BU     TCGA-FD-A5BV 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-FD-A5BX     TCGA-FD-A5BY     TCGA-FD-A5BZ     TCGA-FD-A5C0 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-FD-A5C1     TCGA-FD-A62N     TCGA-FD-A62O     TCGA-FD-A62P 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-FD-A62S     TCGA-FD-A6TA     TCGA-FD-A6TB     TCGA-FD-A6TC 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-FD-A6TD     TCGA-FD-A6TE     TCGA-FD-A6TF     TCGA-FD-A6TG 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-FD-A6TH     TCGA-FD-A6TI     TCGA-FD-A6TK     TCGA-FJ-A3Z7 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-FJ-A3Z9     TCGA-FJ-A871     TCGA-FT-A3EE     TCGA-FT-A61P 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-G2-A2EO     TCGA-G2-A2ES     TCGA-G2-AA3B     TCGA-G2-AA3C 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-G2-AA3D     TCGA-G2-AA3F     TCGA-GC-A3BM     TCGA-GC-A3I6 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-GC-A3OO     TCGA-GC-A3RB     TCGA-GC-A3RC     TCGA-GC-A3RD 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-GC-A3WC     TCGA-GC-A3YS     TCGA-GC-A6I1     TCGA-GC-A6I3 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-GD-A2C5     TCGA-GD-A3OP     TCGA-GD-A3OQ     TCGA-GD-A6C6 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-GD-A76B     TCGA-GU-A42P     TCGA-GU-A42Q     TCGA-GU-A42R 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-GU-A762     TCGA-GU-A763     TCGA-GU-A764     TCGA-GU-A766 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-GU-A767     TCGA-GU-AATO     TCGA-GU-AATP     TCGA-GU-AATQ 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-GV-A3JV     TCGA-GV-A3JW     TCGA-GV-A3JX     TCGA-GV-A3JZ 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-GV-A3QF     TCGA-GV-A3QG     TCGA-GV-A3QI     TCGA-GV-A3QK 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-GV-A40G     TCGA-GV-A6ZA     TCGA-H4-A2HO     TCGA-HQ-A2OE 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-HQ-A2OF     TCGA-HQ-A5ND     TCGA-HQ-A5NE     TCGA-K4-A3WS 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-K4-A3WU     TCGA-K4-A3WV     TCGA-K4-A4AB     TCGA-K4-A4AC 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-K4-A54R     TCGA-K4-A5RH     TCGA-K4-A5RI     TCGA-K4-A5RJ 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-K4-A6FZ     TCGA-K4-A6MB     TCGA-K4-A83P     TCGA-K4-AAQO 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-LC-A66R     TCGA-MV-A51V     TCGA-PQ-A6FI     TCGA-PQ-A6FN 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-R3-A69X     TCGA-S5-A6DX     TCGA-SY-A9G0     TCGA-SY-A9G5 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-UY-A78M     TCGA-UY-A78N     TCGA-UY-A78O     TCGA-UY-A8OB 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-UY-A9PA     TCGA-UY-A9PB     TCGA-UY-A9PD     TCGA-UY-A9PE 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-UY-A9PF     TCGA-XF-A8HH     TCGA-XF-A8HI     TCGA-XF-A9SG 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-XF-A9SH     TCGA-XF-A9SI     TCGA-XF-A9SJ     TCGA-XF-A9SL 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-XF-A9SV     TCGA-XF-A9SW     TCGA-XF-A9SX     TCGA-XF-A9SY 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-XF-A9SZ     TCGA-XF-A9T0     TCGA-XF-A9T2     TCGA-XF-A9T3 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-XF-A9T4     TCGA-XF-A9T5     TCGA-XF-A9T6     TCGA-XF-A9T8 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-XF-AAME     TCGA-XF-AAMF     TCGA-XF-AAMG     TCGA-XF-AAMH 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-XF-AAMJ     TCGA-XF-AAML     TCGA-XF-AAMQ     TCGA-XF-AAMR 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-XF-AAMT     TCGA-XF-AAMW     TCGA-XF-AAMX     TCGA-XF-AAMY 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-XF-AAMZ     TCGA-XF-AAN0     TCGA-XF-AAN1     TCGA-XF-AAN2 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-XF-AAN3     TCGA-XF-AAN4     TCGA-XF-AAN5     TCGA-XF-AAN7 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-XF-AAN8     TCGA-YC-A8S6     TCGA-YF-AA3L     TCGA-YF-AA3M 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-ZF-A9R0     TCGA-ZF-A9R1     TCGA-ZF-A9R2     TCGA-ZF-A9R3 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-ZF-A9R4     TCGA-ZF-A9R5     TCGA-ZF-A9R9     TCGA-ZF-A9RD 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-ZF-A9RF     TCGA-ZF-A9RG     TCGA-ZF-A9RM     TCGA-ZF-A9RN 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-ZF-AA4R     TCGA-ZF-AA4T     TCGA-ZF-AA4U     TCGA-ZF-AA4V 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-ZF-AA4W     TCGA-ZF-AA4X     TCGA-ZF-AA51     TCGA-ZF-AA52 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-ZF-AA53     TCGA-ZF-AA54     TCGA-ZF-AA56     TCGA-ZF-AA58 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-ZF-AA5H     TCGA-ZF-AA5N     TCGA-ZF-AA5P 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
                vv
clus              N0  N1  N2  N3
  FUT5 MUTATED     2   0   0   1
  FUT5 WILD-TYPE 211  41  75   7
D72V5, multiclass
    clus
vv   FUT5 MUTATED FUT5 WILD-TYPE
  N0            2            211
  N1            0             41
  N2            0             75
  N3            1              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"
D72V6, binary
                cls
clus               0   1
  FUT5 MUTATED     0   1
  FUT5 WILD-TYPE 182   9
[1] "tbl2"
                cls
clus             [,1] [,2]
  FUT5 MUTATED      0    1
  FUT5 WILD-TYPE  182    9
   clus
vv  FUT5 MUTATED FUT5 WILD-TYPE
  0            0            182
  1            1              9
[1] 2 2
[1] FALSE
D72V7, binary
                cls
clus               0   1
  FUT5 MUTATED     0   3
  FUT5 WILD-TYPE  96 277
[1] "tbl2"
                cls
clus             [,1] [,2]
  FUT5 MUTATED      0    3
  FUT5 WILD-TYPE   96  277
        clus
vv       FUT5 MUTATED FUT5 WILD-TYPE
  FEMALE            0             96
  MALE              3            277
[1] 2 2
[1] FALSE
D72V8, continuous
D72V9, continuous
[1] "Remove cluster labels:" "FUT5 MUTATED"          
clus
  FUT5 MUTATED FUT5 WILD-TYPE 
             1            204 
    TCGA-2F-A9KO     TCGA-2F-A9KP     TCGA-2F-A9KR     TCGA-4Z-AA7M 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-4Z-AA89     TCGA-BL-A0C8     TCGA-BL-A13I     TCGA-BL-A13J 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-BL-A3JM     TCGA-BL-A5ZZ     TCGA-BT-A20J     TCGA-BT-A20N 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-BT-A2LA     TCGA-BT-A42B     TCGA-BT-A42C     TCGA-BT-A42E 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-C4-A0EZ     TCGA-C4-A0F0     TCGA-C4-A0F1     TCGA-C4-A0F6 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-CF-A3MH     TCGA-CF-A3MI     TCGA-CF-A47W     TCGA-CF-A47X 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-CF-A5UA     TCGA-CF-A9FH     TCGA-CU-A0YN     TCGA-CU-A0YR 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-CU-A3KJ     TCGA-CU-A3QU     TCGA-CU-A3YL     TCGA-CU-A5W6 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-CU-A72E     TCGA-DK-A1A3     TCGA-DK-A1A5     TCGA-DK-A1A6 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-DK-A1AA     TCGA-DK-A1AC     TCGA-DK-A1AE     TCGA-DK-A2HX 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-DK-A2I6     TCGA-DK-A3IL     TCGA-DK-A3IM     TCGA-DK-A3IN 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-DK-A3IQ     TCGA-DK-A3IU     TCGA-DK-A3IV     TCGA-DK-A3WX 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-DK-A3X1     TCGA-DK-A3X2     TCGA-DK-A6AV     TCGA-DK-A6AW 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-DK-A6B0     TCGA-DK-A6B2     TCGA-DK-A6B6     TCGA-DK-AA6L 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-DK-AA6P     TCGA-DK-AA6T     TCGA-DK-AA6U     TCGA-DK-AA74 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-DK-AA76     TCGA-E5-A4TZ     TCGA-E7-A4XJ     TCGA-E7-A519 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-E7-A5KF     TCGA-E7-A678     TCGA-E7-A6ME     TCGA-E7-A6MF 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-E7-A7PW     TCGA-E7-A7XN     TCGA-E7-A85H     TCGA-E7-A97Q 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-FD-A3B3     TCGA-FD-A3B4     TCGA-FD-A3B5     TCGA-FD-A3B6 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-FD-A3B7     TCGA-FD-A3B8     TCGA-FD-A3N5     TCGA-FD-A3N6 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-FD-A3NA     TCGA-FD-A3SJ     TCGA-FD-A3SM     TCGA-FD-A3SN 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-FD-A3SO     TCGA-FD-A3SP     TCGA-FD-A3SQ     TCGA-FD-A3SR 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-FD-A3SS     TCGA-FD-A43N     TCGA-FD-A43P     TCGA-FD-A43S 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-FD-A43U     TCGA-FD-A43X     TCGA-FD-A5BT     TCGA-FD-A5BU 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-FD-A5BV     TCGA-FD-A5BX     TCGA-FD-A5C0     TCGA-FD-A62N 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-FD-A6TB     TCGA-FD-A6TC     TCGA-FD-A6TE     TCGA-FD-A6TG 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-FD-A6TH     TCGA-FD-A6TK     TCGA-FJ-A3Z9     TCGA-FJ-A3ZF 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-FJ-A871     TCGA-FT-A61P     TCGA-G2-A2EF     TCGA-G2-A2EJ 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-G2-A2EL     TCGA-G2-A2ES     TCGA-G2-A3IE     TCGA-G2-AA3B 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-G2-AA3C     TCGA-G2-AA3D     TCGA-G2-AA3F     TCGA-GC-A3BM 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-GC-A3RB     TCGA-GC-A3WC     TCGA-GC-A3YS     TCGA-GD-A2C5 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-GD-A3OQ     TCGA-GD-A3OS     TCGA-GD-A6C6     TCGA-GU-A42P 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-GU-A42Q     TCGA-GU-A42R     TCGA-GU-A763     TCGA-GU-A764 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-GU-AATO     TCGA-GU-AATP     TCGA-GU-AATQ     TCGA-GV-A3JV 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-GV-A3JX     TCGA-GV-A3JZ     TCGA-GV-A3QF     TCGA-GV-A3QG 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-GV-A3QH     TCGA-GV-A3QI     TCGA-GV-A3QK     TCGA-GV-A40E 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-GV-A40G     TCGA-H4-A2HO     TCGA-H4-A2HQ     TCGA-HQ-A5ND 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-HQ-A5NE     TCGA-K4-A3WS     TCGA-K4-A3WV     TCGA-K4-A5RH 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-K4-A5RI     TCGA-K4-A83P     TCGA-K4-AAQO     TCGA-PQ-A6FI 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-PQ-A6FN     TCGA-R3-A69X     TCGA-S5-A6DX     TCGA-SY-A9G0 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-UY-A78N     TCGA-UY-A8OB     TCGA-UY-A9PB     TCGA-UY-A9PE 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-UY-A9PF     TCGA-XF-A9SJ     TCGA-XF-A9SL     TCGA-XF-A9SV 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-XF-A9SX     TCGA-XF-A9SY     TCGA-XF-A9SZ     TCGA-XF-A9T3 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-XF-A9T8     TCGA-XF-AAMF     TCGA-XF-AAMH     TCGA-XF-AAMQ 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-XF-AAMT     TCGA-XF-AAN0     TCGA-XF-AAN1     TCGA-XF-AAN2 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-XF-AAN4     TCGA-XF-AAN5     TCGA-XF-AAN7     TCGA-XF-AAN8 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-YF-AA3L     TCGA-YF-AA3M     TCGA-ZF-A9R0     TCGA-ZF-A9R2 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-ZF-A9R3     TCGA-ZF-A9R5     TCGA-ZF-A9R7     TCGA-ZF-A9R9 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-ZF-A9RD     TCGA-ZF-A9RF     TCGA-ZF-A9RL     TCGA-ZF-A9RM 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-ZF-AA4U     TCGA-ZF-AA4V     TCGA-ZF-AA51     TCGA-ZF-AA52 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-ZF-AA58     TCGA-ZF-AA5H     TCGA-ZF-AA5N     TCGA-ZF-AA5P 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
D72V10, continuous
[1] "Remove cluster labels:" "FUT5 MUTATED"          
clus
  FUT5 MUTATED FUT5 WILD-TYPE 
             2            273 
    TCGA-2F-A9KO     TCGA-2F-A9KP     TCGA-2F-A9KQ     TCGA-2F-A9KR 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-2F-A9KT     TCGA-2F-A9KW     TCGA-4Z-AA7N     TCGA-4Z-AA7O 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-4Z-AA7R     TCGA-4Z-AA7S     TCGA-4Z-AA7W     TCGA-4Z-AA7Y 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-4Z-AA80     TCGA-4Z-AA81     TCGA-4Z-AA82     TCGA-4Z-AA84 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-4Z-AA86     TCGA-4Z-AA87     TCGA-4Z-AA89     TCGA-BL-A0C8 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-BL-A13I     TCGA-BL-A13J     TCGA-BL-A3JM     TCGA-BT-A0S7 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-BT-A0YX     TCGA-BT-A20J     TCGA-BT-A20N     TCGA-BT-A20O 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-BT-A20P     TCGA-BT-A20Q     TCGA-BT-A20T     TCGA-BT-A20V 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-BT-A20W     TCGA-BT-A20X     TCGA-BT-A2LA     TCGA-BT-A2LB 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-BT-A2LD     TCGA-BT-A3PH     TCGA-BT-A3PJ     TCGA-BT-A3PK 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-BT-A42B     TCGA-BT-A42C     TCGA-BT-A42E     TCGA-BT-A42F 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-CU-A0YN     TCGA-CU-A0YO     TCGA-CU-A0YR     TCGA-CU-A3KJ 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-CU-A3QU     TCGA-CU-A3YL     TCGA-CU-A5W6     TCGA-CU-A72E 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-DK-A1A3     TCGA-DK-A1A5     TCGA-DK-A1A6     TCGA-DK-A1A7 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-DK-A1AA     TCGA-DK-A1AB     TCGA-DK-A1AC     TCGA-DK-A1AD 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-DK-A1AE     TCGA-DK-A1AF     TCGA-DK-A1AG     TCGA-DK-A2HX 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-DK-A2I1     TCGA-DK-A2I2     TCGA-DK-A2I4     TCGA-DK-A2I6 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-DK-A3IK     TCGA-DK-A3IL     TCGA-DK-A3IM     TCGA-DK-A3IN 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-DK-A3IQ     TCGA-DK-A3IS     TCGA-DK-A3IT     TCGA-DK-A3IU 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-DK-A3WW     TCGA-DK-A3WX     TCGA-DK-A3WY     TCGA-DK-A3X1 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-DK-A3X2     TCGA-DK-A6AV     TCGA-DK-A6AW     TCGA-DK-A6B0 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-DK-A6B1     TCGA-DK-A6B2     TCGA-DK-A6B5     TCGA-DK-AA6L 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-DK-AA6Q     TCGA-DK-AA6S     TCGA-DK-AA71     TCGA-DK-AA77 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-E5-A2PC     TCGA-E5-A4TZ     TCGA-E5-A4U1     TCGA-E7-A541 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-E7-A7DU     TCGA-E7-A7DV     TCGA-E7-A85H     TCGA-E7-A97Q 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-FD-A3B3     TCGA-FD-A3B4     TCGA-FD-A3B5     TCGA-FD-A3B6 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-FD-A3B7     TCGA-FD-A3B8     TCGA-FD-A3N5     TCGA-FD-A3N6 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-FD-A3NA     TCGA-FD-A3SJ     TCGA-FD-A3SL     TCGA-FD-A3SM 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-FD-A3SN     TCGA-FD-A3SO     TCGA-FD-A3SP     TCGA-FD-A3SQ 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-FD-A3SR     TCGA-FD-A3SS     TCGA-FD-A43N     TCGA-FD-A43P 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-FD-A43S     TCGA-FD-A43U     TCGA-FD-A43X     TCGA-FD-A5BR 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-FD-A5BS     TCGA-FD-A5BT     TCGA-FD-A5BU     TCGA-FD-A5BV 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-FD-A5BX     TCGA-FD-A5BY     TCGA-FD-A5BZ     TCGA-FD-A5C0 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-FD-A5C1     TCGA-FD-A62N     TCGA-FD-A62O     TCGA-FD-A62P 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-FD-A62S     TCGA-FD-A6TA     TCGA-FD-A6TB     TCGA-FD-A6TC 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-FD-A6TD     TCGA-FD-A6TE     TCGA-FD-A6TF     TCGA-FD-A6TG 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-FD-A6TH     TCGA-FD-A6TI     TCGA-FD-A6TK     TCGA-FJ-A3Z7 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-FJ-A3Z9     TCGA-FT-A3EE     TCGA-FT-A61P     TCGA-G2-AA3B 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-G2-AA3C     TCGA-G2-AA3D     TCGA-G2-AA3F     TCGA-GC-A3BM 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-GC-A3I6     TCGA-GC-A3OO     TCGA-GC-A3RB     TCGA-GC-A3RC 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-GC-A3RD     TCGA-GC-A3WC     TCGA-GC-A3YS     TCGA-GC-A6I1 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-GC-A6I3     TCGA-GD-A2C5     TCGA-GD-A3OP     TCGA-GD-A3OQ 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-GD-A6C6     TCGA-GD-A76B     TCGA-GU-A42P     TCGA-GU-A42Q 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-GU-A42R     TCGA-GU-A762     TCGA-GU-A763     TCGA-GU-A764 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-GU-A766     TCGA-GU-A767     TCGA-GU-AATO     TCGA-GU-AATP 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-GU-AATQ     TCGA-GV-A3JV     TCGA-GV-A3JX     TCGA-GV-A3JZ 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-GV-A3QF     TCGA-GV-A3QG     TCGA-GV-A3QI     TCGA-GV-A3QK 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-GV-A40G     TCGA-H4-A2HO     TCGA-HQ-A2OF     TCGA-HQ-A5ND 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-HQ-A5NE     TCGA-K4-A3WS     TCGA-K4-A3WV     TCGA-K4-A4AB 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-K4-A4AC     TCGA-K4-A54R     TCGA-K4-A5RH     TCGA-K4-A5RI 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-K4-A5RJ     TCGA-K4-A6FZ     TCGA-K4-A6MB     TCGA-K4-A83P 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-LC-A66R     TCGA-MV-A51V     TCGA-PQ-A6FI     TCGA-PQ-A6FN 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-R3-A69X     TCGA-S5-A6DX     TCGA-SY-A9G0     TCGA-SY-A9G5 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-UY-A78K     TCGA-UY-A78L     TCGA-UY-A78N     TCGA-UY-A78O 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-XF-A8HH     TCGA-XF-A8HI     TCGA-XF-A9SG     TCGA-XF-A9SH 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-XF-A9SI     TCGA-XF-A9SJ     TCGA-XF-A9SL     TCGA-XF-A9SV 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-XF-A9SW     TCGA-XF-A9SX     TCGA-XF-A9SY     TCGA-XF-A9SZ 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-XF-A9T0     TCGA-XF-A9T2     TCGA-XF-A9T3     TCGA-XF-A9T4 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-XF-A9T5     TCGA-XF-A9T6     TCGA-XF-A9T8     TCGA-XF-AAME 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-XF-AAMF     TCGA-XF-AAMG     TCGA-XF-AAMH     TCGA-XF-AAMJ 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-XF-AAML     TCGA-XF-AAMQ     TCGA-XF-AAMR     TCGA-XF-AAMT 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-XF-AAMW     TCGA-XF-AAMX     TCGA-XF-AAMY     TCGA-XF-AAMZ 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-XF-AAN0     TCGA-XF-AAN1     TCGA-XF-AAN2     TCGA-XF-AAN3 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-XF-AAN4     TCGA-XF-AAN5     TCGA-XF-AAN7     TCGA-XF-AAN8 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-YC-A8S6     TCGA-YF-AA3L     TCGA-ZF-A9R1     TCGA-ZF-A9R2 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-ZF-A9R5     TCGA-ZF-A9R9     TCGA-ZF-A9RD     TCGA-ZF-A9RG 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-ZF-A9RM     TCGA-ZF-AA4R     TCGA-ZF-AA4T     TCGA-ZF-AA4V 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-ZF-AA4W     TCGA-ZF-AA56     TCGA-ZF-AA58     TCGA-ZF-AA5H 
"FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" "FUT5 WILD-TYPE" 
    TCGA-ZF-AA5P 
"FUT5 WILD-TYPE" 
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  FUT5 MUTATED       0                         1     2
  FUT5 WILD-TYPE    38                        20   299
D72V11, multiclass
                           clus
vv                          FUT5 MUTATED FUT5 WILD-TYPE
  ASIAN                                0             38
  BLACK OR AFRICAN AMERICAN            1             20
  WHITE                                2            299
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V12, binary
                cls
clus               0   1
  FUT5 MUTATED     0   3
  FUT5 WILD-TYPE   8 335
[1] "tbl2"
                cls
clus             [,1] [,2]
  FUT5 MUTATED      0    3
  FUT5 WILD-TYPE    8  335
                        clus
vv                       FUT5 MUTATED FUT5 WILD-TYPE
  HISPANIC OR LATINO                0              8
  NOT HISPANIC OR LATINO            3            335
[1] 2 2
[1] FALSE

Clustering(73) Variable = AHR MUTATION ANALYSIS
D73V1, survival
               sevent
clus2             0   1
  AHR MUTATED    11   8
  AHR WILD-TYPE 208 143
  AHR MUTATED AHR WILD-TYPE 
           19           351 
  AHR MUTATED AHR WILD-TYPE 
            8           143 
$`AHR MUTATED`
TCGA-4Z-AA80 TCGA-C4-A0F0 TCGA-CF-A47Y TCGA-DK-A1AB TCGA-DK-A3IU TCGA-DK-A3X1 
        0.62         1.94        12.26        16.70        23.21        48.00 
TCGA-DK-A6AV TCGA-DK-AA76 TCGA-E7-A7DU TCGA-FD-A6TA TCGA-FJ-A3ZE TCGA-GD-A3OP 
       64.18        12.03         0.92        62.86        10.65         2.10 
TCGA-K4-A54R TCGA-LT-A5Z6 TCGA-S5-AA26 TCGA-UY-A8OB TCGA-XF-A9SL TCGA-XF-AAMZ 
       27.68        15.58         3.75        65.75        66.41        44.32 
TCGA-XF-AAN2 
       61.45 

$`AHR WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        91.63       103.50       105.70         8.35 
TCGA-4Z-AA7M TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7S 
       16.27        44.94        16.83        16.77        17.16        34.98 
TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA84 
       27.62        49.12        41.75        51.16        66.54        15.12 
TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J 
       10.22        47.80        33.83        40.08         7.33         2.66 
TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N 
        6.74        12.39         6.58        13.15        19.04        32.84 
TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U 
       12.16        17.88        19.50         5.06        14.89        14.96 
TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A2LD 
        5.06         8.35         8.25        17.16        16.18        20.48 
TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E 
        4.67        12.82         9.96        17.56        28.70        24.26 
TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F1 TCGA-C4-A0F6 TCGA-C4-A0F7 TCGA-CF-A1HR 
       28.41         8.98         2.93        23.01         2.04         0.46 
TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W 
        0.43         0.69        10.95        12.66        12.46        12.10 
TCGA-CF-A47X TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A9FF TCGA-CF-A9FM 
       12.62        13.12        12.00        12.10        11.87        13.08 
TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL 
       12.92         4.90         7.20         5.46         5.19        16.31 
TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 
        1.84        13.58        21.86         2.14        66.41        18.41 
TCGA-DK-A1AA TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG 
       19.00       130.88       112.44        16.14        17.62        15.62 
TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK 
        1.81        10.59         7.79       123.85        87.32         2.20 
TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT 
       13.58         7.82         8.22        17.72        50.27        21.30 
TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X2 TCGA-DK-A6AW 
        9.67        20.81        10.55       140.81        17.98        41.56 
TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L 
       76.60        67.36        15.68        41.06        30.67        38.24 
TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6W 
       15.02        13.58       166.03        12.36        10.49         8.65 
TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA77 TCGA-E5-A2PC TCGA-E5-A4TZ 
        7.53        13.64        43.50        10.62        43.59        15.35 
TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 
       38.83        24.66         0.10         0.49         2.24        16.70 
TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME 
       17.39         0.56         0.66        14.56        13.97        12.99 
TCGA-E7-A6MF TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A97P 
       14.33         1.22        13.68        14.07        12.95        14.37 
TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 
        8.09        32.02        16.77         8.94        33.04         4.01 
TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL 
       12.62        22.52        27.98        60.66        24.30        23.41 
TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR 
       17.98        29.16         5.52        25.74        46.78        19.79 
TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X 
       12.85        22.98        27.35        14.96        20.91         3.62 
TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX 
       26.73        53.88        11.01        19.33         5.36         5.69 
TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O 
        8.25        27.45        18.08        58.92         2.70         7.10 
TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE 
        6.28        13.35        18.81         6.15        12.69        12.36 
TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z7 
        2.27         3.06         4.31         9.67        10.85        31.07 
TCGA-FJ-A3Z9 TCGA-FJ-A3ZF TCGA-FJ-A871 TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EC 
        7.13        17.23         8.94         3.25         6.48        22.88 
TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES 
       61.94        30.61        15.95        26.93        35.24        33.01 
TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3D 
        7.23        20.12        17.62        66.02         6.94        64.44 
TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC 
       19.46        21.40         2.24        15.81         4.50        15.91 
TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 
       14.07        17.75        24.92         8.94        13.91         7.73 
TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42Q 
        3.12        20.98         2.20         7.36        10.92        11.31 
TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 
       11.31         7.63        27.09        20.05         5.62         4.73 
TCGA-GU-AATO TCGA-GU-AATP TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX 
       10.65        32.98         7.00        14.27        21.34        19.10 
TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E 
       19.82        20.28         8.48        10.59        27.35         8.58 
TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF 
       19.07        22.72         1.51        19.40        38.60         3.06 
TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB 
        9.01         8.22        25.02         3.45        21.24         2.76 
TCGA-K4-A4AC TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB 
        9.14         9.07        11.70         1.74         1.81        15.42 
TCGA-K4-A83P TCGA-K4-AAQO TCGA-LC-A66R TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN 
        6.38        11.80        15.32        13.48        12.23        16.67 
TCGA-R3-A69X TCGA-S5-A6DX TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L 
       14.24         1.84        12.43        31.56        17.62        37.05 
TCGA-UY-A78M TCGA-UY-A78N TCGA-UY-A78O TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD 
       22.68        86.83        76.01        35.24        29.56        17.82 
TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH 
        4.54         1.64         1.87        17.88        48.62        64.80 
TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY 
       79.66         3.22        12.76        11.90        23.64        21.04 
TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T5 
       28.24        26.27        18.90         2.24        16.27        66.64 
TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMG TCGA-XF-AAMH 
        2.10        13.74        92.98        10.82       110.60        11.31 
TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMW 
       54.90         7.63        71.57        91.73         2.96         8.32 
TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN3 TCGA-XF-AAN4 
        6.77        98.99        56.48        30.94        86.30        27.06 
TCGA-XF-AAN5 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L 
       75.39        18.81         3.88         9.63         0.66        11.97 
TCGA-YF-AA3M TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R4 
       13.64        18.64         7.36        21.11        24.13        30.28 
TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RE 
       27.19        21.86        28.41        74.56        13.41         3.48 
TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N 
       52.73        52.60        82.49        47.84        20.22         2.89 
TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA4X 
       34.06        19.69         8.61        59.38        60.16        63.02 
TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 
       38.73        35.41        57.90        19.40         8.52        47.15 
TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-ZF-AA5P 
       19.17         5.52        10.13 

  AHR MUTATED AHR WILD-TYPE 
         0.62          0.10 
  AHR MUTATED AHR WILD-TYPE 
        66.41        166.03 
  AHR MUTATED AHR WILD-TYPE 
        16.70         15.62 
[1] "0.6 - 66.4 (16.7)"  "0.1 - 166.0 (15.6)"
[1] "hr=" "1.1"
D73V2, continuous
               vv
clus            STAGE I STAGE II STAGE III STAGE IV
  AHR MUTATED         0        9         3        7
  AHR WILD-TYPE       4      108       119      121
D73V3, multiclass
           clus
vv          AHR MUTATED AHR WILD-TYPE
  STAGE I             0             4
  STAGE II            9           108
  STAGE III           3           119
  STAGE IV            7           121
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            T0+T1+T2  T3  T4
  AHR MUTATED          7   7   2
  AHR WILD-TYPE      107 172  50
D73V4, multiclass
          clus
vv         AHR MUTATED AHR WILD-TYPE
  T0+T1+T2           7           107
  T3                 7           172
  T4                 2            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"
               vv
clus             N0  N1  N2  N3
  AHR MUTATED    11   1   5   1
  AHR WILD-TYPE 202  40  70   7
D73V5, multiclass
    clus
vv   AHR MUTATED AHR WILD-TYPE
  N0          11           202
  N1           1            40
  N2           5            70
  N3           1             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"
D73V6, binary
               cls
clus              0   1
  AHR MUTATED     9   1
  AHR WILD-TYPE 173   9
[1] "tbl2"
               cls
clus            [,1] [,2]
  AHR MUTATED      9    1
  AHR WILD-TYPE  173    9
   clus
vv  AHR MUTATED AHR WILD-TYPE
  0           9           173
  1           1             9
[1] 2 2
[1] FALSE
D73V7, binary
               cls
clus              0   1
  AHR MUTATED     6  13
  AHR WILD-TYPE  90 267
[1] "tbl2"
               cls
clus            [,1] [,2]
  AHR MUTATED      6   13
  AHR WILD-TYPE   90  267
        clus
vv       AHR MUTATED AHR WILD-TYPE
  FEMALE           6            90
  MALE            13           267
[1] 2 2
[1] FALSE
D73V8, continuous
D73V9, continuous
D73V10, continuous
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AHR MUTATED       2                         1    15
  AHR WILD-TYPE    36                        20   286
D73V11, multiclass
                           clus
vv                          AHR MUTATED AHR WILD-TYPE
  ASIAN                               2            36
  BLACK OR AFRICAN AMERICAN           1            20
  WHITE                              15           286
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D73V12, binary
               cls
clus              0   1
  AHR MUTATED     1  16
  AHR WILD-TYPE   7 322
[1] "tbl2"
               cls
clus            [,1] [,2]
  AHR MUTATED      1   16
  AHR WILD-TYPE    7  322
                        clus
vv                       AHR MUTATED AHR WILD-TYPE
  HISPANIC OR LATINO               1             7
  NOT HISPANIC OR LATINO          16           322
[1] 2 2
[1] FALSE

Clustering(74) Variable = THRAP3 MUTATION ANALYSIS
D74V1, survival
                  sevent
clus2                0   1
  THRAP3 MUTATED     9   5
  THRAP3 WILD-TYPE 210 146
  THRAP3 MUTATED THRAP3 WILD-TYPE 
              14              356 
  THRAP3 MUTATED THRAP3 WILD-TYPE 
               5              146 
$`THRAP3 MUTATED`
TCGA-BT-A2LB TCGA-DK-A3X1 TCGA-FD-A3SN TCGA-FD-A43X TCGA-GC-A3RC TCGA-GC-A6I1 
       16.18        48.00        29.16         3.62        15.91         8.94 
TCGA-GU-A767 TCGA-GV-A3QI TCGA-K4-A3WU TCGA-MV-A51V TCGA-UY-A9PF TCGA-XF-AAMG 
        4.73        10.59         3.45        13.48         1.64       110.60 
TCGA-ZF-A9RE TCGA-ZF-AA4W 
        3.48        60.16 

$`THRAP3 WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        91.63       103.50       105.70         8.35 
TCGA-4Z-AA7M TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7S 
       16.27        44.94        16.83        16.77        17.16        34.98 
TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 
       27.62        49.12         0.62        41.75        51.16        66.54 
TCGA-4Z-AA84 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BL-A13I 
       15.12        10.22        47.80        33.83        40.08         7.33 
TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J 
        2.66         6.74        12.39         6.58        13.15        19.04 
TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T 
       32.84        12.16        17.88        19.50         5.06        14.89 
TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LD 
       14.96         5.06         8.35         8.25        17.16        20.48 
TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E 
        4.67        12.82         9.96        17.56        28.70        24.26 
TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-C4-A0F6 TCGA-C4-A0F7 
       28.41         8.98         1.94         2.93        23.01         2.04 
TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V 
        0.46         0.43         0.69        10.95        12.66        12.46 
TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 
       12.10        12.62        12.26        13.12        12.00        12.10 
TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ 
       11.87        13.08        12.92         4.90         7.20         5.46 
TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 
        5.19        16.31         1.84        13.58        21.86         2.14 
TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD 
       66.41        18.41        19.00        16.70       130.88       112.44 
TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 
       16.14        17.62        15.62         1.81        10.59         7.79 
TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN 
      123.85        87.32         2.20        13.58         7.82         8.22 
TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW 
       17.72        50.27        21.30        23.21         9.67        20.81 
TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 
       10.55       140.81        17.98        64.18        41.56        76.60 
TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6P 
       67.36        15.68        41.06        30.67        38.24        15.02 
TCGA-DK-AA6Q TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA6X 
       13.58       166.03        12.36        10.49         8.65         7.53 
TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A2PC TCGA-E5-A4TZ 
       13.64        43.50        12.03        10.62        43.59        15.35 
TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 
       38.83        24.66         0.10         0.49         2.24        16.70 
TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME 
       17.39         0.56         0.66        14.56        13.97        12.99 
TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H 
       14.33         0.92         1.22        13.68        14.07        12.95 
TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 
       14.37         8.09        32.02        16.77         8.94        33.04 
TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ 
        4.01        12.62        22.52        27.98        60.66        24.30 
TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR 
       23.41        17.98         5.52        25.74        46.78        19.79 
TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A5BR 
       12.85        22.98        27.35        14.96        20.91        26.73 
TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY 
       53.88        11.01        19.33         5.36         5.69         8.25 
TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P 
       27.45        18.08        58.92         2.70         7.10         6.28 
TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE 
       13.35        62.86        18.81         6.15        12.69        12.36 
TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z7 
        2.27         3.06         4.31         9.67        10.85        31.07 
TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FJ-A871 TCGA-FT-A3EE TCGA-FT-A61P 
        7.13        10.65        17.23         8.94         3.25         6.48 
TCGA-G2-A2EC TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO 
       22.88        61.94        30.61        15.95        26.93        35.24 
TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3C 
       33.01         7.23        20.12        17.62        66.02         6.94 
TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB 
       64.44        19.46        21.40         2.24        15.81         4.50 
TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP 
       14.07        17.75        24.92        13.91         7.73         2.10 
TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42Q 
        3.12        20.98         2.20         7.36        10.92        11.31 
TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-AATO 
       11.31         7.63        27.09        20.05         5.62        10.65 
TCGA-GU-AATP TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ 
       32.98         7.00        14.27        21.34        19.10        19.82 
TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA 
       20.28         8.48        27.35         8.58        19.07        22.72 
TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE 
        1.51        19.40        38.60         3.06         9.01         8.22 
TCGA-K4-A3WS TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RH 
       25.02        21.24         2.76         9.14        27.68         9.07 
TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO 
       11.70         1.74         1.81        15.42         6.38        11.80 
TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX 
       15.32        15.58        12.23        16.67        14.24         1.84 
TCGA-S5-AA26 TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M 
        3.75        12.43        31.56        17.62        37.05        22.68 
TCGA-UY-A78N TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD 
       86.83        76.01        65.75        35.24        29.56        17.82 
TCGA-UY-A9PE TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI 
        4.54         1.87        17.88        48.62        64.80        79.66 
TCGA-XF-A9SJ TCGA-XF-A9SL TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY 
        3.22        66.41        12.76        11.90        23.64        21.04 
TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T5 
       28.24        26.27        18.90         2.24        16.27        66.64 
TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMJ 
        2.10        13.74        92.98        10.82        11.31        54.90 
TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX 
        7.63        71.57        91.73         2.96         8.32         6.77 
TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 
       98.99        44.32        56.48        30.94        61.45        86.30 
TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YC-A9TC 
       27.06        75.39        18.81         3.88         9.63         0.66 
TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R3 
       11.97        13.64        18.64         7.36        21.11        24.13 
TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RD 
       30.28        27.19        21.86        28.41        74.56        13.41 
TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N 
       52.73        52.60        82.49        47.84        20.22         2.89 
TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4X TCGA-ZF-AA51 
       34.06        19.69         8.61        59.38        63.02        38.73 
TCGA-ZF-AA52 TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H 
       35.41        57.90        19.40         8.52        47.15        19.17 
TCGA-ZF-AA5N TCGA-ZF-AA5P 
        5.52        10.13 

  THRAP3 MUTATED THRAP3 WILD-TYPE 
            1.64             0.10 
  THRAP3 MUTATED THRAP3 WILD-TYPE 
          110.60           166.03 
  THRAP3 MUTATED THRAP3 WILD-TYPE 
          12.035           15.745 
[1] "1.6 - 110.6 (12.0)" "0.1 - 166.0 (15.7)"
[1] "hr=" "1"  
D74V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  THRAP3 MUTATED         0        4         8        2
  THRAP3 WILD-TYPE       4      113       114      126
D74V3, multiclass
           clus
vv          THRAP3 MUTATED THRAP3 WILD-TYPE
  STAGE I                0                4
  STAGE II               4              113
  STAGE III              8              114
  STAGE IV               2              126
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1+T2  T3  T4
  THRAP3 MUTATED          3   8   2
  THRAP3 WILD-TYPE      111 171  50
D74V4, multiclass
          clus
vv         THRAP3 MUTATED THRAP3 WILD-TYPE
  T0+T1+T2              3              111
  T3                    8              171
  T4                    2               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"
                  vv
clus                N0  N1  N2  N3
  THRAP3 MUTATED    11   0   2   0
  THRAP3 WILD-TYPE 202  41  73   8
D74V5, multiclass
    clus
vv   THRAP3 MUTATED THRAP3 WILD-TYPE
  N0             11              202
  N1              0               41
  N2              2               73
  N3              0                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"
D74V6, binary
                  cls
clus                 0   1
  THRAP3 MUTATED     4   0
  THRAP3 WILD-TYPE 178  10
[1] "tbl2"
                  cls
clus               [,1] [,2]
  THRAP3 MUTATED      4    0
  THRAP3 WILD-TYPE  178   10
   clus
vv  THRAP3 MUTATED THRAP3 WILD-TYPE
  0              4              178
  1              0               10
[1] 2 2
[1] FALSE
D74V7, binary
                  cls
clus                 0   1
  THRAP3 MUTATED     4  10
  THRAP3 WILD-TYPE  92 270
[1] "tbl2"
                  cls
clus               [,1] [,2]
  THRAP3 MUTATED      4   10
  THRAP3 WILD-TYPE   92  270
        clus
vv       THRAP3 MUTATED THRAP3 WILD-TYPE
  FEMALE              4               92
  MALE               10              270
[1] 2 2
[1] FALSE
D74V8, continuous
D74V9, continuous
D74V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  THRAP3 MUTATED       0                         0    14
  THRAP3 WILD-TYPE    38                        21   287
D74V11, multiclass
                           clus
vv                          THRAP3 MUTATED THRAP3 WILD-TYPE
  ASIAN                                  0               38
  BLACK OR AFRICAN AMERICAN              0               21
  WHITE                                 14              287
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D74V12, binary
                  cls
clus                 0   1
  THRAP3 MUTATED     2  12
  THRAP3 WILD-TYPE   6 326
[1] "tbl2"
                  cls
clus               [,1] [,2]
  THRAP3 MUTATED      2   12
  THRAP3 WILD-TYPE    6  326
                        clus
vv                       THRAP3 MUTATED THRAP3 WILD-TYPE
  HISPANIC OR LATINO                  2                6
  NOT HISPANIC OR LATINO             12              326
[1] 2 2
[1] FALSE

Clustering(75) Variable = TFPI2 MUTATION ANALYSIS
D75V1, survival
                 sevent
clus2               0   1
  TFPI2 MUTATED     5   1
  TFPI2 WILD-TYPE 214 150
  TFPI2 MUTATED TFPI2 WILD-TYPE 
              6             364 
  TFPI2 MUTATED TFPI2 WILD-TYPE 
              1             150 
$`TFPI2 MUTATED`
TCGA-DK-A1A5 TCGA-DK-A3WW TCGA-DK-AA6U TCGA-GV-A6ZA TCGA-PQ-A6FI TCGA-XF-A9SY 
        2.14        20.81        10.49        22.72        12.23        21.04 

$`TFPI2 WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        91.63       103.50       105.70         8.35 
TCGA-4Z-AA7M TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7S 
       16.27        44.94        16.83        16.77        17.16        34.98 
TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 
       27.62        49.12         0.62        41.75        51.16        66.54 
TCGA-4Z-AA84 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BL-A13I 
       15.12        10.22        47.80        33.83        40.08         7.33 
TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J 
        2.66         6.74        12.39         6.58        13.15        19.04 
TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T 
       32.84        12.16        17.88        19.50         5.06        14.89 
TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB 
       14.96         5.06         8.35         8.25        17.16        16.18 
TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C 
       20.48         4.67        12.82         9.96        17.56        28.70 
TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-C4-A0F6 
       24.26        28.41         8.98         1.94         2.93        23.01 
TCGA-C4-A0F7 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T 
        2.04         0.46         0.43         0.69        10.95        12.66 
TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA 
       12.46        12.10        12.62        12.26        13.12        12.00 
TCGA-CF-A7I0 TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR 
       12.10        11.87        13.08        12.92         4.90         7.20 
TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 
        5.46         5.19        16.31         1.84        13.58        21.86 
TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD 
       66.41        18.41        19.00        16.70       130.88       112.44 
TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 
       16.14        17.62        15.62         1.81        10.59         7.79 
TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN 
      123.85        87.32         2.20        13.58         7.82         8.22 
TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WX 
       17.72        50.27        21.30        23.21         9.67        10.55 
TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 
      140.81        48.00        17.98        64.18        41.56        76.60 
TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6P 
       67.36        15.68        41.06        30.67        38.24        15.02 
TCGA-DK-AA6Q TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA71 
       13.58       166.03        12.36         8.65         7.53        13.64 
TCGA-DK-AA74 TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E5-A4U1 
       43.50        12.03        10.62        43.59        15.35        38.83 
TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 
       24.66         0.10         0.49         2.24        16.70        17.39 
TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF 
        0.56         0.66        14.56        13.97        12.99        14.33 
TCGA-E7-A7DU TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A97P 
        0.92         1.22        13.68        14.07        12.95        14.37 
TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 
        8.09        32.02        16.77         8.94        33.04         4.01 
TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL 
       12.62        22.52        27.98        60.66        24.30        23.41 
TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR 
       17.98        29.16         5.52        25.74        46.78        19.79 
TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X 
       12.85        22.98        27.35        14.96        20.91         3.62 
TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX 
       26.73        53.88        11.01        19.33         5.36         5.69 
TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O 
        8.25        27.45        18.08        58.92         2.70         7.10 
TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD 
        6.28        13.35        62.86        18.81         6.15        12.69 
TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FD-A6TK 
       12.36         2.27         3.06         4.31         9.67        10.85 
TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FJ-A871 TCGA-FT-A3EE 
       31.07         7.13        10.65        17.23         8.94         3.25 
TCGA-FT-A61P TCGA-G2-A2EC TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL 
        6.48        22.88        61.94        30.61        15.95        26.93 
TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B 
       35.24        33.01         7.23        20.12        17.62        66.02 
TCGA-G2-AA3C TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO 
        6.94        64.44        19.46        21.40         2.24        15.81 
TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A6I1 
        4.50        15.91        14.07        17.75        24.92         8.94 
TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 
       13.91         7.73         2.10         3.12        20.98         2.20 
TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 
        7.36        10.92        11.31        11.31         7.63        27.09 
TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATO TCGA-GU-AATP TCGA-GU-AATQ 
       20.05         5.62         4.73        10.65        32.98         7.00 
TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH 
       14.27        21.34        19.10        19.82        20.28         8.48 
TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-H4-A2HO TCGA-H4-A2HQ 
       10.59        27.35         8.58        19.07         1.51        19.40 
TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU 
       38.60         3.06         9.01         8.22        25.02         3.45 
TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RH TCGA-K4-A5RI 
       21.24         2.76         9.14        27.68         9.07        11.70 
TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO TCGA-LC-A66R 
        1.74         1.81        15.42         6.38        11.80        15.32 
TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 
       15.58        13.48        16.67        14.24         1.84         3.75 
TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78N 
       12.43        31.56        17.62        37.05        22.68        86.83 
TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE 
       76.01        65.75        35.24        29.56        17.82         4.54 
TCGA-UY-A9PF TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI 
        1.64         1.87        17.88        48.62        64.80        79.66 
TCGA-XF-A9SJ TCGA-XF-A9SL TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SZ 
        3.22        66.41        12.76        11.90        23.64        28.24 
TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 
       26.27        18.90         2.24        16.27        66.64         2.10 
TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMG TCGA-XF-AAMH TCGA-XF-AAMJ 
       13.74        92.98        10.82       110.60        11.31        54.90 
TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX 
        7.63        71.57        91.73         2.96         8.32         6.77 
TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 
       98.99        44.32        56.48        30.94        61.45        86.30 
TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YC-A9TC 
       27.06        75.39        18.81         3.88         9.63         0.66 
TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R3 
       11.97        13.64        18.64         7.36        21.11        24.13 
TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RD 
       30.28        27.19        21.86        28.41        74.56        13.41 
TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-A9RN 
        3.48        52.73        52.60        82.49        47.84        20.22 
TCGA-ZF-AA4N TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W 
        2.89        34.06        19.69         8.61        59.38        60.16 
TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA56 
       63.02        38.73        35.41        57.90        19.40         8.52 
TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-ZF-AA5P 
       47.15        19.17         5.52        10.13 

  TFPI2 MUTATED TFPI2 WILD-TYPE 
           2.14            0.10 
  TFPI2 MUTATED TFPI2 WILD-TYPE 
          22.72          166.03 
  TFPI2 MUTATED TFPI2 WILD-TYPE 
          16.52           15.65 
[1] "2.1 - 22.7 (16.5)"  "0.1 - 166.0 (15.6)"
[1] "hr=" "2"  
D75V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  TFPI2 MUTATED         1        3         1        1
  TFPI2 WILD-TYPE       3      114       121      127
D75V3, multiclass
           clus
vv          TFPI2 MUTATED TFPI2 WILD-TYPE
  STAGE I               1               3
  STAGE II              3             114
  STAGE III             1             121
  STAGE IV              1             127
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1+T2  T3  T4
  TFPI2 MUTATED          3   2   0
  TFPI2 WILD-TYPE      111 177  52
D75V4, multiclass
          clus
vv         TFPI2 MUTATED TFPI2 WILD-TYPE
  T0+T1+T2             3             111
  T3                   2             177
  T4                   0              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"
                 vv
clus               N0  N1  N2  N3
  TFPI2 MUTATED     5   0   1   0
  TFPI2 WILD-TYPE 208  41  74   8
D75V5, multiclass
    clus
vv   TFPI2 MUTATED TFPI2 WILD-TYPE
  N0             5             208
  N1             0              41
  N2             1              74
  N3             0               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"
D75V6, binary
                 cls
clus                0   1
  TFPI2 MUTATED     3   0
  TFPI2 WILD-TYPE 179  10
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TFPI2 MUTATED      3    0
  TFPI2 WILD-TYPE  179   10
   clus
vv  TFPI2 MUTATED TFPI2 WILD-TYPE
  0             3             179
  1             0              10
[1] 2 2
[1] FALSE
D75V7, binary
                 cls
clus                0   1
  TFPI2 MUTATED     1   5
  TFPI2 WILD-TYPE  95 275
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TFPI2 MUTATED      1    5
  TFPI2 WILD-TYPE   95  275
        clus
vv       TFPI2 MUTATED TFPI2 WILD-TYPE
  FEMALE             1              95
  MALE               5             275
[1] 2 2
[1] FALSE
D75V8, continuous
D75V9, continuous
D75V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TFPI2 MUTATED       0                         0     6
  TFPI2 WILD-TYPE    38                        21   295
D75V11, multiclass
                           clus
vv                          TFPI2 MUTATED TFPI2 WILD-TYPE
  ASIAN                                 0              38
  BLACK OR AFRICAN AMERICAN             0              21
  WHITE                                 6             295
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D75V12, binary
                 cls
clus                0   1
  TFPI2 MUTATED     0   6
  TFPI2 WILD-TYPE   8 332
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TFPI2 MUTATED      0    6
  TFPI2 WILD-TYPE    8  332
                        clus
vv                       TFPI2 MUTATED TFPI2 WILD-TYPE
  HISPANIC OR LATINO                 0               8
  NOT HISPANIC OR LATINO             6             332
[1] 2 2
[1] FALSE

Clustering(76) Variable = NPAS4 MUTATION ANALYSIS
D76V1, survival
                 sevent
clus2               0   1
  NPAS4 MUTATED     9   3
  NPAS4 WILD-TYPE 210 148
  NPAS4 MUTATED NPAS4 WILD-TYPE 
             12             358 
  NPAS4 MUTATED NPAS4 WILD-TYPE 
              3             148 
$`NPAS4 MUTATED`
TCGA-2F-A9KT TCGA-BT-A42C TCGA-DK-A1AC TCGA-DK-A6AW TCGA-DK-AA6P TCGA-E7-A85H 
      105.70        28.70       130.88        41.56        15.02        12.95 
TCGA-FD-A3SJ TCGA-G2-A2EJ TCGA-GD-A3OP TCGA-GU-AATQ TCGA-SY-A9G5 TCGA-ZF-A9R9 
       24.30        30.61         2.10         7.00        31.56        28.41 

$`NPAS4 WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KW TCGA-4Z-AA7M 
       22.29        11.97        91.63       103.50         8.35        16.27 
TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7W 
       44.94        16.83        16.77        17.16        34.98        27.62 
TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA84 
       49.12         0.62        41.75        51.16        66.54        15.12 
TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J 
       10.22        47.80        33.83        40.08         7.33         2.66 
TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N 
        6.74        12.39         6.58        13.15        19.04        32.84 
TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U 
       12.16        17.88        19.50         5.06        14.89        14.96 
TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A2LD 
        5.06         8.35         8.25        17.16        16.18        20.48 
TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42E TCGA-BT-A42F 
        4.67        12.82         9.96        17.56        24.26        28.41 
TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-C4-A0F6 TCGA-C4-A0F7 TCGA-CF-A1HR 
        8.98         1.94         2.93        23.01         2.04         0.46 
TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W 
        0.43         0.69        10.95        12.66        12.46        12.10 
TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A9FF 
       12.62        12.26        13.12        12.00        12.10        11.87 
TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3QU 
       13.08        12.92         4.90         7.20         5.46         5.19 
TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 
       16.31         1.84        13.58        21.86         2.14        66.41 
TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF 
       18.41        19.00        16.70       112.44        16.14        17.62 
TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A2I6 
       15.62         1.81        10.59         7.79       123.85        87.32 
TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS 
        2.20        13.58         7.82         8.22        17.72        50.27 
TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY 
       21.30        23.21         9.67        20.81        10.55       140.81 
TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 
       48.00        17.98        64.18        76.60        67.36        15.68 
TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6Q TCGA-DK-AA6S TCGA-DK-AA6T 
       41.06        30.67        38.24        13.58       166.03        12.36 
TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA76 
       10.49         8.65         7.53        13.64        43.50        12.03 
TCGA-DK-AA77 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 
       10.62        43.59        15.35        38.83        24.66         0.10 
TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF 
        0.49         2.24        16.70        17.39         0.56         0.66 
TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7DV 
       14.56        13.97        12.99        14.33         0.92         1.22 
TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 
       13.68        14.07        14.37         8.09        32.02        16.77 
TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 
        8.94        33.04         4.01        12.62        22.52        27.98 
TCGA-FD-A3NA TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP 
       60.66        23.41        17.98        29.16         5.52        25.74 
TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S 
       46.78        19.79        12.85        22.98        27.35        14.96 
TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU 
       20.91         3.62        26.73        53.88        11.01        19.33 
TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 
        5.36         5.69         8.25        27.45        18.08        58.92 
TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB 
        2.70         7.10         6.28        13.35        62.86        18.81 
TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH 
        6.15        12.69        12.36         2.27         3.06         4.31 
TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF 
        9.67        10.85        31.07         7.13        10.65        17.23 
TCGA-FJ-A871 TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EC TCGA-G2-A2EF TCGA-G2-A2EK 
        8.94         3.25         6.48        22.88        61.94        15.95 
TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY 
       26.93        35.24        33.01         7.23        20.12        17.62 
TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 
       66.02         6.94        64.44        19.46        21.40         2.24 
TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS 
       15.81         4.50        15.91        14.07        17.75        24.92 
TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 
        8.94        13.91         7.73         3.12        20.98         2.20 
TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 
        7.36        10.92        11.31        11.31         7.63        27.09 
TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATO TCGA-GU-AATP TCGA-GV-A3JV 
       20.05         5.62         4.73        10.65        32.98        14.27 
TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI 
       21.34        19.10        19.82        20.28         8.48        10.59 
TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-H4-A2HQ 
       27.35         8.58        19.07        22.72         1.51        19.40 
TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU 
       38.60         3.06         9.01         8.22        25.02         3.45 
TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RH TCGA-K4-A5RI 
       21.24         2.76         9.14        27.68         9.07        11.70 
TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO TCGA-LC-A66R 
        1.74         1.81        15.42         6.38        11.80        15.32 
TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX 
       15.58        13.48        12.23        16.67        14.24         1.84 
TCGA-S5-AA26 TCGA-SY-A9G0 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78N 
        3.75        12.43        17.62        37.05        22.68        86.83 
TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE 
       76.01        65.75        35.24        29.56        17.82         4.54 
TCGA-UY-A9PF TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI 
        1.64         1.87        17.88        48.62        64.80        79.66 
TCGA-XF-A9SJ TCGA-XF-A9SL TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY 
        3.22        66.41        12.76        11.90        23.64        21.04 
TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T5 
       28.24        26.27        18.90         2.24        16.27        66.64 
TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMG TCGA-XF-AAMH 
        2.10        13.74        92.98        10.82       110.60        11.31 
TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMW 
       54.90         7.63        71.57        91.73         2.96         8.32 
TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN2 
        6.77        98.99        44.32        56.48        30.94        61.45 
TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 
       86.30        27.06        75.39        18.81         3.88         9.63 
TCGA-YC-A9TC TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R2 
        0.66        11.97        13.64        18.64         7.36        21.11 
TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9RC TCGA-ZF-A9RD 
       24.13        30.28        27.19        21.86        74.56        13.41 
TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-A9RN 
        3.48        52.73        52.60        82.49        47.84        20.22 
TCGA-ZF-AA4N TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W 
        2.89        34.06        19.69         8.61        59.38        60.16 
TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA56 
       63.02        38.73        35.41        57.90        19.40         8.52 
TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-ZF-AA5P 
       47.15        19.17         5.52        10.13 

  NPAS4 MUTATED NPAS4 WILD-TYPE 
            2.1             0.1 
  NPAS4 MUTATED NPAS4 WILD-TYPE 
         130.88          166.03 
  NPAS4 MUTATED NPAS4 WILD-TYPE 
         28.555          15.500 
[1] "2.1 - 130.9 (28.6)" "0.1 - 166.0 (15.5)"
[1] "hr=" "2.4"
D76V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  NPAS4 MUTATED         0        5         4        3
  NPAS4 WILD-TYPE       4      112       118      125
D76V3, multiclass
           clus
vv          NPAS4 MUTATED NPAS4 WILD-TYPE
  STAGE I               0               4
  STAGE II              5             112
  STAGE III             4             118
  STAGE IV              3             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"
                 vv
clus              T0+T1+T2  T3  T4
  NPAS4 MUTATED          3   4   2
  NPAS4 WILD-TYPE      111 175  50
D76V4, multiclass
          clus
vv         NPAS4 MUTATED NPAS4 WILD-TYPE
  T0+T1+T2             3             111
  T3                   4             175
  T4                   2              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"
                 vv
clus               N0  N1  N2  N3
  NPAS4 MUTATED     9   0   3   0
  NPAS4 WILD-TYPE 204  41  72   8
D76V5, multiclass
    clus
vv   NPAS4 MUTATED NPAS4 WILD-TYPE
  N0             9             204
  N1             0              41
  N2             3              72
  N3             0               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"
D76V6, binary
                 cls
clus                0   1
  NPAS4 MUTATED     8   0
  NPAS4 WILD-TYPE 174  10
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NPAS4 MUTATED      8    0
  NPAS4 WILD-TYPE  174   10
   clus
vv  NPAS4 MUTATED NPAS4 WILD-TYPE
  0             8             174
  1             0              10
[1] 2 2
[1] FALSE
D76V7, binary
                 cls
clus                0   1
  NPAS4 MUTATED     3   9
  NPAS4 WILD-TYPE  93 271
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NPAS4 MUTATED      3    9
  NPAS4 WILD-TYPE   93  271
        clus
vv       NPAS4 MUTATED NPAS4 WILD-TYPE
  FEMALE             3              93
  MALE               9             271
[1] 2 2
[1] FALSE
D76V8, continuous
D76V9, continuous
D76V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  NPAS4 MUTATED       1                         0    11
  NPAS4 WILD-TYPE    37                        21   290
D76V11, multiclass
                           clus
vv                          NPAS4 MUTATED NPAS4 WILD-TYPE
  ASIAN                                 1              37
  BLACK OR AFRICAN AMERICAN             0              21
  WHITE                                11             290
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D76V12, binary
                 cls
clus                0   1
  NPAS4 MUTATED     0  11
  NPAS4 WILD-TYPE   8 327
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NPAS4 MUTATED      0   11
  NPAS4 WILD-TYPE    8  327
                        clus
vv                       NPAS4 MUTATED NPAS4 WILD-TYPE
  HISPANIC OR LATINO                 0               8
  NOT HISPANIC OR LATINO            11             327
[1] 2 2
[1] FALSE

Clustering(77) Variable = NFE2L3 MUTATION ANALYSIS
D77V1, survival
                  sevent
clus2                0   1
  NFE2L3 MUTATED     9   4
  NFE2L3 WILD-TYPE 210 147
  NFE2L3 MUTATED NFE2L3 WILD-TYPE 
              13              357 
  NFE2L3 MUTATED NFE2L3 WILD-TYPE 
               4              147 
$`NFE2L3 MUTATED`
TCGA-BT-A2LB TCGA-DK-A6B6 TCGA-DK-AA6Q TCGA-GC-A3RC TCGA-GD-A6C6 TCGA-GV-A3QH 
       16.18        30.67        13.58        15.91         2.20         8.48 
TCGA-GV-A6ZA TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-UY-A9PF TCGA-XF-A9T6 TCGA-ZF-A9RC 
       22.72        15.58        13.48         1.64         2.10        74.56 
TCGA-ZF-AA51 
       38.73 

$`NFE2L3 WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        91.63       103.50       105.70         8.35 
TCGA-4Z-AA7M TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7S 
       16.27        44.94        16.83        16.77        17.16        34.98 
TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 
       27.62        49.12         0.62        41.75        51.16        66.54 
TCGA-4Z-AA84 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BL-A13I 
       15.12        10.22        47.80        33.83        40.08         7.33 
TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J 
        2.66         6.74        12.39         6.58        13.15        19.04 
TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T 
       32.84        12.16        17.88        19.50         5.06        14.89 
TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LD 
       14.96         5.06         8.35         8.25        17.16        20.48 
TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E 
        4.67        12.82         9.96        17.56        28.70        24.26 
TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-C4-A0F6 TCGA-C4-A0F7 
       28.41         8.98         1.94         2.93        23.01         2.04 
TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V 
        0.46         0.43         0.69        10.95        12.66        12.46 
TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 
       12.10        12.62        12.26        13.12        12.00        12.10 
TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ 
       11.87        13.08        12.92         4.90         7.20         5.46 
TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 
        5.19        16.31         1.84        13.58        21.86         2.14 
TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD 
       66.41        18.41        19.00        16.70       130.88       112.44 
TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 
       16.14        17.62        15.62         1.81        10.59         7.79 
TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN 
      123.85        87.32         2.20        13.58         7.82         8.22 
TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW 
       17.72        50.27        21.30        23.21         9.67        20.81 
TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW 
       10.55       140.81        48.00        17.98        64.18        41.56 
TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-AA6L TCGA-DK-AA6P 
       76.60        67.36        15.68        41.06        38.24        15.02 
TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA71 
      166.03        12.36        10.49         8.65         7.53        13.64 
TCGA-DK-AA74 TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E5-A4U1 
       43.50        12.03        10.62        43.59        15.35        38.83 
TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 
       24.66         0.10         0.49         2.24        16.70        17.39 
TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF 
        0.56         0.66        14.56        13.97        12.99        14.33 
TCGA-E7-A7DU TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A97P 
        0.92         1.22        13.68        14.07        12.95        14.37 
TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 
        8.09        32.02        16.77         8.94        33.04         4.01 
TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL 
       12.62        22.52        27.98        60.66        24.30        23.41 
TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR 
       17.98        29.16         5.52        25.74        46.78        19.79 
TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X 
       12.85        22.98        27.35        14.96        20.91         3.62 
TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX 
       26.73        53.88        11.01        19.33         5.36         5.69 
TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O 
        8.25        27.45        18.08        58.92         2.70         7.10 
TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD 
        6.28        13.35        62.86        18.81         6.15        12.69 
TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FD-A6TK 
       12.36         2.27         3.06         4.31         9.67        10.85 
TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FJ-A871 TCGA-FT-A3EE 
       31.07         7.13        10.65        17.23         8.94         3.25 
TCGA-FT-A61P TCGA-G2-A2EC TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL 
        6.48        22.88        61.94        30.61        15.95        26.93 
TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B 
       35.24        33.01         7.23        20.12        17.62        66.02 
TCGA-G2-AA3C TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO 
        6.94        64.44        19.46        21.40         2.24        15.81 
TCGA-GC-A3RB TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GC-A6I3 
        4.50        14.07        17.75        24.92         8.94        13.91 
TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A76B TCGA-GU-A42P 
        7.73         2.10         3.12        20.98         7.36        10.92 
TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 
       11.31        11.31         7.63        27.09        20.05         5.62 
TCGA-GU-A767 TCGA-GU-AATO TCGA-GU-AATP TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW 
        4.73        10.65        32.98         7.00        14.27        21.34 
TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E 
       19.10        19.82        20.28        10.59        27.35         8.58 
TCGA-GV-A40G TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND 
       19.07         1.51        19.40        38.60         3.06         9.01 
TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC 
        8.22        25.02         3.45        21.24         2.76         9.14 
TCGA-K4-A54R TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB 
       27.68         9.07        11.70         1.74         1.81        15.42 
TCGA-K4-A83P TCGA-K4-AAQO TCGA-LC-A66R TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X 
        6.38        11.80        15.32        12.23        16.67        14.24 
TCGA-S5-A6DX TCGA-S5-AA26 TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L 
        1.84         3.75        12.43        31.56        17.62        37.05 
TCGA-UY-A78M TCGA-UY-A78N TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A9PA TCGA-UY-A9PB 
       22.68        86.83        76.01        65.75        35.24        29.56 
TCGA-UY-A9PD TCGA-UY-A9PE TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH 
       17.82         4.54         1.87        17.88        48.62        64.80 
TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SL TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SX 
       79.66         3.22        66.41        12.76        11.90        23.64 
TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 
       21.04        28.24        26.27        18.90         2.24        16.27 
TCGA-XF-A9T5 TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMG TCGA-XF-AAMH 
       66.64        13.74        92.98        10.82       110.60        11.31 
TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMW 
       54.90         7.63        71.57        91.73         2.96         8.32 
TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN2 
        6.77        98.99        44.32        56.48        30.94        61.45 
TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 
       86.30        27.06        75.39        18.81         3.88         9.63 
TCGA-YC-A9TC TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R2 
        0.66        11.97        13.64        18.64         7.36        21.11 
TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RD 
       24.13        30.28        27.19        21.86        28.41        13.41 
TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-A9RN 
        3.48        52.73        52.60        82.49        47.84        20.22 
TCGA-ZF-AA4N TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W 
        2.89        34.06        19.69         8.61        59.38        60.16 
TCGA-ZF-AA4X TCGA-ZF-AA52 TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 
       63.02        35.41        57.90        19.40         8.52        47.15 
TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-ZF-AA5P 
       19.17         5.52        10.13 

  NFE2L3 MUTATED NFE2L3 WILD-TYPE 
            1.64             0.10 
  NFE2L3 MUTATED NFE2L3 WILD-TYPE 
           74.56           166.03 
  NFE2L3 MUTATED NFE2L3 WILD-TYPE 
           15.58            15.68 
[1] "1.6 - 74.6 (15.6)"  "0.1 - 166.0 (15.7)"
[1] "hr=" "1.2"
D77V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  NFE2L3 MUTATED         0        6         5        3
  NFE2L3 WILD-TYPE       4      111       117      125
D77V3, multiclass
           clus
vv          NFE2L3 MUTATED NFE2L3 WILD-TYPE
  STAGE I                0                4
  STAGE II               6              111
  STAGE III              5              117
  STAGE IV               3              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"
                  vv
clus               T0+T1+T2  T3  T4
  NFE2L3 MUTATED          3   8   0
  NFE2L3 WILD-TYPE      111 171  52
D77V4, multiclass
          clus
vv         NFE2L3 MUTATED NFE2L3 WILD-TYPE
  T0+T1+T2              3              111
  T3                    8              171
  T4                    0               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"
                  vv
clus                N0  N1  N2  N3
  NFE2L3 MUTATED     7   1   1   1
  NFE2L3 WILD-TYPE 206  40  74   7
D77V5, multiclass
    clus
vv   NFE2L3 MUTATED NFE2L3 WILD-TYPE
  N0              7              206
  N1              1               40
  N2              1               74
  N3              1                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"
D77V6, binary
                  cls
clus                 0   1
  NFE2L3 MUTATED     5   0
  NFE2L3 WILD-TYPE 177  10
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NFE2L3 MUTATED      5    0
  NFE2L3 WILD-TYPE  177   10
   clus
vv  NFE2L3 MUTATED NFE2L3 WILD-TYPE
  0              5              177
  1              0               10
[1] 2 2
[1] FALSE
D77V7, binary
                  cls
clus                 0   1
  NFE2L3 MUTATED     4  10
  NFE2L3 WILD-TYPE  92 270
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NFE2L3 MUTATED      4   10
  NFE2L3 WILD-TYPE   92  270
        clus
vv       NFE2L3 MUTATED NFE2L3 WILD-TYPE
  FEMALE              4               92
  MALE               10              270
[1] 2 2
[1] FALSE
D77V8, continuous
D77V9, continuous
D77V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  NFE2L3 MUTATED       0                         0    14
  NFE2L3 WILD-TYPE    38                        21   287
D77V11, multiclass
                           clus
vv                          NFE2L3 MUTATED NFE2L3 WILD-TYPE
  ASIAN                                  0               38
  BLACK OR AFRICAN AMERICAN              0               21
  WHITE                                 14              287
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D77V12, binary
                  cls
clus                 0   1
  NFE2L3 MUTATED     0  14
  NFE2L3 WILD-TYPE   8 324
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NFE2L3 MUTATED      0   14
  NFE2L3 WILD-TYPE    8  324
                        clus
vv                       NFE2L3 MUTATED NFE2L3 WILD-TYPE
  HISPANIC OR LATINO                  0                8
  NOT HISPANIC OR LATINO             14              324
[1] 2 2
[1] FALSE

Clustering(78) Variable = TAF11 MUTATION ANALYSIS
D78V1, survival
                 sevent
clus2               0   1
  TAF11 MUTATED     4   3
  TAF11 WILD-TYPE 215 148
  TAF11 MUTATED TAF11 WILD-TYPE 
              7             363 
  TAF11 MUTATED TAF11 WILD-TYPE 
              3             148 
$`TAF11 MUTATED`
TCGA-4Z-AA80 TCGA-4Z-AA86 TCGA-DK-A2I4 TCGA-K4-A4AB TCGA-XF-A9SW TCGA-XF-A9T5 
        0.62        10.22       123.85         2.76        11.90        66.64 
TCGA-ZF-AA4V 
       59.38 

$`TAF11 WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        91.63       103.50       105.70         8.35 
TCGA-4Z-AA7M TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7S 
       16.27        44.94        16.83        16.77        17.16        34.98 
TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA84 
       27.62        49.12        41.75        51.16        66.54        15.12 
TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM 
       47.80        33.83        40.08         7.33         2.66         6.74 
TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O 
       12.39         6.58        13.15        19.04        32.84        12.16 
TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20V 
       17.88        19.50         5.06        14.89        14.96         5.06 
TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH 
        8.35         8.25        17.16        16.18        20.48         4.67 
TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E TCGA-BT-A42F 
       12.82         9.96        17.56        28.70        24.26        28.41 
TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-C4-A0F6 TCGA-C4-A0F7 TCGA-CF-A1HR 
        8.98         1.94         2.93        23.01         2.04         0.46 
TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W 
        0.43         0.69        10.95        12.66        12.46        12.10 
TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A9FF 
       12.62        12.26        13.12        12.00        12.10        11.87 
TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3QU 
       13.08        12.92         4.90         7.20         5.46         5.19 
TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 
       16.31         1.84        13.58        21.86         2.14        66.41 
TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE 
       18.41        19.00        16.70       130.88       112.44        16.14 
TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I6 
       17.62        15.62         1.81        10.59         7.79        87.32 
TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS 
        2.20        13.58         7.82         8.22        17.72        50.27 
TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY 
       21.30        23.21         9.67        20.81        10.55       140.81 
TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 
       48.00        17.98        64.18        41.56        76.60        67.36 
TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6P TCGA-DK-AA6Q 
       15.68        41.06        30.67        38.24        15.02        13.58 
TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA71 
      166.03        12.36        10.49         8.65         7.53        13.64 
TCGA-DK-AA74 TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E5-A4U1 
       43.50        12.03        10.62        43.59        15.35        38.83 
TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 
       24.66         0.10         0.49         2.24        16.70        17.39 
TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF 
        0.56         0.66        14.56        13.97        12.99        14.33 
TCGA-E7-A7DU TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A97P 
        0.92         1.22        13.68        14.07        12.95        14.37 
TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 
        8.09        32.02        16.77         8.94        33.04         4.01 
TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL 
       12.62        22.52        27.98        60.66        24.30        23.41 
TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR 
       17.98        29.16         5.52        25.74        46.78        19.79 
TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X 
       12.85        22.98        27.35        14.96        20.91         3.62 
TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX 
       26.73        53.88        11.01        19.33         5.36         5.69 
TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O 
        8.25        27.45        18.08        58.92         2.70         7.10 
TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD 
        6.28        13.35        62.86        18.81         6.15        12.69 
TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FD-A6TK 
       12.36         2.27         3.06         4.31         9.67        10.85 
TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FJ-A871 TCGA-FT-A3EE 
       31.07         7.13        10.65        17.23         8.94         3.25 
TCGA-FT-A61P TCGA-G2-A2EC TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL 
        6.48        22.88        61.94        30.61        15.95        26.93 
TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B 
       35.24        33.01         7.23        20.12        17.62        66.02 
TCGA-G2-AA3C TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO 
        6.94        64.44        19.46        21.40         2.24        15.81 
TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A6I1 
        4.50        15.91        14.07        17.75        24.92         8.94 
TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 
       13.91         7.73         2.10         3.12        20.98         2.20 
TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 
        7.36        10.92        11.31        11.31         7.63        27.09 
TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATO TCGA-GU-AATP TCGA-GU-AATQ 
       20.05         5.62         4.73        10.65        32.98         7.00 
TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH 
       14.27        21.34        19.10        19.82        20.28         8.48 
TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO 
       10.59        27.35         8.58        19.07        22.72         1.51 
TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS 
       19.40        38.60         3.06         9.01         8.22        25.02 
TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RH TCGA-K4-A5RI 
        3.45        21.24         9.14        27.68         9.07        11.70 
TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO TCGA-LC-A66R 
        1.74         1.81        15.42         6.38        11.80        15.32 
TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX 
       15.58        13.48        12.23        16.67        14.24         1.84 
TCGA-S5-AA26 TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M 
        3.75        12.43        31.56        17.62        37.05        22.68 
TCGA-UY-A78N TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD 
       86.83        76.01        65.75        35.24        29.56        17.82 
TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH 
        4.54         1.64         1.87        17.88        48.62        64.80 
TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SL TCGA-XF-A9SV TCGA-XF-A9SX TCGA-XF-A9SY 
       79.66         3.22        66.41        12.76        23.64        21.04 
TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T6 
       28.24        26.27        18.90         2.24        16.27         2.10 
TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMG TCGA-XF-AAMH TCGA-XF-AAMJ 
       13.74        92.98        10.82       110.60        11.31        54.90 
TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX 
        7.63        71.57        91.73         2.96         8.32         6.77 
TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 
       98.99        44.32        56.48        30.94        61.45        86.30 
TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YC-A9TC 
       27.06        75.39        18.81         3.88         9.63         0.66 
TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R3 
       11.97        13.64        18.64         7.36        21.11        24.13 
TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RD 
       30.28        27.19        21.86        28.41        74.56        13.41 
TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-A9RN 
        3.48        52.73        52.60        82.49        47.84        20.22 
TCGA-ZF-AA4N TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4U TCGA-ZF-AA4W TCGA-ZF-AA4X 
        2.89        34.06        19.69         8.61        60.16        63.02 
TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 
       38.73        35.41        57.90        19.40         8.52        47.15 
TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-ZF-AA5P 
       19.17         5.52        10.13 

  TAF11 MUTATED TAF11 WILD-TYPE 
           0.62            0.10 
  TAF11 MUTATED TAF11 WILD-TYPE 
         123.85          166.03 
  TAF11 MUTATED TAF11 WILD-TYPE 
          11.90           15.68 
[1] "0.6 - 123.8 (11.9)" "0.1 - 166.0 (15.7)"
[1] "hr=" "1.2"
D78V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  TAF11 MUTATED         0        1         3        3
  TAF11 WILD-TYPE       4      116       119      125
D78V3, multiclass
           clus
vv          TAF11 MUTATED TAF11 WILD-TYPE
  STAGE I               0               4
  STAGE II              1             116
  STAGE III             3             119
  STAGE IV              3             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"
                 vv
clus              T0+T1+T2  T3  T4
  TAF11 MUTATED          1   5   1
  TAF11 WILD-TYPE      113 174  51
D78V4, multiclass
          clus
vv         TAF11 MUTATED TAF11 WILD-TYPE
  T0+T1+T2             1             113
  T3                   5             174
  T4                   1              51
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  TAF11 MUTATED     4   2   1   0
  TAF11 WILD-TYPE 209  39  74   8
D78V5, multiclass
    clus
vv   TAF11 MUTATED TAF11 WILD-TYPE
  N0             4             209
  N1             2              39
  N2             1              74
  N3             0               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"
D78V6, binary
                 cls
clus                0   1
  TAF11 MUTATED     4   0
  TAF11 WILD-TYPE 178  10
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TAF11 MUTATED      4    0
  TAF11 WILD-TYPE  178   10
   clus
vv  TAF11 MUTATED TAF11 WILD-TYPE
  0             4             178
  1             0              10
[1] 2 2
[1] FALSE
D78V7, binary
                 cls
clus                0   1
  TAF11 MUTATED     1   6
  TAF11 WILD-TYPE  95 274
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TAF11 MUTATED      1    6
  TAF11 WILD-TYPE   95  274
        clus
vv       TAF11 MUTATED TAF11 WILD-TYPE
  FEMALE             1              95
  MALE               6             274
[1] 2 2
[1] FALSE
D78V8, continuous
[1] "Remove cluster labels:" "TAF11 MUTATED"         
clus
  TAF11 MUTATED TAF11 WILD-TYPE 
              2             118 
     TCGA-2F-A9KO      TCGA-2F-A9KP      TCGA-2F-A9KQ      TCGA-2F-A9KR 
"TAF11 WILD-TYPE" "TAF11 WILD-TYPE" "TAF11 WILD-TYPE" "TAF11 WILD-TYPE" 
     TCGA-2F-A9KT      TCGA-2F-A9KW      TCGA-CF-A1HS      TCGA-CF-A27C 
"TAF11 WILD-TYPE" "TAF11 WILD-TYPE" "TAF11 WILD-TYPE" "TAF11 WILD-TYPE" 
     TCGA-CF-A3MF      TCGA-CF-A3MG      TCGA-CF-A3MH      TCGA-CF-A3MI 
"TAF11 WILD-TYPE" "TAF11 WILD-TYPE" "TAF11 WILD-TYPE" "TAF11 WILD-TYPE" 
     TCGA-CF-A47S      TCGA-CF-A47T      TCGA-CF-A47V      TCGA-CF-A47W 
"TAF11 WILD-TYPE" "TAF11 WILD-TYPE" "TAF11 WILD-TYPE" "TAF11 WILD-TYPE" 
     TCGA-CF-A47X      TCGA-CF-A47Y      TCGA-CF-A5U8      TCGA-CF-A5UA 
"TAF11 WILD-TYPE" "TAF11 WILD-TYPE" "TAF11 WILD-TYPE" "TAF11 WILD-TYPE" 
     TCGA-CF-A7I0      TCGA-DK-A2HX      TCGA-DK-A3IN      TCGA-DK-A3IV 
"TAF11 WILD-TYPE" "TAF11 WILD-TYPE" "TAF11 WILD-TYPE" "TAF11 WILD-TYPE" 
     TCGA-DK-A3WX      TCGA-DK-A3X2      TCGA-DK-A6B2      TCGA-DK-A6B5 
"TAF11 WILD-TYPE" "TAF11 WILD-TYPE" "TAF11 WILD-TYPE" "TAF11 WILD-TYPE" 
     TCGA-DK-A6B6      TCGA-DK-AA6P      TCGA-DK-AA6S      TCGA-DK-AA6U 
"TAF11 WILD-TYPE" "TAF11 WILD-TYPE" "TAF11 WILD-TYPE" "TAF11 WILD-TYPE" 
     TCGA-DK-AA6W      TCGA-DK-AA76      TCGA-E5-A2PC      TCGA-E5-A4TZ 
"TAF11 WILD-TYPE" "TAF11 WILD-TYPE" "TAF11 WILD-TYPE" "TAF11 WILD-TYPE" 
     TCGA-E5-A4U1      TCGA-E7-A519      TCGA-E7-A541      TCGA-E7-A7DU 
"TAF11 WILD-TYPE" "TAF11 WILD-TYPE" "TAF11 WILD-TYPE" "TAF11 WILD-TYPE" 
     TCGA-E7-A7DV      TCGA-FT-A61P      TCGA-G2-A2EC      TCGA-G2-A2EF 
"TAF11 WILD-TYPE" "TAF11 WILD-TYPE" "TAF11 WILD-TYPE" "TAF11 WILD-TYPE" 
     TCGA-G2-A2EJ      TCGA-G2-A2EK      TCGA-G2-A2EL      TCGA-G2-A2EO 
"TAF11 WILD-TYPE" "TAF11 WILD-TYPE" "TAF11 WILD-TYPE" "TAF11 WILD-TYPE" 
     TCGA-G2-A2ES      TCGA-G2-A3IB      TCGA-G2-A3IE      TCGA-G2-A3VY 
"TAF11 WILD-TYPE" "TAF11 WILD-TYPE" "TAF11 WILD-TYPE" "TAF11 WILD-TYPE" 
     TCGA-GC-A3BM      TCGA-GC-A3I6      TCGA-GC-A3OO      TCGA-GC-A3RC 
"TAF11 WILD-TYPE" "TAF11 WILD-TYPE" "TAF11 WILD-TYPE" "TAF11 WILD-TYPE" 
     TCGA-GC-A3RD      TCGA-GC-A3YS      TCGA-GC-A6I1      TCGA-GC-A6I3 
"TAF11 WILD-TYPE" "TAF11 WILD-TYPE" "TAF11 WILD-TYPE" "TAF11 WILD-TYPE" 
     TCGA-GD-A3OS      TCGA-GD-A6C6      TCGA-GV-A3JV      TCGA-GV-A3JW 
"TAF11 WILD-TYPE" "TAF11 WILD-TYPE" "TAF11 WILD-TYPE" "TAF11 WILD-TYPE" 
     TCGA-GV-A3JX      TCGA-GV-A3JZ      TCGA-GV-A3QF      TCGA-GV-A3QH 
"TAF11 WILD-TYPE" "TAF11 WILD-TYPE" "TAF11 WILD-TYPE" "TAF11 WILD-TYPE" 
     TCGA-GV-A3QI      TCGA-GV-A3QK      TCGA-GV-A40E      TCGA-GV-A40G 
"TAF11 WILD-TYPE" "TAF11 WILD-TYPE" "TAF11 WILD-TYPE" "TAF11 WILD-TYPE" 
     TCGA-GV-A6ZA      TCGA-SY-A9G0      TCGA-SY-A9G5      TCGA-UY-A78L 
"TAF11 WILD-TYPE" "TAF11 WILD-TYPE" "TAF11 WILD-TYPE" "TAF11 WILD-TYPE" 
     TCGA-UY-A78M      TCGA-UY-A78N      TCGA-XF-A8HH      TCGA-XF-A8HI 
"TAF11 WILD-TYPE" "TAF11 WILD-TYPE" "TAF11 WILD-TYPE" "TAF11 WILD-TYPE" 
     TCGA-XF-A9SG      TCGA-XF-A9SH      TCGA-XF-A9SI      TCGA-XF-A9SJ 
"TAF11 WILD-TYPE" "TAF11 WILD-TYPE" "TAF11 WILD-TYPE" "TAF11 WILD-TYPE" 
     TCGA-XF-A9SL      TCGA-XF-A9SV      TCGA-XF-A9SX      TCGA-XF-A9SY 
"TAF11 WILD-TYPE" "TAF11 WILD-TYPE" "TAF11 WILD-TYPE" "TAF11 WILD-TYPE" 
     TCGA-XF-A9SZ      TCGA-XF-A9T0      TCGA-XF-A9T2      TCGA-XF-A9T3 
"TAF11 WILD-TYPE" "TAF11 WILD-TYPE" "TAF11 WILD-TYPE" "TAF11 WILD-TYPE" 
     TCGA-XF-A9T4      TCGA-XF-A9T6      TCGA-XF-A9T8      TCGA-XF-AAME 
"TAF11 WILD-TYPE" "TAF11 WILD-TYPE" "TAF11 WILD-TYPE" "TAF11 WILD-TYPE" 
     TCGA-XF-AAMF      TCGA-XF-AAMG      TCGA-XF-AAMH      TCGA-XF-AAMJ 
"TAF11 WILD-TYPE" "TAF11 WILD-TYPE" "TAF11 WILD-TYPE" "TAF11 WILD-TYPE" 
     TCGA-XF-AAML      TCGA-XF-AAMQ      TCGA-XF-AAMR      TCGA-XF-AAMT 
"TAF11 WILD-TYPE" "TAF11 WILD-TYPE" "TAF11 WILD-TYPE" "TAF11 WILD-TYPE" 
     TCGA-XF-AAMW      TCGA-XF-AAMX      TCGA-XF-AAMY      TCGA-XF-AAMZ 
"TAF11 WILD-TYPE" "TAF11 WILD-TYPE" "TAF11 WILD-TYPE" "TAF11 WILD-TYPE" 
     TCGA-XF-AAN0      TCGA-XF-AAN1      TCGA-XF-AAN2      TCGA-XF-AAN3 
"TAF11 WILD-TYPE" "TAF11 WILD-TYPE" "TAF11 WILD-TYPE" "TAF11 WILD-TYPE" 
     TCGA-XF-AAN4      TCGA-XF-AAN5      TCGA-XF-AAN7      TCGA-XF-AAN8 
"TAF11 WILD-TYPE" "TAF11 WILD-TYPE" "TAF11 WILD-TYPE" "TAF11 WILD-TYPE" 
     TCGA-YF-AA3L      TCGA-YF-AA3M 
"TAF11 WILD-TYPE" "TAF11 WILD-TYPE" 
D78V9, continuous
[1] "Remove cluster labels:" "TAF11 MUTATED"         
clus
  TAF11 MUTATED TAF11 WILD-TYPE 
              1             204 
     TCGA-2F-A9KO      TCGA-2F-A9KP      TCGA-2F-A9KR      TCGA-4Z-AA7M 
"TAF11 WILD-TYPE" "TAF11 WILD-TYPE" "TAF11 WILD-TYPE" "TAF11 WILD-TYPE" 
     TCGA-4Z-AA89      TCGA-BL-A0C8      TCGA-BL-A13I      TCGA-BL-A13J 
"TAF11 WILD-TYPE" "TAF11 WILD-TYPE" "TAF11 WILD-TYPE" "TAF11 WILD-TYPE" 
     TCGA-BL-A3JM      TCGA-BL-A5ZZ      TCGA-BT-A20J      TCGA-BT-A20N 
"TAF11 WILD-TYPE" "TAF11 WILD-TYPE" "TAF11 WILD-TYPE" "TAF11 WILD-TYPE" 
     TCGA-BT-A2LA      TCGA-BT-A42B      TCGA-BT-A42C      TCGA-BT-A42E 
"TAF11 WILD-TYPE" "TAF11 WILD-TYPE" "TAF11 WILD-TYPE" "TAF11 WILD-TYPE" 
     TCGA-C4-A0EZ      TCGA-C4-A0F0      TCGA-C4-A0F1      TCGA-C4-A0F6 
"TAF11 WILD-TYPE" "TAF11 WILD-TYPE" "TAF11 WILD-TYPE" "TAF11 WILD-TYPE" 
     TCGA-CF-A3MH      TCGA-CF-A3MI      TCGA-CF-A47W      TCGA-CF-A47X 
"TAF11 WILD-TYPE" "TAF11 WILD-TYPE" "TAF11 WILD-TYPE" "TAF11 WILD-TYPE" 
     TCGA-CF-A5UA      TCGA-CF-A9FH      TCGA-CU-A0YN      TCGA-CU-A0YR 
"TAF11 WILD-TYPE" "TAF11 WILD-TYPE" "TAF11 WILD-TYPE" "TAF11 WILD-TYPE" 
     TCGA-CU-A3KJ      TCGA-CU-A3QU      TCGA-CU-A3YL      TCGA-CU-A5W6 
"TAF11 WILD-TYPE" "TAF11 WILD-TYPE" "TAF11 WILD-TYPE" "TAF11 WILD-TYPE" 
     TCGA-CU-A72E      TCGA-DK-A1A3      TCGA-DK-A1A5      TCGA-DK-A1A6 
"TAF11 WILD-TYPE" "TAF11 WILD-TYPE" "TAF11 WILD-TYPE" "TAF11 WILD-TYPE" 
     TCGA-DK-A1AA      TCGA-DK-A1AC      TCGA-DK-A1AE      TCGA-DK-A2HX 
"TAF11 WILD-TYPE" "TAF11 WILD-TYPE" "TAF11 WILD-TYPE" "TAF11 WILD-TYPE" 
     TCGA-DK-A2I6      TCGA-DK-A3IL      TCGA-DK-A3IM      TCGA-DK-A3IN 
"TAF11 WILD-TYPE" "TAF11 WILD-TYPE" "TAF11 WILD-TYPE" "TAF11 WILD-TYPE" 
     TCGA-DK-A3IQ      TCGA-DK-A3IU      TCGA-DK-A3IV      TCGA-DK-A3WX 
"TAF11 WILD-TYPE" "TAF11 WILD-TYPE" "TAF11 WILD-TYPE" "TAF11 WILD-TYPE" 
     TCGA-DK-A3X1      TCGA-DK-A3X2      TCGA-DK-A6AV      TCGA-DK-A6AW 
"TAF11 WILD-TYPE" "TAF11 WILD-TYPE" "TAF11 WILD-TYPE" "TAF11 WILD-TYPE" 
     TCGA-DK-A6B0      TCGA-DK-A6B2      TCGA-DK-A6B6      TCGA-DK-AA6L 
"TAF11 WILD-TYPE" "TAF11 WILD-TYPE" "TAF11 WILD-TYPE" "TAF11 WILD-TYPE" 
     TCGA-DK-AA6P      TCGA-DK-AA6T      TCGA-DK-AA6U      TCGA-DK-AA74 
"TAF11 WILD-TYPE" "TAF11 WILD-TYPE" "TAF11 WILD-TYPE" "TAF11 WILD-TYPE" 
     TCGA-DK-AA76      TCGA-E5-A4TZ      TCGA-E7-A4XJ      TCGA-E7-A519 
"TAF11 WILD-TYPE" "TAF11 WILD-TYPE" "TAF11 WILD-TYPE" "TAF11 WILD-TYPE" 
     TCGA-E7-A5KF      TCGA-E7-A678      TCGA-E7-A6ME      TCGA-E7-A6MF 
"TAF11 WILD-TYPE" "TAF11 WILD-TYPE" "TAF11 WILD-TYPE" "TAF11 WILD-TYPE" 
     TCGA-E7-A7PW      TCGA-E7-A7XN      TCGA-E7-A85H      TCGA-E7-A97Q 
"TAF11 WILD-TYPE" "TAF11 WILD-TYPE" "TAF11 WILD-TYPE" "TAF11 WILD-TYPE" 
     TCGA-FD-A3B3      TCGA-FD-A3B4      TCGA-FD-A3B5      TCGA-FD-A3B6 
"TAF11 WILD-TYPE" "TAF11 WILD-TYPE" "TAF11 WILD-TYPE" "TAF11 WILD-TYPE" 
     TCGA-FD-A3B7      TCGA-FD-A3B8      TCGA-FD-A3N5      TCGA-FD-A3N6 
"TAF11 WILD-TYPE" "TAF11 WILD-TYPE" "TAF11 WILD-TYPE" "TAF11 WILD-TYPE" 
     TCGA-FD-A3NA      TCGA-FD-A3SJ      TCGA-FD-A3SM      TCGA-FD-A3SN 
"TAF11 WILD-TYPE" "TAF11 WILD-TYPE" "TAF11 WILD-TYPE" "TAF11 WILD-TYPE" 
     TCGA-FD-A3SO      TCGA-FD-A3SP      TCGA-FD-A3SQ      TCGA-FD-A3SR 
"TAF11 WILD-TYPE" "TAF11 WILD-TYPE" "TAF11 WILD-TYPE" "TAF11 WILD-TYPE" 
     TCGA-FD-A3SS      TCGA-FD-A43N      TCGA-FD-A43P      TCGA-FD-A43S 
"TAF11 WILD-TYPE" "TAF11 WILD-TYPE" "TAF11 WILD-TYPE" "TAF11 WILD-TYPE" 
     TCGA-FD-A43U      TCGA-FD-A43X      TCGA-FD-A5BT      TCGA-FD-A5BU 
"TAF11 WILD-TYPE" "TAF11 WILD-TYPE" "TAF11 WILD-TYPE" "TAF11 WILD-TYPE" 
     TCGA-FD-A5BV      TCGA-FD-A5BX      TCGA-FD-A5C0      TCGA-FD-A62N 
"TAF11 WILD-TYPE" "TAF11 WILD-TYPE" "TAF11 WILD-TYPE" "TAF11 WILD-TYPE" 
     TCGA-FD-A6TB      TCGA-FD-A6TC      TCGA-FD-A6TE      TCGA-FD-A6TG 
"TAF11 WILD-TYPE" "TAF11 WILD-TYPE" "TAF11 WILD-TYPE" "TAF11 WILD-TYPE" 
     TCGA-FD-A6TH      TCGA-FD-A6TK      TCGA-FJ-A3Z9      TCGA-FJ-A3ZE 
"TAF11 WILD-TYPE" "TAF11 WILD-TYPE" "TAF11 WILD-TYPE" "TAF11 WILD-TYPE" 
     TCGA-FJ-A3ZF      TCGA-FJ-A871      TCGA-FT-A61P      TCGA-G2-A2EF 
"TAF11 WILD-TYPE" "TAF11 WILD-TYPE" "TAF11 WILD-TYPE" "TAF11 WILD-TYPE" 
     TCGA-G2-A2EJ      TCGA-G2-A2EL      TCGA-G2-A2ES      TCGA-G2-A3IE 
"TAF11 WILD-TYPE" "TAF11 WILD-TYPE" "TAF11 WILD-TYPE" "TAF11 WILD-TYPE" 
     TCGA-G2-AA3B      TCGA-G2-AA3C      TCGA-G2-AA3D      TCGA-G2-AA3F 
"TAF11 WILD-TYPE" "TAF11 WILD-TYPE" "TAF11 WILD-TYPE" "TAF11 WILD-TYPE" 
     TCGA-GC-A3BM      TCGA-GC-A3RB      TCGA-GC-A3WC      TCGA-GC-A3YS 
"TAF11 WILD-TYPE" "TAF11 WILD-TYPE" "TAF11 WILD-TYPE" "TAF11 WILD-TYPE" 
     TCGA-GD-A2C5      TCGA-GD-A3OQ      TCGA-GD-A3OS      TCGA-GD-A6C6 
"TAF11 WILD-TYPE" "TAF11 WILD-TYPE" "TAF11 WILD-TYPE" "TAF11 WILD-TYPE" 
     TCGA-GU-A42P      TCGA-GU-A42Q      TCGA-GU-A42R      TCGA-GU-A763 
"TAF11 WILD-TYPE" "TAF11 WILD-TYPE" "TAF11 WILD-TYPE" "TAF11 WILD-TYPE" 
     TCGA-GU-A764      TCGA-GU-AATO      TCGA-GU-AATP      TCGA-GU-AATQ 
"TAF11 WILD-TYPE" "TAF11 WILD-TYPE" "TAF11 WILD-TYPE" "TAF11 WILD-TYPE" 
     TCGA-GV-A3JV      TCGA-GV-A3JX      TCGA-GV-A3JZ      TCGA-GV-A3QF 
"TAF11 WILD-TYPE" "TAF11 WILD-TYPE" "TAF11 WILD-TYPE" "TAF11 WILD-TYPE" 
     TCGA-GV-A3QG      TCGA-GV-A3QH      TCGA-GV-A3QI      TCGA-GV-A3QK 
"TAF11 WILD-TYPE" "TAF11 WILD-TYPE" "TAF11 WILD-TYPE" "TAF11 WILD-TYPE" 
     TCGA-GV-A40E      TCGA-GV-A40G      TCGA-H4-A2HO      TCGA-H4-A2HQ 
"TAF11 WILD-TYPE" "TAF11 WILD-TYPE" "TAF11 WILD-TYPE" "TAF11 WILD-TYPE" 
     TCGA-HQ-A5ND      TCGA-HQ-A5NE      TCGA-K4-A3WS      TCGA-K4-A3WV 
"TAF11 WILD-TYPE" "TAF11 WILD-TYPE" "TAF11 WILD-TYPE" "TAF11 WILD-TYPE" 
     TCGA-K4-A5RH      TCGA-K4-A5RI      TCGA-K4-A83P      TCGA-K4-AAQO 
"TAF11 WILD-TYPE" "TAF11 WILD-TYPE" "TAF11 WILD-TYPE" "TAF11 WILD-TYPE" 
     TCGA-PQ-A6FI      TCGA-PQ-A6FN      TCGA-R3-A69X      TCGA-S5-A6DX 
"TAF11 WILD-TYPE" "TAF11 WILD-TYPE" "TAF11 WILD-TYPE" "TAF11 WILD-TYPE" 
     TCGA-SY-A9G0      TCGA-UY-A78N      TCGA-UY-A8OB      TCGA-UY-A9PB 
"TAF11 WILD-TYPE" "TAF11 WILD-TYPE" "TAF11 WILD-TYPE" "TAF11 WILD-TYPE" 
     TCGA-UY-A9PE      TCGA-UY-A9PF      TCGA-XF-A9SJ      TCGA-XF-A9SL 
"TAF11 WILD-TYPE" "TAF11 WILD-TYPE" "TAF11 WILD-TYPE" "TAF11 WILD-TYPE" 
     TCGA-XF-A9SV      TCGA-XF-A9SX      TCGA-XF-A9SY      TCGA-XF-A9SZ 
"TAF11 WILD-TYPE" "TAF11 WILD-TYPE" "TAF11 WILD-TYPE" "TAF11 WILD-TYPE" 
     TCGA-XF-A9T3      TCGA-XF-A9T8      TCGA-XF-AAMF      TCGA-XF-AAMH 
"TAF11 WILD-TYPE" "TAF11 WILD-TYPE" "TAF11 WILD-TYPE" "TAF11 WILD-TYPE" 
     TCGA-XF-AAMQ      TCGA-XF-AAMT      TCGA-XF-AAN0      TCGA-XF-AAN1 
"TAF11 WILD-TYPE" "TAF11 WILD-TYPE" "TAF11 WILD-TYPE" "TAF11 WILD-TYPE" 
     TCGA-XF-AAN2      TCGA-XF-AAN4      TCGA-XF-AAN5      TCGA-XF-AAN7 
"TAF11 WILD-TYPE" "TAF11 WILD-TYPE" "TAF11 WILD-TYPE" "TAF11 WILD-TYPE" 
     TCGA-XF-AAN8      TCGA-YF-AA3L      TCGA-YF-AA3M      TCGA-ZF-A9R0 
"TAF11 WILD-TYPE" "TAF11 WILD-TYPE" "TAF11 WILD-TYPE" "TAF11 WILD-TYPE" 
     TCGA-ZF-A9R2      TCGA-ZF-A9R3      TCGA-ZF-A9R5      TCGA-ZF-A9R7 
"TAF11 WILD-TYPE" "TAF11 WILD-TYPE" "TAF11 WILD-TYPE" "TAF11 WILD-TYPE" 
     TCGA-ZF-A9R9      TCGA-ZF-A9RD      TCGA-ZF-A9RF      TCGA-ZF-A9RL 
"TAF11 WILD-TYPE" "TAF11 WILD-TYPE" "TAF11 WILD-TYPE" "TAF11 WILD-TYPE" 
     TCGA-ZF-A9RM      TCGA-ZF-AA4U      TCGA-ZF-AA51      TCGA-ZF-AA52 
"TAF11 WILD-TYPE" "TAF11 WILD-TYPE" "TAF11 WILD-TYPE" "TAF11 WILD-TYPE" 
     TCGA-ZF-AA58      TCGA-ZF-AA5H      TCGA-ZF-AA5N      TCGA-ZF-AA5P 
"TAF11 WILD-TYPE" "TAF11 WILD-TYPE" "TAF11 WILD-TYPE" "TAF11 WILD-TYPE" 
D78V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TAF11 MUTATED       0                         1     6
  TAF11 WILD-TYPE    38                        20   295
D78V11, multiclass
                           clus
vv                          TAF11 MUTATED TAF11 WILD-TYPE
  ASIAN                                 0              38
  BLACK OR AFRICAN AMERICAN             1              20
  WHITE                                 6             295
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D78V12, binary
                 cls
clus                0   1
  TAF11 MUTATED     0   5
  TAF11 WILD-TYPE   8 333
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TAF11 MUTATED      0    5
  TAF11 WILD-TYPE    8  333
                        clus
vv                       TAF11 MUTATED TAF11 WILD-TYPE
  HISPANIC OR LATINO                 0               8
  NOT HISPANIC OR LATINO             5             333
[1] 2 2
[1] FALSE

Clustering(79) Variable = BCL2L1 MUTATION ANALYSIS
D79V1, survival
                  sevent
clus2                0   1
  BCL2L1 MUTATED     1   2
  BCL2L1 WILD-TYPE 218 149
  BCL2L1 MUTATED BCL2L1 WILD-TYPE 
               3              367 
  BCL2L1 MUTATED BCL2L1 WILD-TYPE 
               2              149 
$`BCL2L1 MUTATED`
TCGA-BT-A20N TCGA-FD-A62O TCGA-GC-A3I6 
       32.84         7.10         2.24 

$`BCL2L1 WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        91.63       103.50       105.70         8.35 
TCGA-4Z-AA7M TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7S 
       16.27        44.94        16.83        16.77        17.16        34.98 
TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 
       27.62        49.12         0.62        41.75        51.16        66.54 
TCGA-4Z-AA84 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BL-A13I 
       15.12        10.22        47.80        33.83        40.08         7.33 
TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J 
        2.66         6.74        12.39         6.58        13.15        19.04 
TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U 
       12.16        17.88        19.50         5.06        14.89        14.96 
TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A2LD 
        5.06         8.35         8.25        17.16        16.18        20.48 
TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E 
        4.67        12.82         9.96        17.56        28.70        24.26 
TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-C4-A0F6 TCGA-C4-A0F7 
       28.41         8.98         1.94         2.93        23.01         2.04 
TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V 
        0.46         0.43         0.69        10.95        12.66        12.46 
TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 
       12.10        12.62        12.26        13.12        12.00        12.10 
TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ 
       11.87        13.08        12.92         4.90         7.20         5.46 
TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 
        5.19        16.31         1.84        13.58        21.86         2.14 
TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD 
       66.41        18.41        19.00        16.70       130.88       112.44 
TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 
       16.14        17.62        15.62         1.81        10.59         7.79 
TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN 
      123.85        87.32         2.20        13.58         7.82         8.22 
TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW 
       17.72        50.27        21.30        23.21         9.67        20.81 
TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW 
       10.55       140.81        48.00        17.98        64.18        41.56 
TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L 
       76.60        67.36        15.68        41.06        30.67        38.24 
TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6W 
       15.02        13.58       166.03        12.36        10.49         8.65 
TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A2PC 
        7.53        13.64        43.50        12.03        10.62        43.59 
TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ 
       15.35        38.83        24.66         0.10         0.49         2.24 
TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 
       16.70        17.39         0.56         0.66        14.56        13.97 
TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A7XN 
       12.99        14.33         0.92         1.22        13.68        14.07 
TCGA-E7-A85H TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 
       12.95        14.37         8.09        32.02        16.77         8.94 
TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA 
       33.04         4.01        12.62        22.52        27.98        60.66 
TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP 
       24.30        23.41        17.98        29.16         5.52        25.74 
TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S 
       46.78        19.79        12.85        22.98        27.35        14.96 
TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU 
       20.91         3.62        26.73        53.88        11.01        19.33 
TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 
        5.36         5.69         8.25        27.45        18.08        58.92 
TCGA-FD-A62N TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC 
        2.70         6.28        13.35        62.86        18.81         6.15 
TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI 
       12.69        12.36         2.27         3.06         4.31         9.67 
TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FJ-A871 
       10.85        31.07         7.13        10.65        17.23         8.94 
TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EC TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK 
        3.25         6.48        22.88        61.94        30.61        15.95 
TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY 
       26.93        35.24        33.01         7.23        20.12        17.62 
TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3OO 
       66.02         6.94        64.44        19.46        21.40        15.81 
TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A6I1 
        4.50        15.91        14.07        17.75        24.92         8.94 
TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 
       13.91         7.73         2.10         3.12        20.98         2.20 
TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 
        7.36        10.92        11.31        11.31         7.63        27.09 
TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATO TCGA-GU-AATP TCGA-GU-AATQ 
       20.05         5.62         4.73        10.65        32.98         7.00 
TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH 
       14.27        21.34        19.10        19.82        20.28         8.48 
TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO 
       10.59        27.35         8.58        19.07        22.72         1.51 
TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS 
       19.40        38.60         3.06         9.01         8.22        25.02 
TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RH 
        3.45        21.24         2.76         9.14        27.68         9.07 
TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO 
       11.70         1.74         1.81        15.42         6.38        11.80 
TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X 
       15.32        15.58        13.48        12.23        16.67        14.24 
TCGA-S5-A6DX TCGA-S5-AA26 TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L 
        1.84         3.75        12.43        31.56        17.62        37.05 
TCGA-UY-A78M TCGA-UY-A78N TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A9PA TCGA-UY-A9PB 
       22.68        86.83        76.01        65.75        35.24        29.56 
TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG 
       17.82         4.54         1.64         1.87        17.88        48.62 
TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SL TCGA-XF-A9SV TCGA-XF-A9SW 
       64.80        79.66         3.22        66.41        12.76        11.90 
TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 
       23.64        21.04        28.24        26.27        18.90         2.24 
TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMF 
       16.27        66.64         2.10        13.74        92.98        10.82 
TCGA-XF-AAMG TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR 
      110.60        11.31        54.90         7.63        71.57        91.73 
TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN0 
        2.96         8.32         6.77        98.99        44.32        56.48 
TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN7 
       30.94        61.45        86.30        27.06        75.39        18.81 
TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R0 
        3.88         9.63         0.66        11.97        13.64        18.64 
TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R7 
        7.36        21.11        24.13        30.28        27.19        21.86 
TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RG 
       28.41        74.56        13.41         3.48        52.73        52.60 
TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4R TCGA-ZF-AA4T 
       82.49        47.84        20.22         2.89        34.06        19.69 
TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 
        8.61        59.38        60.16        63.02        38.73        35.41 
TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N 
       57.90        19.40         8.52        47.15        19.17         5.52 
TCGA-ZF-AA5P 
       10.13 

  BCL2L1 MUTATED BCL2L1 WILD-TYPE 
            2.24             0.10 
  BCL2L1 MUTATED BCL2L1 WILD-TYPE 
           32.84           166.03 
  BCL2L1 MUTATED BCL2L1 WILD-TYPE 
            7.10            15.68 
[1] "2.2 - 32.8 (7.1)"   "0.1 - 166.0 (15.7)"
[1] "hr=" "2.5"
D79V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  BCL2L1 MUTATED         0        0         2        1
  BCL2L1 WILD-TYPE       4      117       120      127
D79V3, multiclass
           clus
vv          BCL2L1 MUTATED BCL2L1 WILD-TYPE
  STAGE I                0                4
  STAGE II               0              117
  STAGE III              2              120
  STAGE IV               1              127
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1+T2  T3  T4
  BCL2L1 MUTATED          0   3   0
  BCL2L1 WILD-TYPE      114 176  52
D79V4, multiclass
          clus
vv         BCL2L1 MUTATED BCL2L1 WILD-TYPE
  T0+T1+T2              0              114
  T3                    3              176
  T4                    0               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"
                  vv
clus                N0  N1  N2  N3
  BCL2L1 MUTATED     2   0   1   0
  BCL2L1 WILD-TYPE 211  41  74   8
D79V5, multiclass
    clus
vv   BCL2L1 MUTATED BCL2L1 WILD-TYPE
  N0              2              211
  N1              0               41
  N2              1               74
  N3              0                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"
D79V6, binary
                  cls
clus                 0   1
  BCL2L1 MUTATED     1   0
  BCL2L1 WILD-TYPE 181  10
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BCL2L1 MUTATED      1    0
  BCL2L1 WILD-TYPE  181   10
   clus
vv  BCL2L1 MUTATED BCL2L1 WILD-TYPE
  0              1              181
  1              0               10
[1] 2 2
[1] FALSE
D79V7, binary
                  cls
clus                 0   1
  BCL2L1 MUTATED     0   3
  BCL2L1 WILD-TYPE  96 277
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BCL2L1 MUTATED      0    3
  BCL2L1 WILD-TYPE   96  277
        clus
vv       BCL2L1 MUTATED BCL2L1 WILD-TYPE
  FEMALE              0               96
  MALE                3              277
[1] 2 2
[1] FALSE
D79V8, continuous
[1] "Remove cluster labels:" "BCL2L1 MUTATED"        
clus
  BCL2L1 MUTATED BCL2L1 WILD-TYPE 
               1              119 
      TCGA-2F-A9KO       TCGA-2F-A9KP       TCGA-2F-A9KQ       TCGA-2F-A9KR 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-2F-A9KT       TCGA-2F-A9KW       TCGA-CF-A1HS       TCGA-CF-A27C 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-CF-A3MF       TCGA-CF-A3MG       TCGA-CF-A3MH       TCGA-CF-A3MI 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-CF-A47S       TCGA-CF-A47T       TCGA-CF-A47V       TCGA-CF-A47W 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-CF-A47X       TCGA-CF-A47Y       TCGA-CF-A5U8       TCGA-CF-A5UA 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-CF-A7I0       TCGA-DK-A2HX       TCGA-DK-A3IN       TCGA-DK-A3IV 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-DK-A3WX       TCGA-DK-A3X2       TCGA-DK-A6B2       TCGA-DK-A6B5 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-DK-A6B6       TCGA-DK-AA6P       TCGA-DK-AA6S       TCGA-DK-AA6U 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-DK-AA6W       TCGA-DK-AA76       TCGA-E5-A2PC       TCGA-E5-A4TZ 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-E5-A4U1       TCGA-E7-A519       TCGA-E7-A541       TCGA-E7-A7DU 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-E7-A7DV       TCGA-FT-A61P       TCGA-G2-A2EC       TCGA-G2-A2EF 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-G2-A2EJ       TCGA-G2-A2EK       TCGA-G2-A2EL       TCGA-G2-A2EO 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-G2-A2ES       TCGA-G2-A3IB       TCGA-G2-A3IE       TCGA-G2-A3VY 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-GC-A3BM       TCGA-GC-A3OO       TCGA-GC-A3RC       TCGA-GC-A3RD 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-GC-A3YS       TCGA-GC-A6I1       TCGA-GC-A6I3       TCGA-GD-A3OS 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-GD-A6C6       TCGA-GV-A3JV       TCGA-GV-A3JW       TCGA-GV-A3JX 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-GV-A3JZ       TCGA-GV-A3QF       TCGA-GV-A3QH       TCGA-GV-A3QI 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-GV-A3QK       TCGA-GV-A40E       TCGA-GV-A40G       TCGA-GV-A6ZA 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-SY-A9G0       TCGA-SY-A9G5       TCGA-UY-A78L       TCGA-UY-A78M 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-UY-A78N       TCGA-XF-A8HH       TCGA-XF-A8HI       TCGA-XF-A9SG 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-XF-A9SH       TCGA-XF-A9SI       TCGA-XF-A9SJ       TCGA-XF-A9SL 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-XF-A9SV       TCGA-XF-A9SW       TCGA-XF-A9SX       TCGA-XF-A9SY 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-XF-A9SZ       TCGA-XF-A9T0       TCGA-XF-A9T2       TCGA-XF-A9T3 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-XF-A9T4       TCGA-XF-A9T5       TCGA-XF-A9T6       TCGA-XF-A9T8 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-XF-AAME       TCGA-XF-AAMF       TCGA-XF-AAMG       TCGA-XF-AAMH 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-XF-AAMJ       TCGA-XF-AAML       TCGA-XF-AAMQ       TCGA-XF-AAMR 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-XF-AAMT       TCGA-XF-AAMW       TCGA-XF-AAMX       TCGA-XF-AAMY 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-XF-AAMZ       TCGA-XF-AAN0       TCGA-XF-AAN1       TCGA-XF-AAN2 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-XF-AAN3       TCGA-XF-AAN4       TCGA-XF-AAN5       TCGA-XF-AAN7 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-XF-AAN8       TCGA-YF-AA3L       TCGA-YF-AA3M 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
D79V9, continuous
[1] "Remove cluster labels:" "BCL2L1 MUTATED"        
clus
  BCL2L1 MUTATED BCL2L1 WILD-TYPE 
               1              204 
      TCGA-2F-A9KO       TCGA-2F-A9KP       TCGA-2F-A9KR       TCGA-4Z-AA7M 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-4Z-AA89       TCGA-BL-A0C8       TCGA-BL-A13I       TCGA-BL-A13J 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-BL-A3JM       TCGA-BL-A5ZZ       TCGA-BT-A20J       TCGA-BT-A2LA 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-BT-A42B       TCGA-BT-A42C       TCGA-BT-A42E       TCGA-C4-A0EZ 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-C4-A0F0       TCGA-C4-A0F1       TCGA-C4-A0F6       TCGA-CF-A3MH 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-CF-A3MI       TCGA-CF-A47W       TCGA-CF-A47X       TCGA-CF-A5UA 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-CF-A9FH       TCGA-CU-A0YN       TCGA-CU-A0YR       TCGA-CU-A3KJ 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-CU-A3QU       TCGA-CU-A3YL       TCGA-CU-A5W6       TCGA-CU-A72E 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-DK-A1A3       TCGA-DK-A1A5       TCGA-DK-A1A6       TCGA-DK-A1AA 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-DK-A1AC       TCGA-DK-A1AE       TCGA-DK-A2HX       TCGA-DK-A2I6 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-DK-A3IL       TCGA-DK-A3IM       TCGA-DK-A3IN       TCGA-DK-A3IQ 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-DK-A3IU       TCGA-DK-A3IV       TCGA-DK-A3WX       TCGA-DK-A3X1 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-DK-A3X2       TCGA-DK-A6AV       TCGA-DK-A6AW       TCGA-DK-A6B0 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-DK-A6B2       TCGA-DK-A6B6       TCGA-DK-AA6L       TCGA-DK-AA6P 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-DK-AA6T       TCGA-DK-AA6U       TCGA-DK-AA74       TCGA-DK-AA76 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-E5-A4TZ       TCGA-E7-A4XJ       TCGA-E7-A519       TCGA-E7-A5KF 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-E7-A678       TCGA-E7-A6ME       TCGA-E7-A6MF       TCGA-E7-A7PW 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-E7-A7XN       TCGA-E7-A85H       TCGA-E7-A97Q       TCGA-FD-A3B3 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-FD-A3B4       TCGA-FD-A3B5       TCGA-FD-A3B6       TCGA-FD-A3B7 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-FD-A3B8       TCGA-FD-A3N5       TCGA-FD-A3N6       TCGA-FD-A3NA 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-FD-A3SJ       TCGA-FD-A3SM       TCGA-FD-A3SN       TCGA-FD-A3SO 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-FD-A3SP       TCGA-FD-A3SQ       TCGA-FD-A3SR       TCGA-FD-A3SS 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-FD-A43N       TCGA-FD-A43P       TCGA-FD-A43S       TCGA-FD-A43U 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-FD-A43X       TCGA-FD-A5BT       TCGA-FD-A5BU       TCGA-FD-A5BV 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-FD-A5BX       TCGA-FD-A5C0       TCGA-FD-A62N       TCGA-FD-A6TB 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-FD-A6TC       TCGA-FD-A6TE       TCGA-FD-A6TG       TCGA-FD-A6TH 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-FD-A6TK       TCGA-FJ-A3Z9       TCGA-FJ-A3ZE       TCGA-FJ-A3ZF 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-FJ-A871       TCGA-FT-A61P       TCGA-G2-A2EF       TCGA-G2-A2EJ 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-G2-A2EL       TCGA-G2-A2ES       TCGA-G2-A3IE       TCGA-G2-AA3B 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-G2-AA3C       TCGA-G2-AA3D       TCGA-G2-AA3F       TCGA-GC-A3BM 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-GC-A3RB       TCGA-GC-A3WC       TCGA-GC-A3YS       TCGA-GD-A2C5 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-GD-A3OQ       TCGA-GD-A3OS       TCGA-GD-A6C6       TCGA-GU-A42P 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-GU-A42Q       TCGA-GU-A42R       TCGA-GU-A763       TCGA-GU-A764 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-GU-AATO       TCGA-GU-AATP       TCGA-GU-AATQ       TCGA-GV-A3JV 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-GV-A3JX       TCGA-GV-A3JZ       TCGA-GV-A3QF       TCGA-GV-A3QG 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-GV-A3QH       TCGA-GV-A3QI       TCGA-GV-A3QK       TCGA-GV-A40E 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-GV-A40G       TCGA-H4-A2HO       TCGA-H4-A2HQ       TCGA-HQ-A5ND 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-HQ-A5NE       TCGA-K4-A3WS       TCGA-K4-A3WV       TCGA-K4-A5RH 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-K4-A5RI       TCGA-K4-A83P       TCGA-K4-AAQO       TCGA-PQ-A6FI 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-PQ-A6FN       TCGA-R3-A69X       TCGA-S5-A6DX       TCGA-SY-A9G0 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-UY-A78N       TCGA-UY-A8OB       TCGA-UY-A9PB       TCGA-UY-A9PE 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-UY-A9PF       TCGA-XF-A9SJ       TCGA-XF-A9SL       TCGA-XF-A9SV 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-XF-A9SX       TCGA-XF-A9SY       TCGA-XF-A9SZ       TCGA-XF-A9T3 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-XF-A9T8       TCGA-XF-AAMF       TCGA-XF-AAMH       TCGA-XF-AAMQ 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-XF-AAMT       TCGA-XF-AAN0       TCGA-XF-AAN1       TCGA-XF-AAN2 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-XF-AAN4       TCGA-XF-AAN5       TCGA-XF-AAN7       TCGA-XF-AAN8 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-YF-AA3L       TCGA-YF-AA3M       TCGA-ZF-A9R0       TCGA-ZF-A9R2 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-ZF-A9R3       TCGA-ZF-A9R5       TCGA-ZF-A9R7       TCGA-ZF-A9R9 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-ZF-A9RD       TCGA-ZF-A9RF       TCGA-ZF-A9RL       TCGA-ZF-A9RM 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-ZF-AA4U       TCGA-ZF-AA4V       TCGA-ZF-AA51       TCGA-ZF-AA52 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-ZF-AA58       TCGA-ZF-AA5H       TCGA-ZF-AA5N       TCGA-ZF-AA5P 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
D79V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  BCL2L1 MUTATED       0                         0     2
  BCL2L1 WILD-TYPE    38                        21   299
D79V11, multiclass
[1] "Remove cluster labels:" "BCL2L1 MUTATED"        
clus
  BCL2L1 MUTATED BCL2L1 WILD-TYPE 
               2              358 
      TCGA-2F-A9KO       TCGA-2F-A9KP       TCGA-2F-A9KQ       TCGA-2F-A9KT 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-2F-A9KW       TCGA-4Z-AA7M       TCGA-4Z-AA7N       TCGA-4Z-AA7O 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-4Z-AA7Q       TCGA-4Z-AA7R       TCGA-4Z-AA7S       TCGA-4Z-AA7W 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-4Z-AA7Y       TCGA-4Z-AA80       TCGA-4Z-AA81       TCGA-4Z-AA82 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-4Z-AA83       TCGA-4Z-AA84       TCGA-4Z-AA86       TCGA-4Z-AA87 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-4Z-AA89       TCGA-BL-A0C8       TCGA-BL-A13I       TCGA-BL-A13J 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-BL-A3JM       TCGA-BL-A5ZZ       TCGA-BT-A0S7       TCGA-BT-A0YX 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-BT-A20J       TCGA-BT-A20O       TCGA-BT-A20P       TCGA-BT-A20Q 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-BT-A20R       TCGA-BT-A20T       TCGA-BT-A20U       TCGA-BT-A20V 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-BT-A20W       TCGA-BT-A20X       TCGA-BT-A2LA       TCGA-BT-A2LB 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-BT-A2LD       TCGA-BT-A3PH       TCGA-BT-A3PJ       TCGA-BT-A3PK 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-BT-A42B       TCGA-BT-A42C       TCGA-BT-A42E       TCGA-BT-A42F 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-CF-A1HR       TCGA-CF-A1HS       TCGA-CF-A27C       TCGA-CF-A3MF 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-CF-A3MG       TCGA-CF-A3MH       TCGA-CF-A3MI       TCGA-CF-A47S 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-CF-A47T       TCGA-CF-A47V       TCGA-CF-A47W       TCGA-CF-A47X 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-CF-A47Y       TCGA-CF-A5U8       TCGA-CF-A5UA       TCGA-CF-A7I0 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-CF-A9FF       TCGA-CF-A9FH       TCGA-CF-A9FM       TCGA-CU-A0YN 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-CU-A0YO       TCGA-CU-A0YR       TCGA-CU-A3KJ       TCGA-CU-A3QU 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-CU-A3YL       TCGA-CU-A5W6       TCGA-CU-A72E       TCGA-DK-A1A3 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-DK-A1A5       TCGA-DK-A1A6       TCGA-DK-A1A7       TCGA-DK-A1AA 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-DK-A1AB       TCGA-DK-A1AC       TCGA-DK-A1AD       TCGA-DK-A1AE 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-DK-A1AF       TCGA-DK-A1AG       TCGA-DK-A2HX       TCGA-DK-A2I1 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-DK-A2I2       TCGA-DK-A2I4       TCGA-DK-A2I6       TCGA-DK-A3IK 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-DK-A3IL       TCGA-DK-A3IM       TCGA-DK-A3IN       TCGA-DK-A3IQ 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-DK-A3IS       TCGA-DK-A3IT       TCGA-DK-A3IU       TCGA-DK-A3IV 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-DK-A3WW       TCGA-DK-A3WX       TCGA-DK-A3WY       TCGA-DK-A3X1 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-DK-A3X2       TCGA-DK-A6AV       TCGA-DK-A6AW       TCGA-DK-A6B0 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-DK-A6B1       TCGA-DK-A6B2       TCGA-DK-A6B5       TCGA-DK-A6B6 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-DK-AA6L       TCGA-DK-AA6P       TCGA-DK-AA6Q       TCGA-DK-AA6S 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-DK-AA6T       TCGA-DK-AA6U       TCGA-DK-AA6W       TCGA-DK-AA6X 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-DK-AA71       TCGA-DK-AA74       TCGA-DK-AA76       TCGA-DK-AA77 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-E5-A2PC       TCGA-E5-A4TZ       TCGA-E7-A3X6       TCGA-E7-A3Y1 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-E7-A4IJ       TCGA-E7-A4XJ       TCGA-E7-A519       TCGA-E7-A541 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-E7-A5KE       TCGA-E7-A5KF       TCGA-E7-A677       TCGA-E7-A678 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-E7-A6ME       TCGA-E7-A6MF       TCGA-E7-A7DU       TCGA-E7-A7DV 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-E7-A7PW       TCGA-E7-A7XN       TCGA-E7-A85H       TCGA-E7-A97P 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-E7-A97Q       TCGA-FD-A3B3       TCGA-FD-A3B4       TCGA-FD-A3B5 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-FD-A3B6       TCGA-FD-A3B7       TCGA-FD-A3B8       TCGA-FD-A3N5 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-FD-A3N6       TCGA-FD-A3NA       TCGA-FD-A3SJ       TCGA-FD-A3SL 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-FD-A3SM       TCGA-FD-A3SN       TCGA-FD-A3SO       TCGA-FD-A3SP 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-FD-A3SQ       TCGA-FD-A3SR       TCGA-FD-A3SS       TCGA-FD-A43N 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-FD-A43P       TCGA-FD-A43S       TCGA-FD-A43U       TCGA-FD-A43X 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-FD-A5BR       TCGA-FD-A5BS       TCGA-FD-A5BT       TCGA-FD-A5BU 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-FD-A5BV       TCGA-FD-A5BX       TCGA-FD-A5BY       TCGA-FD-A5BZ 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-FD-A5C0       TCGA-FD-A5C1       TCGA-FD-A62N       TCGA-FD-A62P 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-FD-A62S       TCGA-FD-A6TA       TCGA-FD-A6TB       TCGA-FD-A6TC 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-FD-A6TD       TCGA-FD-A6TE       TCGA-FD-A6TF       TCGA-FD-A6TG 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-FD-A6TH       TCGA-FD-A6TI       TCGA-FD-A6TK       TCGA-FJ-A3Z7 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-FJ-A3Z9       TCGA-FJ-A3ZE       TCGA-FJ-A3ZF       TCGA-FJ-A871 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-FT-A3EE       TCGA-FT-A61P       TCGA-G2-A2EC       TCGA-G2-A2EF 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-G2-A2EJ       TCGA-G2-A2EK       TCGA-G2-A2EL       TCGA-G2-A2EO 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-G2-A2ES       TCGA-G2-A3IB       TCGA-G2-A3IE       TCGA-G2-A3VY 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-G2-AA3B       TCGA-G2-AA3C       TCGA-G2-AA3D       TCGA-G2-AA3F 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-GC-A3BM       TCGA-GC-A3OO       TCGA-GC-A3RB       TCGA-GC-A3RC 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-GC-A3RD       TCGA-GC-A3WC       TCGA-GC-A3YS       TCGA-GC-A6I1 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-GC-A6I3       TCGA-GD-A2C5       TCGA-GD-A3OP       TCGA-GD-A3OQ 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-GD-A3OS       TCGA-GD-A6C6       TCGA-GD-A76B       TCGA-GU-A42P 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-GU-A42Q       TCGA-GU-A42R       TCGA-GU-A762       TCGA-GU-A763 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-GU-A764       TCGA-GU-A766       TCGA-GU-A767       TCGA-GU-AATO 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-GU-AATP       TCGA-GU-AATQ       TCGA-GV-A3JV       TCGA-GV-A3JW 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-GV-A3JX       TCGA-GV-A3JZ       TCGA-GV-A3QF       TCGA-GV-A3QG 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-GV-A3QH       TCGA-GV-A3QI       TCGA-GV-A3QK       TCGA-GV-A40E 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-GV-A40G       TCGA-GV-A6ZA       TCGA-H4-A2HO       TCGA-H4-A2HQ 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-K4-A3WS       TCGA-K4-A3WU       TCGA-K4-A3WV       TCGA-K4-A4AB 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-K4-A4AC       TCGA-K4-A54R       TCGA-K4-A5RH       TCGA-K4-A5RI 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-K4-A5RJ       TCGA-K4-A6FZ       TCGA-K4-A6MB       TCGA-K4-A83P 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-K4-AAQO       TCGA-LC-A66R       TCGA-LT-A5Z6       TCGA-MV-A51V 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-PQ-A6FI       TCGA-PQ-A6FN       TCGA-R3-A69X       TCGA-S5-A6DX 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-S5-AA26       TCGA-SY-A9G0       TCGA-SY-A9G5       TCGA-UY-A78K 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-UY-A78L       TCGA-UY-A78M       TCGA-UY-A78N       TCGA-UY-A78O 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-UY-A8OB       TCGA-UY-A9PA       TCGA-UY-A9PB       TCGA-UY-A9PD 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-UY-A9PE       TCGA-UY-A9PF       TCGA-XF-A8HH       TCGA-XF-A8HI 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-XF-A9SH       TCGA-XF-A9SI       TCGA-XF-A9SJ       TCGA-XF-A9SL 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-XF-A9SV       TCGA-XF-A9SW       TCGA-XF-A9SX       TCGA-XF-A9SY 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-XF-A9SZ       TCGA-XF-A9T0       TCGA-XF-A9T2       TCGA-XF-A9T3 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-XF-A9T4       TCGA-XF-A9T5       TCGA-XF-A9T6       TCGA-XF-A9T8 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-XF-AAME       TCGA-XF-AAMF       TCGA-XF-AAMG       TCGA-XF-AAMH 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-XF-AAMJ       TCGA-XF-AAML       TCGA-XF-AAMQ       TCGA-XF-AAMR 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-XF-AAMT       TCGA-XF-AAMW       TCGA-XF-AAMX       TCGA-XF-AAMY 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-XF-AAMZ       TCGA-XF-AAN0       TCGA-XF-AAN2       TCGA-XF-AAN3 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-XF-AAN4       TCGA-XF-AAN5       TCGA-XF-AAN7       TCGA-XF-AAN8 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-YC-A8S6       TCGA-YC-A9TC       TCGA-ZF-A9R0       TCGA-ZF-A9R1 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-ZF-A9R2       TCGA-ZF-A9R3       TCGA-ZF-A9R4       TCGA-ZF-A9R5 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-ZF-A9R7       TCGA-ZF-A9R9       TCGA-ZF-A9RC       TCGA-ZF-A9RD 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-ZF-A9RE       TCGA-ZF-A9RF       TCGA-ZF-A9RG       TCGA-ZF-A9RL 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-ZF-A9RM       TCGA-ZF-A9RN       TCGA-ZF-AA4N       TCGA-ZF-AA4R 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-ZF-AA4T       TCGA-ZF-AA4U       TCGA-ZF-AA4V       TCGA-ZF-AA4W 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-ZF-AA4X       TCGA-ZF-AA51       TCGA-ZF-AA52       TCGA-ZF-AA53 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-ZF-AA54       TCGA-ZF-AA56       TCGA-ZF-AA58       TCGA-ZF-AA5H 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
      TCGA-ZF-AA5N       TCGA-ZF-AA5P 
"BCL2L1 WILD-TYPE" "BCL2L1 WILD-TYPE" 
D79V12, binary
                  cls
clus                 0   1
  BCL2L1 MUTATED     0   2
  BCL2L1 WILD-TYPE   8 336
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BCL2L1 MUTATED      0    2
  BCL2L1 WILD-TYPE    8  336
                        clus
vv                       BCL2L1 MUTATED BCL2L1 WILD-TYPE
  HISPANIC OR LATINO                  0                8
  NOT HISPANIC OR LATINO              2              336
[1] 2 2
[1] FALSE

Clustering(80) Variable = TRERF1 MUTATION ANALYSIS
D80V1, survival
                  sevent
clus2                0   1
  TRERF1 MUTATED    14   7
  TRERF1 WILD-TYPE 205 144
  TRERF1 MUTATED TRERF1 WILD-TYPE 
              21              349 
  TRERF1 MUTATED TRERF1 WILD-TYPE 
               7              144 
$`TRERF1 MUTATED`
TCGA-2F-A9KR TCGA-BL-A0C8 TCGA-BT-A20N TCGA-CF-A47X TCGA-DK-A2I1 TCGA-DK-A2I4 
      103.50        40.08        32.84        12.62        10.59       123.85 
TCGA-E5-A2PC TCGA-E7-A3Y1 TCGA-E7-A678 TCGA-FD-A3B5 TCGA-FD-A3SS TCGA-G2-A2EC 
       43.59         0.10        13.97         8.94        12.85        22.88 
TCGA-GV-A3QF TCGA-GV-A3QK TCGA-K4-A54R TCGA-MV-A51V TCGA-UY-A9PB TCGA-UY-A9PE 
       20.28        27.35        27.68        13.48        29.56         4.54 
TCGA-XF-AAMT TCGA-ZF-A9RG TCGA-ZF-AA52 
        2.96        52.60        35.41 

$`TRERF1 WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KT TCGA-2F-A9KW TCGA-4Z-AA7M 
       22.29        11.97        91.63       105.70         8.35        16.27 
TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7W 
       44.94        16.83        16.77        17.16        34.98        27.62 
TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA84 
       49.12         0.62        41.75        51.16        66.54        15.12 
TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM 
       10.22        47.80        33.83         7.33         2.66         6.74 
TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20P 
       12.39         6.58        13.15        19.04        12.16        17.88 
TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20W 
       19.50         5.06        14.89        14.96         5.06         8.35 
TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PJ 
        8.25        17.16        16.18        20.48         4.67        12.82 
TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ 
        9.96        17.56        28.70        24.26        28.41         8.98 
TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-C4-A0F6 TCGA-C4-A0F7 TCGA-CF-A1HR TCGA-CF-A1HS 
        1.94         2.93        23.01         2.04         0.46         0.43 
TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47Y 
        0.69        10.95        12.66        12.46        12.10        12.26 
TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A0YN 
       13.12        12.00        12.10        11.87        13.08        12.92 
TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 
        4.90         7.20         5.46         5.19        16.31         1.84 
TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA 
       13.58        21.86         2.14        66.41        18.41        19.00 
TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG 
       16.70       130.88       112.44        16.14        17.62        15.62 
TCGA-DK-A2HX TCGA-DK-A2I2 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM 
        1.81         7.79        87.32         2.20        13.58         7.82 
TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV 
        8.22        17.72        50.27        21.30        23.21         9.67 
TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV 
       20.81        10.55       140.81        48.00        17.98        64.18 
TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 
       41.56        76.60        67.36        15.68        41.06        30.67 
TCGA-DK-AA6L TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6U 
       38.24        15.02        13.58       166.03        12.36        10.49 
TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA76 TCGA-DK-AA77 
        8.65         7.53        13.64        43.50        12.03        10.62 
TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 
       15.35        38.83        24.66         0.49         2.24        16.70 
TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A6ME TCGA-E7-A6MF 
       17.39         0.56         0.66        14.56        12.99        14.33 
TCGA-E7-A7DU TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A97P 
        0.92         1.22        13.68        14.07        12.95        14.37 
TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 
        8.09        32.02        16.77        33.04         4.01        12.62 
TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM 
       22.52        27.98        60.66        24.30        23.41        17.98 
TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A43N 
       29.16         5.52        25.74        46.78        19.79        22.98 
TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS 
       27.35        14.96        20.91         3.62        26.73        53.88 
TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ 
       11.01        19.33         5.36         5.69         8.25        27.45 
TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S 
       18.08        58.92         2.70         7.10         6.28        13.35 
TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF 
       62.86        18.81         6.15        12.69        12.36         2.27 
TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 
        3.06         4.31         9.67        10.85        31.07         7.13 
TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FJ-A871 TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EF 
       10.65        17.23         8.94         3.25         6.48        61.94 
TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB 
       30.61        15.95        26.93        35.24        33.01         7.23 
TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3D TCGA-G2-AA3F 
       20.12        17.62        66.02         6.94        64.44        19.46 
TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD 
       21.40         2.24        15.81         4.50        15.91        14.07 
TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP 
       17.75        24.92         8.94        13.91         7.73         2.10 
TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42Q 
        3.12        20.98         2.20         7.36        10.92        11.31 
TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 
       11.31         7.63        27.09        20.05         5.62         4.73 
TCGA-GU-AATO TCGA-GU-AATP TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX 
       10.65        32.98         7.00        14.27        21.34        19.10 
TCGA-GV-A3JZ TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA 
       19.82         8.48        10.59         8.58        19.07        22.72 
TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE 
        1.51        19.40        38.60         3.06         9.01         8.22 
TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A5RH 
       25.02         3.45        21.24         2.76         9.14         9.07 
TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO 
       11.70         1.74         1.81        15.42         6.38        11.80 
TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX 
       15.32        15.58        12.23        16.67        14.24         1.84 
TCGA-S5-AA26 TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M 
        3.75        12.43        31.56        17.62        37.05        22.68 
TCGA-UY-A78N TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A9PA TCGA-UY-A9PD TCGA-UY-A9PF 
       86.83        76.01        65.75        35.24        17.82         1.64 
TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SJ 
        1.87        17.88        48.62        64.80        79.66         3.22 
TCGA-XF-A9SL TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ 
       66.41        12.76        11.90        23.64        21.04        28.24 
TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 
       26.27        18.90         2.24        16.27        66.64         2.10 
TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMG TCGA-XF-AAMH TCGA-XF-AAMJ 
       13.74        92.98        10.82       110.60        11.31        54.90 
TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAMY 
        7.63        71.57        91.73         8.32         6.77        98.99 
TCGA-XF-AAMZ TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN4 
       44.32        56.48        30.94        61.45        86.30        27.06 
TCGA-XF-AAN5 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L 
       75.39        18.81         3.88         9.63         0.66        11.97 
TCGA-YF-AA3M TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R4 
       13.64        18.64         7.36        21.11        24.13        30.28 
TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RE 
       27.19        21.86        28.41        74.56        13.41         3.48 
TCGA-ZF-A9RF TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4R 
       52.73        82.49        47.84        20.22         2.89        34.06 
TCGA-ZF-AA4T TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA51 
       19.69         8.61        59.38        60.16        63.02        38.73 
TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N 
       57.90        19.40         8.52        47.15        19.17         5.52 
TCGA-ZF-AA5P 
       10.13 

  TRERF1 MUTATED TRERF1 WILD-TYPE 
            0.10             0.43 
  TRERF1 MUTATED TRERF1 WILD-TYPE 
          123.85           166.03 
  TRERF1 MUTATED TRERF1 WILD-TYPE 
           22.88            15.58 
[1] "0.1 - 123.8 (22.9)" "0.4 - 166.0 (15.6)"
[1] "hr=" "1.5"
D80V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  TRERF1 MUTATED         1        5         8        7
  TRERF1 WILD-TYPE       3      112       114      121
D80V3, multiclass
           clus
vv          TRERF1 MUTATED TRERF1 WILD-TYPE
  STAGE I                1                3
  STAGE II               5              112
  STAGE III              8              114
  STAGE IV               7              121
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1+T2  T3  T4
  TRERF1 MUTATED          7  10   2
  TRERF1 WILD-TYPE      107 169  50
D80V4, multiclass
          clus
vv         TRERF1 MUTATED TRERF1 WILD-TYPE
  T0+T1+T2              7              107
  T3                   10              169
  T4                    2               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"
                  vv
clus                N0  N1  N2  N3
  TRERF1 MUTATED    12   2   4   1
  TRERF1 WILD-TYPE 201  39  71   7
D80V5, multiclass
    clus
vv   TRERF1 MUTATED TRERF1 WILD-TYPE
  N0             12              201
  N1              2               39
  N2              4               71
  N3              1                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"
D80V6, binary
                  cls
clus                 0   1
  TRERF1 MUTATED    10   0
  TRERF1 WILD-TYPE 172  10
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRERF1 MUTATED     10    0
  TRERF1 WILD-TYPE  172   10
   clus
vv  TRERF1 MUTATED TRERF1 WILD-TYPE
  0             10              172
  1              0               10
[1] 2 2
[1] FALSE
D80V7, binary
                  cls
clus                 0   1
  TRERF1 MUTATED     7  14
  TRERF1 WILD-TYPE  89 266
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRERF1 MUTATED      7   14
  TRERF1 WILD-TYPE   89  266
        clus
vv       TRERF1 MUTATED TRERF1 WILD-TYPE
  FEMALE              7               89
  MALE               14              266
[1] 2 2
[1] FALSE
D80V8, continuous
D80V9, continuous
D80V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TRERF1 MUTATED       2                         2    15
  TRERF1 WILD-TYPE    36                        19   286
D80V11, multiclass
                           clus
vv                          TRERF1 MUTATED TRERF1 WILD-TYPE
  ASIAN                                  2               36
  BLACK OR AFRICAN AMERICAN              2               19
  WHITE                                 15              286
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D80V12, binary
                  cls
clus                 0   1
  TRERF1 MUTATED     0  19
  TRERF1 WILD-TYPE   8 319
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRERF1 MUTATED      0   19
  TRERF1 WILD-TYPE    8  319
                        clus
vv                       TRERF1 MUTATED TRERF1 WILD-TYPE
  HISPANIC OR LATINO                  0                8
  NOT HISPANIC OR LATINO             19              319
[1] 2 2
[1] FALSE

Clustering(81) Variable = CHD2 MUTATION ANALYSIS
D81V1, survival
                sevent
clus2              0   1
  CHD2 MUTATED    19   6
  CHD2 WILD-TYPE 200 145
  CHD2 MUTATED CHD2 WILD-TYPE 
            25            345 
  CHD2 MUTATED CHD2 WILD-TYPE 
             6            145 
$`CHD2 MUTATED`
TCGA-2F-A9KT TCGA-4Z-AA86 TCGA-BT-A3PK TCGA-CU-A3QU TCGA-DK-A1A3 TCGA-DK-A1AE 
      105.70        10.22         9.96         5.19        21.86        16.14 
TCGA-DK-A2HX TCGA-DK-A2I4 TCGA-DK-A3IT TCGA-DK-A3WW TCGA-E5-A4U1 TCGA-E7-A7PW 
        1.81       123.85        21.30        20.81        38.83        13.68 
TCGA-FD-A3SJ TCGA-FD-A62N TCGA-G2-A3VY TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GU-A42Q 
       24.30         2.70        17.62        13.91         7.73        11.31 
TCGA-GV-A6ZA TCGA-K4-A6FZ TCGA-XF-A9SI TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-ZF-AA4V 
       22.72         1.81        79.66         2.10        13.74        59.38 
TCGA-ZF-AA51 
       38.73 

$`CHD2 WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KW TCGA-4Z-AA7M 
       22.29        11.97        91.63       103.50         8.35        16.27 
TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7W 
       44.94        16.83        16.77        17.16        34.98        27.62 
TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA84 
       49.12         0.62        41.75        51.16        66.54        15.12 
TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM 
       47.80        33.83        40.08         7.33         2.66         6.74 
TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O 
       12.39         6.58        13.15        19.04        32.84        12.16 
TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20V 
       17.88        19.50         5.06        14.89        14.96         5.06 
TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH 
        8.35         8.25        17.16        16.18        20.48         4.67 
TCGA-BT-A3PJ TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ 
       12.82        17.56        28.70        24.26        28.41         8.98 
TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-C4-A0F6 TCGA-C4-A0F7 TCGA-CF-A1HR TCGA-CF-A1HS 
        1.94         2.93        23.01         2.04         0.46         0.43 
TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X 
        0.69        10.95        12.66        12.46        12.10        12.62 
TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A9FF TCGA-CF-A9FM 
       12.26        13.12        12.00        12.10        11.87        13.08 
TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3YL TCGA-CU-A5W6 
       12.92         4.90         7.20         5.46        16.31         1.84 
TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB 
       13.58         2.14        66.41        18.41        19.00        16.70 
TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I1 TCGA-DK-A2I2 
      130.88       112.44        17.62        15.62        10.59         7.79 
TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ 
       87.32         2.20        13.58         7.82         8.22        17.72 
TCGA-DK-A3IS TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 
       50.27        23.21         9.67        10.55       140.81        48.00 
TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 
       17.98        64.18        41.56        76.60        67.36        15.68 
TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6S 
       41.06        30.67        38.24        15.02        13.58       166.03 
TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA74 
       12.36        10.49         8.65         7.53        13.64        43.50 
TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E7-A3X6 TCGA-E7-A3Y1 
       12.03        10.62        43.59        15.35        24.66         0.10 
TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF 
        0.49         2.24        16.70        17.39         0.56         0.66 
TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7DV 
       14.56        13.97        12.99        14.33         0.92         1.22 
TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 
       14.07        12.95        14.37         8.09        32.02        16.77 
TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 
        8.94        33.04         4.01        12.62        22.52        27.98 
TCGA-FD-A3NA TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP 
       60.66        23.41        17.98        29.16         5.52        25.74 
TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S 
       46.78        19.79        12.85        22.98        27.35        14.96 
TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU 
       20.91         3.62        26.73        53.88        11.01        19.33 
TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 
        5.36         5.69         8.25        27.45        18.08        58.92 
TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC 
        7.10         6.28        13.35        62.86        18.81         6.15 
TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI 
       12.69        12.36         2.27         3.06         4.31         9.67 
TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FJ-A871 
       10.85        31.07         7.13        10.65        17.23         8.94 
TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EC TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK 
        3.25         6.48        22.88        61.94        30.61        15.95 
TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3B 
       26.93        35.24        33.01         7.23        20.12        66.02 
TCGA-G2-AA3C TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO 
        6.94        64.44        19.46        21.40         2.24        15.81 
TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A6I1 
        4.50        15.91        14.07        17.75        24.92         8.94 
TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42P 
        2.10         3.12        20.98         2.20         7.36        10.92 
TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 
       11.31         7.63        27.09        20.05         5.62         4.73 
TCGA-GU-AATO TCGA-GU-AATP TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX 
       10.65        32.98         7.00        14.27        21.34        19.10 
TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E 
       19.82        20.28         8.48        10.59        27.35         8.58 
TCGA-GV-A40G TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND 
       19.07         1.51        19.40        38.60         3.06         9.01 
TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC 
        8.22        25.02         3.45        21.24         2.76         9.14 
TCGA-K4-A54R TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6MB TCGA-K4-A83P 
       27.68         9.07        11.70         1.74        15.42         6.38 
TCGA-K4-AAQO TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN 
       11.80        15.32        15.58        13.48        12.23        16.67 
TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78K 
       14.24         1.84         3.75        12.43        31.56        17.62 
TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78N TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A9PA 
       37.05        22.68        86.83        76.01        65.75        35.24 
TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HH TCGA-XF-A8HI 
       29.56        17.82         4.54         1.64         1.87        17.88 
TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SJ TCGA-XF-A9SL TCGA-XF-A9SV TCGA-XF-A9SW 
       48.62        64.80         3.22        66.41        12.76        11.90 
TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 
       23.64        21.04        28.24        26.27        18.90         2.24 
TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMG TCGA-XF-AAMH 
       16.27        66.64        92.98        10.82       110.60        11.31 
TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMW 
       54.90         7.63        71.57        91.73         2.96         8.32 
TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN2 
        6.77        98.99        44.32        56.48        30.94        61.45 
TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 
       86.30        27.06        75.39        18.81         3.88         9.63 
TCGA-YC-A9TC TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R2 
        0.66        11.97        13.64        18.64         7.36        21.11 
TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RC 
       24.13        30.28        27.19        21.86        28.41        74.56 
TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-A9RM 
       13.41         3.48        52.73        52.60        82.49        47.84 
TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4U TCGA-ZF-AA4W 
       20.22         2.89        34.06        19.69         8.61        60.16 
TCGA-ZF-AA4X TCGA-ZF-AA52 TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 
       63.02        35.41        57.90        19.40         8.52        47.15 
TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-ZF-AA5P 
       19.17         5.52        10.13 

  CHD2 MUTATED CHD2 WILD-TYPE 
          1.81           0.10 
  CHD2 MUTATED CHD2 WILD-TYPE 
        123.85         166.03 
  CHD2 MUTATED CHD2 WILD-TYPE 
         16.14          15.62 
[1] "1.8 - 123.8 (16.1)" "0.1 - 166.0 (15.6)"
[1] "hr=" "1.9"
D81V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  CHD2 MUTATED         0        7        11        7
  CHD2 WILD-TYPE       4      110       111      121
D81V3, multiclass
           clus
vv          CHD2 MUTATED CHD2 WILD-TYPE
  STAGE I              0              4
  STAGE II             7            110
  STAGE III           11            111
  STAGE IV             7            121
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1+T2  T3  T4
  CHD2 MUTATED          8  16   0
  CHD2 WILD-TYPE      106 163  52
D81V4, multiclass
          clus
vv         CHD2 MUTATED CHD2 WILD-TYPE
  T0+T1+T2            8            106
  T3                 16            163
  T4                  0             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"
                vv
clus              N0  N1  N2  N3
  CHD2 MUTATED    15   3   4   0
  CHD2 WILD-TYPE 198  38  71   8
D81V5, multiclass
    clus
vv   CHD2 MUTATED CHD2 WILD-TYPE
  N0           15            198
  N1            3             38
  N2            4             71
  N3            0              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"
D81V6, binary
                cls
clus               0   1
  CHD2 MUTATED    14   0
  CHD2 WILD-TYPE 168  10
[1] "tbl2"
                cls
clus             [,1] [,2]
  CHD2 MUTATED     14    0
  CHD2 WILD-TYPE  168   10
   clus
vv  CHD2 MUTATED CHD2 WILD-TYPE
  0           14            168
  1            0             10
[1] 2 2
[1] FALSE
D81V7, binary
                cls
clus               0   1
  CHD2 MUTATED     7  18
  CHD2 WILD-TYPE  89 262
[1] "tbl2"
                cls
clus             [,1] [,2]
  CHD2 MUTATED      7   18
  CHD2 WILD-TYPE   89  262
        clus
vv       CHD2 MUTATED CHD2 WILD-TYPE
  FEMALE            7             89
  MALE             18            262
[1] 2 2
[1] FALSE
D81V8, continuous
D81V9, continuous
D81V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CHD2 MUTATED       4                         2    18
  CHD2 WILD-TYPE    34                        19   283
D81V11, multiclass
                           clus
vv                          CHD2 MUTATED CHD2 WILD-TYPE
  ASIAN                                4             34
  BLACK OR AFRICAN AMERICAN            2             19
  WHITE                               18            283
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D81V12, binary
                cls
clus               0   1
  CHD2 MUTATED     0  24
  CHD2 WILD-TYPE   8 314
[1] "tbl2"
                cls
clus             [,1] [,2]
  CHD2 MUTATED      0   24
  CHD2 WILD-TYPE    8  314
                        clus
vv                       CHD2 MUTATED CHD2 WILD-TYPE
  HISPANIC OR LATINO                0              8
  NOT HISPANIC OR LATINO           24            314
[1] 2 2
[1] FALSE

Clustering(82) Variable = USP28 MUTATION ANALYSIS
D82V1, survival
                 sevent
clus2               0   1
  USP28 MUTATED     9   4
  USP28 WILD-TYPE 210 147
  USP28 MUTATED USP28 WILD-TYPE 
             13             357 
  USP28 MUTATED USP28 WILD-TYPE 
              4             147 
$`USP28 MUTATED`
TCGA-2F-A9KO TCGA-4Z-AA7O TCGA-BT-A0YX TCGA-DK-AA71 TCGA-DK-AA74 TCGA-FD-A6TF 
       22.29        16.83        13.15        13.64        43.50         2.27 
TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QI TCGA-SY-A9G5 TCGA-UY-A78M TCGA-XF-AAN2 
       19.10        19.82        10.59        31.56        22.68        61.45 
TCGA-ZF-A9R4 
       30.28 

$`USP28 WILD-TYPE`
TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW TCGA-4Z-AA7M 
       11.97        91.63       103.50       105.70         8.35        16.27 
TCGA-4Z-AA7N TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7W TCGA-4Z-AA7Y 
       44.94        16.77        17.16        34.98        27.62        49.12 
TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA84 TCGA-4Z-AA86 
        0.62        41.75        51.16        66.54        15.12        10.22 
TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM 
       47.80        33.83        40.08         7.33         2.66         6.74 
TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P 
       12.39         6.58        19.04        32.84        12.16        17.88 
TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20W 
       19.50         5.06        14.89        14.96         5.06         8.35 
TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PJ 
        8.25        17.16        16.18        20.48         4.67        12.82 
TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ 
        9.96        17.56        28.70        24.26        28.41         8.98 
TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-C4-A0F6 TCGA-C4-A0F7 TCGA-CF-A1HR TCGA-CF-A1HS 
        1.94         2.93        23.01         2.04         0.46         0.43 
TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X 
        0.69        10.95        12.66        12.46        12.10        12.62 
TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A9FF TCGA-CF-A9FM 
       12.26        13.12        12.00        12.10        11.87        13.08 
TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL 
       12.92         4.90         7.20         5.46         5.19        16.31 
TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 
        1.84        13.58        21.86         2.14        66.41        18.41 
TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF 
       19.00        16.70       130.88       112.44        16.14        17.62 
TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A2I6 
       15.62         1.81        10.59         7.79       123.85        87.32 
TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS 
        2.20        13.58         7.82         8.22        17.72        50.27 
TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY 
       21.30        23.21         9.67        20.81        10.55       140.81 
TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 
       48.00        17.98        64.18        41.56        76.60        67.36 
TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6P TCGA-DK-AA6Q 
       15.68        41.06        30.67        38.24        15.02        13.58 
TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA76 
      166.03        12.36        10.49         8.65         7.53        12.03 
TCGA-DK-AA77 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 
       10.62        43.59        15.35        38.83        24.66         0.10 
TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF 
        0.49         2.24        16.70        17.39         0.56         0.66 
TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7DV 
       14.56        13.97        12.99        14.33         0.92         1.22 
TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B3 
       13.68        14.07        12.95        14.37         8.09        32.02 
TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 
       16.77         8.94        33.04         4.01        12.62        22.52 
TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN 
       27.98        60.66        24.30        23.41        17.98        29.16 
TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N 
        5.52        25.74        46.78        19.79        12.85        22.98 
TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS 
       27.35        14.96        20.91         3.62        26.73        53.88 
TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ 
       11.01        19.33         5.36         5.69         8.25        27.45 
TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S 
       18.08        58.92         2.70         7.10         6.28        13.35 
TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TG 
       62.86        18.81         6.15        12.69        12.36         3.06 
TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE 
        4.31         9.67        10.85        31.07         7.13        10.65 
TCGA-FJ-A3ZF TCGA-FJ-A871 TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EC TCGA-G2-A2EF 
       17.23         8.94         3.25         6.48        22.88        61.94 
TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB 
       30.61        15.95        26.93        35.24        33.01         7.23 
TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3D TCGA-G2-AA3F 
       20.12        17.62        66.02         6.94        64.44        19.46 
TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD 
       21.40         2.24        15.81         4.50        15.91        14.07 
TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP 
       17.75        24.92         8.94        13.91         7.73         2.10 
TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42Q 
        3.12        20.98         2.20         7.36        10.92        11.31 
TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 
       11.31         7.63        27.09        20.05         5.62         4.73 
TCGA-GU-AATO TCGA-GU-AATP TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3QF 
       10.65        32.98         7.00        14.27        21.34        20.28 
TCGA-GV-A3QH TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO 
        8.48        27.35         8.58        19.07        22.72         1.51 
TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS 
       19.40        38.60         3.06         9.01         8.22        25.02 
TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RH 
        3.45        21.24         2.76         9.14        27.68         9.07 
TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO 
       11.70         1.74         1.81        15.42         6.38        11.80 
TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X 
       15.32        15.58        13.48        12.23        16.67        14.24 
TCGA-S5-A6DX TCGA-S5-AA26 TCGA-SY-A9G0 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78N 
        1.84         3.75        12.43        17.62        37.05        86.83 
TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE 
       76.01        65.75        35.24        29.56        17.82         4.54 
TCGA-UY-A9PF TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI 
        1.64         1.87        17.88        48.62        64.80        79.66 
TCGA-XF-A9SJ TCGA-XF-A9SL TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY 
        3.22        66.41        12.76        11.90        23.64        21.04 
TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T5 
       28.24        26.27        18.90         2.24        16.27        66.64 
TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMG TCGA-XF-AAMH 
        2.10        13.74        92.98        10.82       110.60        11.31 
TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMW 
       54.90         7.63        71.57        91.73         2.96         8.32 
TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN3 
        6.77        98.99        44.32        56.48        30.94        86.30 
TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YC-A9TC 
       27.06        75.39        18.81         3.88         9.63         0.66 
TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R3 
       11.97        13.64        18.64         7.36        21.11        24.13 
TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RE 
       27.19        21.86        28.41        74.56        13.41         3.48 
TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N 
       52.73        52.60        82.49        47.84        20.22         2.89 
TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA4X 
       34.06        19.69         8.61        59.38        60.16        63.02 
TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 
       38.73        35.41        57.90        19.40         8.52        47.15 
TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-ZF-AA5P 
       19.17         5.52        10.13 

  USP28 MUTATED USP28 WILD-TYPE 
           2.27            0.10 
  USP28 MUTATED USP28 WILD-TYPE 
          61.45          166.03 
  USP28 MUTATED USP28 WILD-TYPE 
          19.82           15.42 
[1] "2.3 - 61.5 (19.8)"  "0.1 - 166.0 (15.4)"
[1] "hr=" "1.5"
D82V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  USP28 MUTATED         0        4         5        4
  USP28 WILD-TYPE       4      113       117      124
D82V3, multiclass
           clus
vv          USP28 MUTATED USP28 WILD-TYPE
  STAGE I               0               4
  STAGE II              4             113
  STAGE III             5             117
  STAGE IV              4             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"
                 vv
clus              T0+T1+T2  T3  T4
  USP28 MUTATED          5   6   2
  USP28 WILD-TYPE      109 173  50
D82V4, multiclass
          clus
vv         USP28 MUTATED USP28 WILD-TYPE
  T0+T1+T2             5             109
  T3                   6             173
  T4                   2              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"
                 vv
clus               N0  N1  N2  N3
  USP28 MUTATED     8   1   2   1
  USP28 WILD-TYPE 205  40  73   7
D82V5, multiclass
    clus
vv   USP28 MUTATED USP28 WILD-TYPE
  N0             8             205
  N1             1              40
  N2             2              73
  N3             1               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"
D82V6, binary
                 cls
clus                0   1
  USP28 MUTATED     7   1
  USP28 WILD-TYPE 175   9
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP28 MUTATED      7    1
  USP28 WILD-TYPE  175    9
   clus
vv  USP28 MUTATED USP28 WILD-TYPE
  0             7             175
  1             1               9
[1] 2 2
[1] FALSE
D82V7, binary
                 cls
clus                0   1
  USP28 MUTATED     3  10
  USP28 WILD-TYPE  93 270
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP28 MUTATED      3   10
  USP28 WILD-TYPE   93  270
        clus
vv       USP28 MUTATED USP28 WILD-TYPE
  FEMALE             3              93
  MALE              10             270
[1] 2 2
[1] FALSE
D82V8, continuous
D82V9, continuous
D82V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  USP28 MUTATED       1                         1    11
  USP28 WILD-TYPE    37                        20   290
D82V11, multiclass
                           clus
vv                          USP28 MUTATED USP28 WILD-TYPE
  ASIAN                                 1              37
  BLACK OR AFRICAN AMERICAN             1              20
  WHITE                                11             290
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D82V12, binary
                 cls
clus                0   1
  USP28 MUTATED     0  12
  USP28 WILD-TYPE   8 326
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP28 MUTATED      0   12
  USP28 WILD-TYPE    8  326
                        clus
vv                       USP28 MUTATED USP28 WILD-TYPE
  HISPANIC OR LATINO                 0               8
  NOT HISPANIC OR LATINO            12             326
[1] 2 2
[1] FALSE

Clustering(83) Variable = GPS2 MUTATION ANALYSIS
D83V1, survival
                sevent
clus2              0   1
  GPS2 MUTATED     7   3
  GPS2 WILD-TYPE 212 148
  GPS2 MUTATED GPS2 WILD-TYPE 
            10            360 
  GPS2 MUTATED GPS2 WILD-TYPE 
             3            148 
$`GPS2 MUTATED`
TCGA-BT-A20T TCGA-BT-A42C TCGA-CF-A27C TCGA-DK-A1A3 TCGA-DK-A6B1 TCGA-DK-AA6S 
       14.89        28.70         0.69        21.86        67.36       166.03 
TCGA-FD-A62O TCGA-GU-AATP TCGA-XF-A9T5 TCGA-ZF-AA58 
        7.10        32.98        66.64        47.15 

$`GPS2 WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        91.63       103.50       105.70         8.35 
TCGA-4Z-AA7M TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7S 
       16.27        44.94        16.83        16.77        17.16        34.98 
TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 
       27.62        49.12         0.62        41.75        51.16        66.54 
TCGA-4Z-AA84 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BL-A13I 
       15.12        10.22        47.80        33.83        40.08         7.33 
TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J 
        2.66         6.74        12.39         6.58        13.15        19.04 
TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20U 
       32.84        12.16        17.88        19.50         5.06        14.96 
TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A2LD 
        5.06         8.35         8.25        17.16        16.18        20.48 
TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42E TCGA-BT-A42F 
        4.67        12.82         9.96        17.56        24.26        28.41 
TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-C4-A0F6 TCGA-C4-A0F7 TCGA-CF-A1HR 
        8.98         1.94         2.93        23.01         2.04         0.46 
TCGA-CF-A1HS TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X 
        0.43        10.95        12.66        12.46        12.10        12.62 
TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A9FF TCGA-CF-A9FM 
       12.26        13.12        12.00        12.10        11.87        13.08 
TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL 
       12.92         4.90         7.20         5.46         5.19        16.31 
TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA 
        1.84        13.58         2.14        66.41        18.41        19.00 
TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG 
       16.70       130.88       112.44        16.14        17.62        15.62 
TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK 
        1.81        10.59         7.79       123.85        87.32         2.20 
TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT 
       13.58         7.82         8.22        17.72        50.27        21.30 
TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 
       23.21         9.67        20.81        10.55       140.81        48.00 
TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B2 TCGA-DK-A6B5 
       17.98        64.18        41.56        76.60        15.68        41.06 
TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-DK-AA6U 
       30.67        38.24        15.02        13.58        12.36        10.49 
TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA76 TCGA-DK-AA77 
        8.65         7.53        13.64        43.50        12.03        10.62 
TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ 
       43.59        15.35        38.83        24.66         0.10         0.49 
TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 
        2.24        16.70        17.39         0.56         0.66        14.56 
TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7DV TCGA-E7-A7PW 
       13.97        12.99        14.33         0.92         1.22        13.68 
TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 
       14.07        12.95        14.37         8.09        32.02        16.77 
TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 
        8.94        33.04         4.01        12.62        22.52        27.98 
TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO 
       60.66        24.30        23.41        17.98        29.16         5.52 
TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P 
       25.74        46.78        19.79        12.85        22.98        27.35 
TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT 
       14.96        20.91         3.62        26.73        53.88        11.01 
TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 
       19.33         5.36         5.69         8.25        27.45        18.08 
TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB 
       58.92         2.70         6.28        13.35        62.86        18.81 
TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH 
        6.15        12.69        12.36         2.27         3.06         4.31 
TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF 
        9.67        10.85        31.07         7.13        10.65        17.23 
TCGA-FJ-A871 TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EC TCGA-G2-A2EF TCGA-G2-A2EJ 
        8.94         3.25         6.48        22.88        61.94        30.61 
TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE 
       15.95        26.93        35.24        33.01         7.23        20.12 
TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3BM 
       17.62        66.02         6.94        64.44        19.46        21.40 
TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC 
        2.24        15.81         4.50        15.91        14.07        17.75 
TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ 
       24.92         8.94        13.91         7.73         2.10         3.12 
TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R 
       20.98         2.20         7.36        10.92        11.31        11.31 
TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATO 
        7.63        27.09        20.05         5.62         4.73        10.65 
TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF 
        7.00        14.27        21.34        19.10        19.82        20.28 
TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA 
        8.48        10.59        27.35         8.58        19.07        22.72 
TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE 
        1.51        19.40        38.60         3.06         9.01         8.22 
TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R 
       25.02         3.45        21.24         2.76         9.14        27.68 
TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P 
        9.07        11.70         1.74         1.81        15.42         6.38 
TCGA-K4-AAQO TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN 
       11.80        15.32        15.58        13.48        12.23        16.67 
TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78K 
       14.24         1.84         3.75        12.43        31.56        17.62 
TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78N TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A9PA 
       37.05        22.68        86.83        76.01        65.75        35.24 
TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HH TCGA-XF-A8HI 
       29.56        17.82         4.54         1.64         1.87        17.88 
TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SL TCGA-XF-A9SV 
       48.62        64.80        79.66         3.22        66.41        12.76 
TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 
       11.90        23.64        21.04        28.24        26.27        18.90 
TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMF 
        2.24        16.27         2.10        13.74        92.98        10.82 
TCGA-XF-AAMG TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR 
      110.60        11.31        54.90         7.63        71.57        91.73 
TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN0 
        2.96         8.32         6.77        98.99        44.32        56.48 
TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN7 
       30.94        61.45        86.30        27.06        75.39        18.81 
TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R0 
        3.88         9.63         0.66        11.97        13.64        18.64 
TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R7 
        7.36        21.11        24.13        30.28        27.19        21.86 
TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RG 
       28.41        74.56        13.41         3.48        52.73        52.60 
TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4R TCGA-ZF-AA4T 
       82.49        47.84        20.22         2.89        34.06        19.69 
TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 
        8.61        59.38        60.16        63.02        38.73        35.41 
TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-ZF-AA5P 
       57.90        19.40         8.52        19.17         5.52        10.13 

  GPS2 MUTATED GPS2 WILD-TYPE 
          0.69           0.10 
  GPS2 MUTATED GPS2 WILD-TYPE 
        166.03         140.81 
  GPS2 MUTATED GPS2 WILD-TYPE 
         30.84          15.50 
[1] "0.7 - 166.0 (30.8)" "0.1 - 140.8 (15.5)"
[1] "hr=" "2.1"
D83V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  GPS2 MUTATED         0        2         1        6
  GPS2 WILD-TYPE       4      115       121      122
D83V3, multiclass
           clus
vv          GPS2 MUTATED GPS2 WILD-TYPE
  STAGE I              0              4
  STAGE II             2            115
  STAGE III            1            121
  STAGE IV             6            122
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1+T2  T3  T4
  GPS2 MUTATED          2   7   0
  GPS2 WILD-TYPE      112 172  52
D83V4, multiclass
          clus
vv         GPS2 MUTATED GPS2 WILD-TYPE
  T0+T1+T2            2            112
  T3                  7            172
  T4                  0             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"
                vv
clus              N0  N1  N2  N3
  GPS2 MUTATED     4   2   4   0
  GPS2 WILD-TYPE 209  39  71   8
D83V5, multiclass
    clus
vv   GPS2 MUTATED GPS2 WILD-TYPE
  N0            4            209
  N1            2             39
  N2            4             71
  N3            0              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"
D83V6, binary
                cls
clus               0   1
  GPS2 MUTATED     6   0
  GPS2 WILD-TYPE 176  10
[1] "tbl2"
                cls
clus             [,1] [,2]
  GPS2 MUTATED      6    0
  GPS2 WILD-TYPE  176   10
   clus
vv  GPS2 MUTATED GPS2 WILD-TYPE
  0            6            176
  1            0             10
[1] 2 2
[1] FALSE
D83V7, binary
                cls
clus               0   1
  GPS2 MUTATED     2   8
  GPS2 WILD-TYPE  94 272
[1] "tbl2"
                cls
clus             [,1] [,2]
  GPS2 MUTATED      2    8
  GPS2 WILD-TYPE   94  272
        clus
vv       GPS2 MUTATED GPS2 WILD-TYPE
  FEMALE            2             94
  MALE              8            272
[1] 2 2
[1] FALSE
D83V8, continuous
D83V9, continuous
D83V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  GPS2 MUTATED       1                         0     9
  GPS2 WILD-TYPE    37                        21   292
D83V11, multiclass
                           clus
vv                          GPS2 MUTATED GPS2 WILD-TYPE
  ASIAN                                1             37
  BLACK OR AFRICAN AMERICAN            0             21
  WHITE                                9            292
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D83V12, binary
                cls
clus               0   1
  GPS2 MUTATED     0  10
  GPS2 WILD-TYPE   8 328
[1] "tbl2"
                cls
clus             [,1] [,2]
  GPS2 MUTATED      0   10
  GPS2 WILD-TYPE    8  328
                        clus
vv                       GPS2 MUTATED GPS2 WILD-TYPE
  HISPANIC OR LATINO                0              8
  NOT HISPANIC OR LATINO           10            328
[1] 2 2
[1] FALSE

Clustering(84) Variable = F7 MUTATION ANALYSIS
D84V1, survival
              sevent
clus2            0   1
  F7 MUTATED     4   3
  F7 WILD-TYPE 215 148
  F7 MUTATED F7 WILD-TYPE 
           7          363 
  F7 MUTATED F7 WILD-TYPE 
           3          148 
$`F7 MUTATED`
TCGA-BL-A5ZZ TCGA-DK-A3X2 TCGA-E7-A7XN TCGA-MV-A51V TCGA-XF-AAML TCGA-XF-AAMQ 
       12.39        17.98        14.07        13.48         7.63        71.57 
TCGA-XF-AAN7 
       18.81 

$`F7 WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        91.63       103.50       105.70         8.35 
TCGA-4Z-AA7M TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7S 
       16.27        44.94        16.83        16.77        17.16        34.98 
TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 
       27.62        49.12         0.62        41.75        51.16        66.54 
TCGA-4Z-AA84 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BL-A13I 
       15.12        10.22        47.80        33.83        40.08         7.33 
TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N 
        2.66         6.74         6.58        13.15        19.04        32.84 
TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U 
       12.16        17.88        19.50         5.06        14.89        14.96 
TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A2LD 
        5.06         8.35         8.25        17.16        16.18        20.48 
TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E 
        4.67        12.82         9.96        17.56        28.70        24.26 
TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-C4-A0F6 TCGA-C4-A0F7 
       28.41         8.98         1.94         2.93        23.01         2.04 
TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V 
        0.46         0.43         0.69        10.95        12.66        12.46 
TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 
       12.10        12.62        12.26        13.12        12.00        12.10 
TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ 
       11.87        13.08        12.92         4.90         7.20         5.46 
TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 
        5.19        16.31         1.84        13.58        21.86         2.14 
TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD 
       66.41        18.41        19.00        16.70       130.88       112.44 
TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 
       16.14        17.62        15.62         1.81        10.59         7.79 
TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN 
      123.85        87.32         2.20        13.58         7.82         8.22 
TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW 
       17.72        50.27        21.30        23.21         9.67        20.81 
TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 
       10.55       140.81        48.00        64.18        41.56        76.60 
TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6P 
       67.36        15.68        41.06        30.67        38.24        15.02 
TCGA-DK-AA6Q TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA6X 
       13.58       166.03        12.36        10.49         8.65         7.53 
TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A2PC TCGA-E5-A4TZ 
       13.64        43.50        12.03        10.62        43.59        15.35 
TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 
       38.83        24.66         0.10         0.49         2.24        16.70 
TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME 
       17.39         0.56         0.66        14.56        13.97        12.99 
TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A85H TCGA-E7-A97P 
       14.33         0.92         1.22        13.68        12.95        14.37 
TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 
        8.09        32.02        16.77         8.94        33.04         4.01 
TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL 
       12.62        22.52        27.98        60.66        24.30        23.41 
TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR 
       17.98        29.16         5.52        25.74        46.78        19.79 
TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X 
       12.85        22.98        27.35        14.96        20.91         3.62 
TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX 
       26.73        53.88        11.01        19.33         5.36         5.69 
TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O 
        8.25        27.45        18.08        58.92         2.70         7.10 
TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD 
        6.28        13.35        62.86        18.81         6.15        12.69 
TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FD-A6TK 
       12.36         2.27         3.06         4.31         9.67        10.85 
TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FJ-A871 TCGA-FT-A3EE 
       31.07         7.13        10.65        17.23         8.94         3.25 
TCGA-FT-A61P TCGA-G2-A2EC TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL 
        6.48        22.88        61.94        30.61        15.95        26.93 
TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B 
       35.24        33.01         7.23        20.12        17.62        66.02 
TCGA-G2-AA3C TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO 
        6.94        64.44        19.46        21.40         2.24        15.81 
TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A6I1 
        4.50        15.91        14.07        17.75        24.92         8.94 
TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 
       13.91         7.73         2.10         3.12        20.98         2.20 
TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 
        7.36        10.92        11.31        11.31         7.63        27.09 
TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATO TCGA-GU-AATP TCGA-GU-AATQ 
       20.05         5.62         4.73        10.65        32.98         7.00 
TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH 
       14.27        21.34        19.10        19.82        20.28         8.48 
TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO 
       10.59        27.35         8.58        19.07        22.72         1.51 
TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS 
       19.40        38.60         3.06         9.01         8.22        25.02 
TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RH 
        3.45        21.24         2.76         9.14        27.68         9.07 
TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO 
       11.70         1.74         1.81        15.42         6.38        11.80 
TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX 
       15.32        15.58        12.23        16.67        14.24         1.84 
TCGA-S5-AA26 TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M 
        3.75        12.43        31.56        17.62        37.05        22.68 
TCGA-UY-A78N TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD 
       86.83        76.01        65.75        35.24        29.56        17.82 
TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH 
        4.54         1.64         1.87        17.88        48.62        64.80 
TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SL TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SX 
       79.66         3.22        66.41        12.76        11.90        23.64 
TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 
       21.04        28.24        26.27        18.90         2.24        16.27 
TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMG 
       66.64         2.10        13.74        92.98        10.82       110.60 
TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX 
       11.31        54.90        91.73         2.96         8.32         6.77 
TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 
       98.99        44.32        56.48        30.94        61.45        86.30 
TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L 
       27.06        75.39         3.88         9.63         0.66        11.97 
TCGA-YF-AA3M TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R4 
       13.64        18.64         7.36        21.11        24.13        30.28 
TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RE 
       27.19        21.86        28.41        74.56        13.41         3.48 
TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N 
       52.73        52.60        82.49        47.84        20.22         2.89 
TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA4X 
       34.06        19.69         8.61        59.38        60.16        63.02 
TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 
       38.73        35.41        57.90        19.40         8.52        47.15 
TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-ZF-AA5P 
       19.17         5.52        10.13 

  F7 MUTATED F7 WILD-TYPE 
        7.63         0.10 
  F7 MUTATED F7 WILD-TYPE 
       71.57       166.03 
  F7 MUTATED F7 WILD-TYPE 
       14.07        15.68 
[1] "7.6 - 71.6 (14.1)"  "0.1 - 166.0 (15.7)"
[1] "hr=" "1.1"
D84V2, continuous
              vv
clus           STAGE I STAGE II STAGE III STAGE IV
  F7 MUTATED         0        2         3        2
  F7 WILD-TYPE       4      115       119      126
D84V3, multiclass
           clus
vv          F7 MUTATED F7 WILD-TYPE
  STAGE I            0            4
  STAGE II           2          115
  STAGE III          3          119
  STAGE IV           2          126
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
              vv
clus           T0+T1+T2  T3  T4
  F7 MUTATED          2   4   1
  F7 WILD-TYPE      112 175  51
D84V4, multiclass
          clus
vv         F7 MUTATED F7 WILD-TYPE
  T0+T1+T2          2          112
  T3                4          175
  T4                1           51
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
              vv
clus            N0  N1  N2  N3
  F7 MUTATED     5   1   1   0
  F7 WILD-TYPE 208  40  74   8
D84V5, multiclass
    clus
vv   F7 MUTATED F7 WILD-TYPE
  N0          5          208
  N1          1           40
  N2          1           74
  N3          0            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"
D84V6, binary
              cls
clus             0   1
  F7 MUTATED     3   0
  F7 WILD-TYPE 179  10
[1] "tbl2"
              cls
clus           [,1] [,2]
  F7 MUTATED      3    0
  F7 WILD-TYPE  179   10
   clus
vv  F7 MUTATED F7 WILD-TYPE
  0          3          179
  1          0           10
[1] 2 2
[1] FALSE
D84V7, binary
              cls
clus             0   1
  F7 MUTATED     2   5
  F7 WILD-TYPE  94 275
[1] "tbl2"
              cls
clus           [,1] [,2]
  F7 MUTATED      2    5
  F7 WILD-TYPE   94  275
        clus
vv       F7 MUTATED F7 WILD-TYPE
  FEMALE          2           94
  MALE            5          275
[1] 2 2
[1] FALSE
D84V8, continuous
D84V9, continuous
D84V10, continuous
              vv
clus           ASIAN BLACK OR AFRICAN AMERICAN WHITE
  F7 MUTATED       1                         0     6
  F7 WILD-TYPE    37                        21   295
D84V11, multiclass
                           clus
vv                          F7 MUTATED F7 WILD-TYPE
  ASIAN                              1           37
  BLACK OR AFRICAN AMERICAN          0           21
  WHITE                              6          295
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D84V12, binary
              cls
clus             0   1
  F7 MUTATED     0   7
  F7 WILD-TYPE   8 331
[1] "tbl2"
              cls
clus           [,1] [,2]
  F7 MUTATED      0    7
  F7 WILD-TYPE    8  331
                        clus
vv                       F7 MUTATED F7 WILD-TYPE
  HISPANIC OR LATINO              0            8
  NOT HISPANIC OR LATINO          7          331
[1] 2 2
[1] FALSE

Clustering(85) Variable = IRX4 MUTATION ANALYSIS
D85V1, survival
                sevent
clus2              0   1
  IRX4 MUTATED     4   4
  IRX4 WILD-TYPE 215 147
  IRX4 MUTATED IRX4 WILD-TYPE 
             8            362 
  IRX4 MUTATED IRX4 WILD-TYPE 
             4            147 
$`IRX4 MUTATED`
TCGA-4Z-AA87 TCGA-C4-A0F7 TCGA-DK-A3WW TCGA-FD-A3SJ TCGA-GU-AATO TCGA-K4-A5RI 
       47.80         2.04        20.81        24.30        10.65        11.70 
TCGA-LT-A5Z6 TCGA-ZF-AA4V 
       15.58        59.38 

$`IRX4 WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        91.63       103.50       105.70         8.35 
TCGA-4Z-AA7M TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7S 
       16.27        44.94        16.83        16.77        17.16        34.98 
TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 
       27.62        49.12         0.62        41.75        51.16        66.54 
TCGA-4Z-AA84 TCGA-4Z-AA86 TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J 
       15.12        10.22        33.83        40.08         7.33         2.66 
TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N 
        6.74        12.39         6.58        13.15        19.04        32.84 
TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U 
       12.16        17.88        19.50         5.06        14.89        14.96 
TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A2LD 
        5.06         8.35         8.25        17.16        16.18        20.48 
TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E 
        4.67        12.82         9.96        17.56        28.70        24.26 
TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-C4-A0F6 TCGA-CF-A1HR 
       28.41         8.98         1.94         2.93        23.01         0.46 
TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W 
        0.43         0.69        10.95        12.66        12.46        12.10 
TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A9FF 
       12.62        12.26        13.12        12.00        12.10        11.87 
TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3QU 
       13.08        12.92         4.90         7.20         5.46         5.19 
TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 
       16.31         1.84        13.58        21.86         2.14        66.41 
TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE 
       18.41        19.00        16.70       130.88       112.44        16.14 
TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 
       17.62        15.62         1.81        10.59         7.79       123.85 
TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ 
       87.32         2.20        13.58         7.82         8.22        17.72 
TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WX TCGA-DK-A3WY 
       50.27        21.30        23.21         9.67        10.55       140.81 
TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 
       48.00        17.98        64.18        41.56        76.60        67.36 
TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6P TCGA-DK-AA6Q 
       15.68        41.06        30.67        38.24        15.02        13.58 
TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA71 
      166.03        12.36        10.49         8.65         7.53        13.64 
TCGA-DK-AA74 TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E5-A4U1 
       43.50        12.03        10.62        43.59        15.35        38.83 
TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 
       24.66         0.10         0.49         2.24        16.70        17.39 
TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF 
        0.56         0.66        14.56        13.97        12.99        14.33 
TCGA-E7-A7DU TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A97P 
        0.92         1.22        13.68        14.07        12.95        14.37 
TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 
        8.09        32.02        16.77         8.94        33.04         4.01 
TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SL TCGA-FD-A3SM 
       12.62        22.52        27.98        60.66        23.41        17.98 
TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS 
       29.16         5.52        25.74        46.78        19.79        12.85 
TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BR 
       22.98        27.35        14.96        20.91         3.62        26.73 
TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY 
       53.88        11.01        19.33         5.36         5.69         8.25 
TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P 
       27.45        18.08        58.92         2.70         7.10         6.28 
TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE 
       13.35        62.86        18.81         6.15        12.69        12.36 
TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z7 
        2.27         3.06         4.31         9.67        10.85        31.07 
TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FJ-A871 TCGA-FT-A3EE TCGA-FT-A61P 
        7.13        10.65        17.23         8.94         3.25         6.48 
TCGA-G2-A2EC TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO 
       22.88        61.94        30.61        15.95        26.93        35.24 
TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3C 
       33.01         7.23        20.12        17.62        66.02         6.94 
TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB 
       64.44        19.46        21.40         2.24        15.81         4.50 
TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GC-A6I3 
       15.91        14.07        17.75        24.92         8.94        13.91 
TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GD-A76B 
        7.73         2.10         3.12        20.98         2.20         7.36 
TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A764 
       10.92        11.31        11.31         7.63        27.09        20.05 
TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATP TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW 
        5.62         4.73        32.98         7.00        14.27        21.34 
TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK 
       19.10        19.82        20.28         8.48        10.59        27.35 
TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE 
        8.58        19.07        22.72         1.51        19.40        38.60 
TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV 
        3.06         9.01         8.22        25.02         3.45        21.24 
TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RH TCGA-K4-A5RJ TCGA-K4-A6FZ 
        2.76         9.14        27.68         9.07         1.74         1.81 
TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO TCGA-LC-A66R TCGA-MV-A51V TCGA-PQ-A6FI 
       15.42         6.38        11.80        15.32        13.48        12.23 
TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 TCGA-SY-A9G0 TCGA-SY-A9G5 
       16.67        14.24         1.84         3.75        12.43        31.56 
TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78N TCGA-UY-A78O TCGA-UY-A8OB 
       17.62        37.05        22.68        86.83        76.01        65.75 
TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HH 
       35.24        29.56        17.82         4.54         1.64         1.87 
TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SL 
       17.88        48.62        64.80        79.66         3.22        66.41 
TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T0 
       12.76        11.90        23.64        21.04        28.24        26.27 
TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 
       18.90         2.24        16.27        66.64         2.10        13.74 
TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMG TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML 
       92.98        10.82       110.60        11.31        54.90         7.63 
TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAMY 
       71.57        91.73         2.96         8.32         6.77        98.99 
TCGA-XF-AAMZ TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN4 
       44.32        56.48        30.94        61.45        86.30        27.06 
TCGA-XF-AAN5 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L 
       75.39        18.81         3.88         9.63         0.66        11.97 
TCGA-YF-AA3M TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R4 
       13.64        18.64         7.36        21.11        24.13        30.28 
TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RE 
       27.19        21.86        28.41        74.56        13.41         3.48 
TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N 
       52.73        52.60        82.49        47.84        20.22         2.89 
TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4U TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA51 
       34.06        19.69         8.61        60.16        63.02        38.73 
TCGA-ZF-AA52 TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H 
       35.41        57.90        19.40         8.52        47.15        19.17 
TCGA-ZF-AA5N TCGA-ZF-AA5P 
        5.52        10.13 

  IRX4 MUTATED IRX4 WILD-TYPE 
          2.04           0.10 
  IRX4 MUTATED IRX4 WILD-TYPE 
         59.38         166.03 
  IRX4 MUTATED IRX4 WILD-TYPE 
        18.195         15.650 
[1] "2.0 - 59.4 (18.2)"  "0.1 - 166.0 (15.6)"
[1] "hr=" "1.1"
D85V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  IRX4 MUTATED         0        1         4        3
  IRX4 WILD-TYPE       4      116       118      125
D85V3, multiclass
           clus
vv          IRX4 MUTATED IRX4 WILD-TYPE
  STAGE I              0              4
  STAGE II             1            116
  STAGE III            4            118
  STAGE IV             3            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"
                vv
clus             T0+T1+T2  T3  T4
  IRX4 MUTATED          1   3   3
  IRX4 WILD-TYPE      113 176  49
D85V4, multiclass
          clus
vv         IRX4 MUTATED IRX4 WILD-TYPE
  T0+T1+T2            1            113
  T3                  3            176
  T4                  3             49
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  IRX4 MUTATED     4   0   3   0
  IRX4 WILD-TYPE 209  41  72   8
D85V5, multiclass
    clus
vv   IRX4 MUTATED IRX4 WILD-TYPE
  N0            4            209
  N1            0             41
  N2            3             72
  N3            0              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"
D85V6, binary
                cls
clus               0   1
  IRX4 MUTATED     4   0
  IRX4 WILD-TYPE 178  10
[1] "tbl2"
                cls
clus             [,1] [,2]
  IRX4 MUTATED      4    0
  IRX4 WILD-TYPE  178   10
   clus
vv  IRX4 MUTATED IRX4 WILD-TYPE
  0            4            178
  1            0             10
[1] 2 2
[1] FALSE
D85V7, binary
                cls
clus               0   1
  IRX4 MUTATED     1   7
  IRX4 WILD-TYPE  95 273
[1] "tbl2"
                cls
clus             [,1] [,2]
  IRX4 MUTATED      1    7
  IRX4 WILD-TYPE   95  273
        clus
vv       IRX4 MUTATED IRX4 WILD-TYPE
  FEMALE            1             95
  MALE              7            273
[1] 2 2
[1] FALSE
D85V8, continuous
D85V9, continuous
D85V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  IRX4 MUTATED       0                         1     6
  IRX4 WILD-TYPE    38                        20   295
D85V11, multiclass
                           clus
vv                          IRX4 MUTATED IRX4 WILD-TYPE
  ASIAN                                0             38
  BLACK OR AFRICAN AMERICAN            1             20
  WHITE                                6            295
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D85V12, binary
                cls
clus               0   1
  IRX4 MUTATED     0   6
  IRX4 WILD-TYPE   8 332
[1] "tbl2"
                cls
clus             [,1] [,2]
  IRX4 MUTATED      0    6
  IRX4 WILD-TYPE    8  332
                        clus
vv                       IRX4 MUTATED IRX4 WILD-TYPE
  HISPANIC OR LATINO                0              8
  NOT HISPANIC OR LATINO            6            332
[1] 2 2
[1] FALSE

Clustering(86) Variable = HSP90AA1 MUTATION ANALYSIS
D86V1, survival
                    sevent
clus2                  0   1
  HSP90AA1 MUTATED    18   4
  HSP90AA1 WILD-TYPE 201 147
  HSP90AA1 MUTATED HSP90AA1 WILD-TYPE 
                22                348 
  HSP90AA1 MUTATED HSP90AA1 WILD-TYPE 
                 4                147 
$`HSP90AA1 MUTATED`
TCGA-2F-A9KT TCGA-BT-A3PJ TCGA-CF-A47X TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IT 
      105.70        12.82        12.62       123.85        87.32        21.30 
TCGA-DK-AA71 TCGA-E7-A5KE TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43X TCGA-FD-A6TC 
       13.64         0.56        19.79        12.85         3.62         6.15 
TCGA-FD-A6TE TCGA-GC-A3YS TCGA-GU-A766 TCGA-GV-A3JV TCGA-K4-A6MB TCGA-MV-A51V 
       12.36        24.92         5.62        14.27        15.42        13.48 
TCGA-SY-A9G5 TCGA-XF-AAMG TCGA-XF-AAN0 TCGA-ZF-AA4W 
       31.56       110.60        56.48        60.16 

$`HSP90AA1 WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KW TCGA-4Z-AA7M 
       22.29        11.97        91.63       103.50         8.35        16.27 
TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7W 
       44.94        16.83        16.77        17.16        34.98        27.62 
TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA84 
       49.12         0.62        41.75        51.16        66.54        15.12 
TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J 
       10.22        47.80        33.83        40.08         7.33         2.66 
TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N 
        6.74        12.39         6.58        13.15        19.04        32.84 
TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U 
       12.16        17.88        19.50         5.06        14.89        14.96 
TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A2LD 
        5.06         8.35         8.25        17.16        16.18        20.48 
TCGA-BT-A3PH TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E TCGA-BT-A42F 
        4.67         9.96        17.56        28.70        24.26        28.41 
TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-C4-A0F6 TCGA-C4-A0F7 TCGA-CF-A1HR 
        8.98         1.94         2.93        23.01         2.04         0.46 
TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W 
        0.43         0.69        10.95        12.66        12.46        12.10 
TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A9FF TCGA-CF-A9FM 
       12.26        13.12        12.00        12.10        11.87        13.08 
TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL 
       12.92         4.90         7.20         5.46         5.19        16.31 
TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 
        1.84        13.58        21.86         2.14        66.41        18.41 
TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF 
       19.00        16.70       130.88       112.44        16.14        17.62 
TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A3IK TCGA-DK-A3IL 
       15.62         1.81        10.59         7.79         2.20        13.58 
TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IU TCGA-DK-A3IV 
        7.82         8.22        17.72        50.27        23.21         9.67 
TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV 
       20.81        10.55       140.81        48.00        17.98        64.18 
TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 
       41.56        76.60        67.36        15.68        41.06        30.67 
TCGA-DK-AA6L TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6U 
       38.24        15.02        13.58       166.03        12.36        10.49 
TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA74 TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A2PC 
        8.65         7.53        43.50        12.03        10.62        43.59 
TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ 
       15.35        38.83        24.66         0.10         0.49         2.24 
TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME 
       16.70        17.39         0.66        14.56        13.97        12.99 
TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H 
       14.33         0.92         1.22        13.68        14.07        12.95 
TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 
       14.37         8.09        32.02        16.77         8.94        33.04 
TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ 
        4.01        12.62        22.52        27.98        60.66        24.30 
TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ 
       23.41        17.98        29.16         5.52        25.74        46.78 
TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A5BR TCGA-FD-A5BS 
       22.98        27.35        14.96        20.91        26.73        53.88 
TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ 
       11.01        19.33         5.36         5.69         8.25        27.45 
TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S 
       18.08        58.92         2.70         7.10         6.28        13.35 
TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TD TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH 
       62.86        18.81        12.69         2.27         3.06         4.31 
TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF 
        9.67        10.85        31.07         7.13        10.65        17.23 
TCGA-FJ-A871 TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EC TCGA-G2-A2EF TCGA-G2-A2EJ 
        8.94         3.25         6.48        22.88        61.94        30.61 
TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE 
       15.95        26.93        35.24        33.01         7.23        20.12 
TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3BM 
       17.62        66.02         6.94        64.44        19.46        21.40 
TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC 
        2.24        15.81         4.50        15.91        14.07        17.75 
TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS 
        8.94        13.91         7.73         2.10         3.12        20.98 
TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 
        2.20         7.36        10.92        11.31        11.31         7.63 
TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A767 TCGA-GU-AATO TCGA-GU-AATP TCGA-GU-AATQ 
       27.09        20.05         4.73        10.65        32.98         7.00 
TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI 
       21.34        19.10        19.82        20.28         8.48        10.59 
TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-H4-A2HQ 
       27.35         8.58        19.07        22.72         1.51        19.40 
TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU 
       38.60         3.06         9.01         8.22        25.02         3.45 
TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RH TCGA-K4-A5RI 
       21.24         2.76         9.14        27.68         9.07        11.70 
TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A83P TCGA-K4-AAQO TCGA-LC-A66R TCGA-LT-A5Z6 
        1.74         1.81         6.38        11.80        15.32        15.58 
TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 TCGA-SY-A9G0 
       12.23        16.67        14.24         1.84         3.75        12.43 
TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78N TCGA-UY-A78O TCGA-UY-A8OB 
       17.62        37.05        22.68        86.83        76.01        65.75 
TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HH 
       35.24        29.56        17.82         4.54         1.64         1.87 
TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SL 
       17.88        48.62        64.80        79.66         3.22        66.41 
TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T0 
       12.76        11.90        23.64        21.04        28.24        26.27 
TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 
       18.90         2.24        16.27        66.64         2.10        13.74 
TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ 
       92.98        10.82        11.31        54.90         7.63        71.57 
TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAMZ 
       91.73         2.96         8.32         6.77        98.99        44.32 
TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN7 
       30.94        61.45        86.30        27.06        75.39        18.81 
TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R0 
        3.88         9.63         0.66        11.97        13.64        18.64 
TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R7 
        7.36        21.11        24.13        30.28        27.19        21.86 
TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RG 
       28.41        74.56        13.41         3.48        52.73        52.60 
TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4R TCGA-ZF-AA4T 
       82.49        47.84        20.22         2.89        34.06        19.69 
TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA53 
        8.61        59.38        63.02        38.73        35.41        57.90 
TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-ZF-AA5P 
       19.40         8.52        47.15        19.17         5.52        10.13 

  HSP90AA1 MUTATED HSP90AA1 WILD-TYPE 
              0.56               0.10 
  HSP90AA1 MUTATED HSP90AA1 WILD-TYPE 
            123.85             166.03 
  HSP90AA1 MUTATED HSP90AA1 WILD-TYPE 
            14.845             15.745 
[1] "0.6 - 123.8 (14.8)" "0.1 - 166.0 (15.7)"
[1] "hr=" "2.9"
D86V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  HSP90AA1 MUTATED         0        6         8        8
  HSP90AA1 WILD-TYPE       4      111       114      120
D86V3, multiclass
           clus
vv          HSP90AA1 MUTATED HSP90AA1 WILD-TYPE
  STAGE I                  0                  4
  STAGE II                 6                111
  STAGE III                8                114
  STAGE IV                 8                120
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1+T2  T3  T4
  HSP90AA1 MUTATED          7   9   6
  HSP90AA1 WILD-TYPE      107 170  46
D86V4, multiclass
          clus
vv         HSP90AA1 MUTATED HSP90AA1 WILD-TYPE
  T0+T1+T2                7                107
  T3                      9                170
  T4                      6                 46
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  HSP90AA1 MUTATED    13   4   3   2
  HSP90AA1 WILD-TYPE 200  37  72   6
D86V5, multiclass
    clus
vv   HSP90AA1 MUTATED HSP90AA1 WILD-TYPE
  N0               13                200
  N1                4                 37
  N2                3                 72
  N3                2                  6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D86V6, binary
                    cls
clus                   0   1
  HSP90AA1 MUTATED    11   0
  HSP90AA1 WILD-TYPE 171  10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HSP90AA1 MUTATED     11    0
  HSP90AA1 WILD-TYPE  171   10
   clus
vv  HSP90AA1 MUTATED HSP90AA1 WILD-TYPE
  0               11                171
  1                0                 10
[1] 2 2
[1] FALSE
D86V7, binary
                    cls
clus                   0   1
  HSP90AA1 MUTATED     2  20
  HSP90AA1 WILD-TYPE  94 260
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HSP90AA1 MUTATED      2   20
  HSP90AA1 WILD-TYPE   94  260
        clus
vv       HSP90AA1 MUTATED HSP90AA1 WILD-TYPE
  FEMALE                2                 94
  MALE                 20                260
[1] 2 2
[1] FALSE
D86V8, continuous
D86V9, continuous
D86V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  HSP90AA1 MUTATED       2                         0    20
  HSP90AA1 WILD-TYPE    36                        21   281
D86V11, multiclass
                           clus
vv                          HSP90AA1 MUTATED HSP90AA1 WILD-TYPE
  ASIAN                                    2                 36
  BLACK OR AFRICAN AMERICAN                0                 21
  WHITE                                   20                281
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D86V12, binary
                    cls
clus                   0   1
  HSP90AA1 MUTATED     1  21
  HSP90AA1 WILD-TYPE   7 317
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HSP90AA1 MUTATED      1   21
  HSP90AA1 WILD-TYPE    7  317
                        clus
vv                       HSP90AA1 MUTATED HSP90AA1 WILD-TYPE
  HISPANIC OR LATINO                    1                  7
  NOT HISPANIC OR LATINO               21                317
[1] 2 2
[1] FALSE

Clustering(87) Variable = TTYH1 MUTATION ANALYSIS
D87V1, survival
                 sevent
clus2               0   1
  TTYH1 MUTATED     5   2
  TTYH1 WILD-TYPE 214 149
  TTYH1 MUTATED TTYH1 WILD-TYPE 
              7             363 
  TTYH1 MUTATED TTYH1 WILD-TYPE 
              2             149 
$`TTYH1 MUTATED`
TCGA-CU-A3KJ TCGA-DK-A1AB TCGA-DK-A2I4 TCGA-FD-A5BX TCGA-G2-A2EO TCGA-K4-A6MB 
        5.46        16.70       123.85         5.69        35.24        15.42 
TCGA-XF-A9T3 
        2.24 

$`TTYH1 WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        91.63       103.50       105.70         8.35 
TCGA-4Z-AA7M TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7S 
       16.27        44.94        16.83        16.77        17.16        34.98 
TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 
       27.62        49.12         0.62        41.75        51.16        66.54 
TCGA-4Z-AA84 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BL-A13I 
       15.12        10.22        47.80        33.83        40.08         7.33 
TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J 
        2.66         6.74        12.39         6.58        13.15        19.04 
TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T 
       32.84        12.16        17.88        19.50         5.06        14.89 
TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB 
       14.96         5.06         8.35         8.25        17.16        16.18 
TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C 
       20.48         4.67        12.82         9.96        17.56        28.70 
TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-C4-A0F6 
       24.26        28.41         8.98         1.94         2.93        23.01 
TCGA-C4-A0F7 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T 
        2.04         0.46         0.43         0.69        10.95        12.66 
TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA 
       12.46        12.10        12.62        12.26        13.12        12.00 
TCGA-CF-A7I0 TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR 
       12.10        11.87        13.08        12.92         4.90         7.20 
TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 
        5.19        16.31         1.84        13.58        21.86         2.14 
TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE 
       66.41        18.41        19.00       130.88       112.44        16.14 
TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I6 
       17.62        15.62         1.81        10.59         7.79        87.32 
TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS 
        2.20        13.58         7.82         8.22        17.72        50.27 
TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY 
       21.30        23.21         9.67        20.81        10.55       140.81 
TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 
       48.00        17.98        64.18        41.56        76.60        67.36 
TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6P TCGA-DK-AA6Q 
       15.68        41.06        30.67        38.24        15.02        13.58 
TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA71 
      166.03        12.36        10.49         8.65         7.53        13.64 
TCGA-DK-AA74 TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E5-A4U1 
       43.50        12.03        10.62        43.59        15.35        38.83 
TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 
       24.66         0.10         0.49         2.24        16.70        17.39 
TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF 
        0.56         0.66        14.56        13.97        12.99        14.33 
TCGA-E7-A7DU TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A97P 
        0.92         1.22        13.68        14.07        12.95        14.37 
TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 
        8.09        32.02        16.77         8.94        33.04         4.01 
TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL 
       12.62        22.52        27.98        60.66        24.30        23.41 
TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR 
       17.98        29.16         5.52        25.74        46.78        19.79 
TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X 
       12.85        22.98        27.35        14.96        20.91         3.62 
TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BY 
       26.73        53.88        11.01        19.33         5.36         8.25 
TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P 
       27.45        18.08        58.92         2.70         7.10         6.28 
TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE 
       13.35        62.86        18.81         6.15        12.69        12.36 
TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z7 
        2.27         3.06         4.31         9.67        10.85        31.07 
TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FJ-A871 TCGA-FT-A3EE TCGA-FT-A61P 
        7.13        10.65        17.23         8.94         3.25         6.48 
TCGA-G2-A2EC TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2ES 
       22.88        61.94        30.61        15.95        26.93        33.01 
TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3D 
        7.23        20.12        17.62        66.02         6.94        64.44 
TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC 
       19.46        21.40         2.24        15.81         4.50        15.91 
TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 
       14.07        17.75        24.92         8.94        13.91         7.73 
TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42P 
        2.10         3.12        20.98         2.20         7.36        10.92 
TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 
       11.31        11.31         7.63        27.09        20.05         5.62 
TCGA-GU-A767 TCGA-GU-AATO TCGA-GU-AATP TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW 
        4.73        10.65        32.98         7.00        14.27        21.34 
TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK 
       19.10        19.82        20.28         8.48        10.59        27.35 
TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE 
        8.58        19.07        22.72         1.51        19.40        38.60 
TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV 
        3.06         9.01         8.22        25.02         3.45        21.24 
TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ 
        2.76         9.14        27.68         9.07        11.70         1.74 
TCGA-K4-A6FZ TCGA-K4-A83P TCGA-K4-AAQO TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V 
        1.81         6.38        11.80        15.32        15.58        13.48 
TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 TCGA-SY-A9G0 
       12.23        16.67        14.24         1.84         3.75        12.43 
TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78N TCGA-UY-A78O 
       31.56        17.62        37.05        22.68        86.83        76.01 
TCGA-UY-A8OB TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF 
       65.75        35.24        29.56        17.82         4.54         1.64 
TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SJ 
        1.87        17.88        48.62        64.80        79.66         3.22 
TCGA-XF-A9SL TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ 
       66.41        12.76        11.90        23.64        21.04        28.24 
TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 
       26.27        18.90        16.27        66.64         2.10        13.74 
TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMG TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML 
       92.98        10.82       110.60        11.31        54.90         7.63 
TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAMY 
       71.57        91.73         2.96         8.32         6.77        98.99 
TCGA-XF-AAMZ TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN4 
       44.32        56.48        30.94        61.45        86.30        27.06 
TCGA-XF-AAN5 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L 
       75.39        18.81         3.88         9.63         0.66        11.97 
TCGA-YF-AA3M TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R4 
       13.64        18.64         7.36        21.11        24.13        30.28 
TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RE 
       27.19        21.86        28.41        74.56        13.41         3.48 
TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N 
       52.73        52.60        82.49        47.84        20.22         2.89 
TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA4X 
       34.06        19.69         8.61        59.38        60.16        63.02 
TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 
       38.73        35.41        57.90        19.40         8.52        47.15 
TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-ZF-AA5P 
       19.17         5.52        10.13 

  TTYH1 MUTATED TTYH1 WILD-TYPE 
           2.24            0.10 
  TTYH1 MUTATED TTYH1 WILD-TYPE 
         123.85          166.03 
  TTYH1 MUTATED TTYH1 WILD-TYPE 
          15.42           15.68 
[1] "2.2 - 123.8 (15.4)" "0.1 - 166.0 (15.7)"
[1] "hr=" "1.4"
D87V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  TTYH1 MUTATED         0        0         3        4
  TTYH1 WILD-TYPE       4      117       119      124
D87V3, multiclass
           clus
vv          TTYH1 MUTATED TTYH1 WILD-TYPE
  STAGE I               0               4
  STAGE II              0             117
  STAGE III             3             119
  STAGE IV              4             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"
                 vv
clus              T0+T1+T2  T3  T4
  TTYH1 MUTATED          0   6   1
  TTYH1 WILD-TYPE      114 173  51
D87V4, multiclass
          clus
vv         TTYH1 MUTATED TTYH1 WILD-TYPE
  T0+T1+T2             0             114
  T3                   6             173
  T4                   1              51
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  TTYH1 MUTATED     3   2   2   0
  TTYH1 WILD-TYPE 210  39  73   8
D87V5, multiclass
    clus
vv   TTYH1 MUTATED TTYH1 WILD-TYPE
  N0             3             210
  N1             2              39
  N2             2              73
  N3             0               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"
D87V6, binary
                 cls
clus                0   1
  TTYH1 MUTATED     4   0
  TTYH1 WILD-TYPE 178  10
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TTYH1 MUTATED      4    0
  TTYH1 WILD-TYPE  178   10
   clus
vv  TTYH1 MUTATED TTYH1 WILD-TYPE
  0             4             178
  1             0              10
[1] 2 2
[1] FALSE
D87V7, binary
                 cls
clus                0   1
  TTYH1 MUTATED     2   5
  TTYH1 WILD-TYPE  94 275
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TTYH1 MUTATED      2    5
  TTYH1 WILD-TYPE   94  275
        clus
vv       TTYH1 MUTATED TTYH1 WILD-TYPE
  FEMALE             2              94
  MALE               5             275
[1] 2 2
[1] FALSE
D87V8, continuous
[1] "Remove cluster labels:" "TTYH1 MUTATED"         
clus
  TTYH1 MUTATED TTYH1 WILD-TYPE 
              2             118 
     TCGA-2F-A9KO      TCGA-2F-A9KP      TCGA-2F-A9KQ      TCGA-2F-A9KR 
"TTYH1 WILD-TYPE" "TTYH1 WILD-TYPE" "TTYH1 WILD-TYPE" "TTYH1 WILD-TYPE" 
     TCGA-2F-A9KT      TCGA-2F-A9KW      TCGA-CF-A1HS      TCGA-CF-A27C 
"TTYH1 WILD-TYPE" "TTYH1 WILD-TYPE" "TTYH1 WILD-TYPE" "TTYH1 WILD-TYPE" 
     TCGA-CF-A3MF      TCGA-CF-A3MG      TCGA-CF-A3MH      TCGA-CF-A3MI 
"TTYH1 WILD-TYPE" "TTYH1 WILD-TYPE" "TTYH1 WILD-TYPE" "TTYH1 WILD-TYPE" 
     TCGA-CF-A47S      TCGA-CF-A47T      TCGA-CF-A47V      TCGA-CF-A47W 
"TTYH1 WILD-TYPE" "TTYH1 WILD-TYPE" "TTYH1 WILD-TYPE" "TTYH1 WILD-TYPE" 
     TCGA-CF-A47X      TCGA-CF-A47Y      TCGA-CF-A5U8      TCGA-CF-A5UA 
"TTYH1 WILD-TYPE" "TTYH1 WILD-TYPE" "TTYH1 WILD-TYPE" "TTYH1 WILD-TYPE" 
     TCGA-CF-A7I0      TCGA-DK-A2HX      TCGA-DK-A3IN      TCGA-DK-A3IV 
"TTYH1 WILD-TYPE" "TTYH1 WILD-TYPE" "TTYH1 WILD-TYPE" "TTYH1 WILD-TYPE" 
     TCGA-DK-A3WX      TCGA-DK-A3X2      TCGA-DK-A6B2      TCGA-DK-A6B5 
"TTYH1 WILD-TYPE" "TTYH1 WILD-TYPE" "TTYH1 WILD-TYPE" "TTYH1 WILD-TYPE" 
     TCGA-DK-A6B6      TCGA-DK-AA6P      TCGA-DK-AA6S      TCGA-DK-AA6U 
"TTYH1 WILD-TYPE" "TTYH1 WILD-TYPE" "TTYH1 WILD-TYPE" "TTYH1 WILD-TYPE" 
     TCGA-DK-AA6W      TCGA-DK-AA76      TCGA-E5-A2PC      TCGA-E5-A4TZ 
"TTYH1 WILD-TYPE" "TTYH1 WILD-TYPE" "TTYH1 WILD-TYPE" "TTYH1 WILD-TYPE" 
     TCGA-E5-A4U1      TCGA-E7-A519      TCGA-E7-A541      TCGA-E7-A7DU 
"TTYH1 WILD-TYPE" "TTYH1 WILD-TYPE" "TTYH1 WILD-TYPE" "TTYH1 WILD-TYPE" 
     TCGA-E7-A7DV      TCGA-FT-A61P      TCGA-G2-A2EC      TCGA-G2-A2EF 
"TTYH1 WILD-TYPE" "TTYH1 WILD-TYPE" "TTYH1 WILD-TYPE" "TTYH1 WILD-TYPE" 
     TCGA-G2-A2EJ      TCGA-G2-A2EK      TCGA-G2-A2EL      TCGA-G2-A2ES 
"TTYH1 WILD-TYPE" "TTYH1 WILD-TYPE" "TTYH1 WILD-TYPE" "TTYH1 WILD-TYPE" 
     TCGA-G2-A3IB      TCGA-G2-A3IE      TCGA-G2-A3VY      TCGA-GC-A3BM 
"TTYH1 WILD-TYPE" "TTYH1 WILD-TYPE" "TTYH1 WILD-TYPE" "TTYH1 WILD-TYPE" 
     TCGA-GC-A3I6      TCGA-GC-A3OO      TCGA-GC-A3RC      TCGA-GC-A3RD 
"TTYH1 WILD-TYPE" "TTYH1 WILD-TYPE" "TTYH1 WILD-TYPE" "TTYH1 WILD-TYPE" 
     TCGA-GC-A3YS      TCGA-GC-A6I1      TCGA-GC-A6I3      TCGA-GD-A3OS 
"TTYH1 WILD-TYPE" "TTYH1 WILD-TYPE" "TTYH1 WILD-TYPE" "TTYH1 WILD-TYPE" 
     TCGA-GD-A6C6      TCGA-GV-A3JV      TCGA-GV-A3JW      TCGA-GV-A3JX 
"TTYH1 WILD-TYPE" "TTYH1 WILD-TYPE" "TTYH1 WILD-TYPE" "TTYH1 WILD-TYPE" 
     TCGA-GV-A3JZ      TCGA-GV-A3QF      TCGA-GV-A3QH      TCGA-GV-A3QI 
"TTYH1 WILD-TYPE" "TTYH1 WILD-TYPE" "TTYH1 WILD-TYPE" "TTYH1 WILD-TYPE" 
     TCGA-GV-A3QK      TCGA-GV-A40E      TCGA-GV-A40G      TCGA-GV-A6ZA 
"TTYH1 WILD-TYPE" "TTYH1 WILD-TYPE" "TTYH1 WILD-TYPE" "TTYH1 WILD-TYPE" 
     TCGA-SY-A9G0      TCGA-SY-A9G5      TCGA-UY-A78L      TCGA-UY-A78M 
"TTYH1 WILD-TYPE" "TTYH1 WILD-TYPE" "TTYH1 WILD-TYPE" "TTYH1 WILD-TYPE" 
     TCGA-UY-A78N      TCGA-XF-A8HH      TCGA-XF-A8HI      TCGA-XF-A9SG 
"TTYH1 WILD-TYPE" "TTYH1 WILD-TYPE" "TTYH1 WILD-TYPE" "TTYH1 WILD-TYPE" 
     TCGA-XF-A9SH      TCGA-XF-A9SI      TCGA-XF-A9SJ      TCGA-XF-A9SL 
"TTYH1 WILD-TYPE" "TTYH1 WILD-TYPE" "TTYH1 WILD-TYPE" "TTYH1 WILD-TYPE" 
     TCGA-XF-A9SV      TCGA-XF-A9SW      TCGA-XF-A9SX      TCGA-XF-A9SY 
"TTYH1 WILD-TYPE" "TTYH1 WILD-TYPE" "TTYH1 WILD-TYPE" "TTYH1 WILD-TYPE" 
     TCGA-XF-A9SZ      TCGA-XF-A9T0      TCGA-XF-A9T2      TCGA-XF-A9T4 
"TTYH1 WILD-TYPE" "TTYH1 WILD-TYPE" "TTYH1 WILD-TYPE" "TTYH1 WILD-TYPE" 
     TCGA-XF-A9T5      TCGA-XF-A9T6      TCGA-XF-A9T8      TCGA-XF-AAME 
"TTYH1 WILD-TYPE" "TTYH1 WILD-TYPE" "TTYH1 WILD-TYPE" "TTYH1 WILD-TYPE" 
     TCGA-XF-AAMF      TCGA-XF-AAMG      TCGA-XF-AAMH      TCGA-XF-AAMJ 
"TTYH1 WILD-TYPE" "TTYH1 WILD-TYPE" "TTYH1 WILD-TYPE" "TTYH1 WILD-TYPE" 
     TCGA-XF-AAML      TCGA-XF-AAMQ      TCGA-XF-AAMR      TCGA-XF-AAMT 
"TTYH1 WILD-TYPE" "TTYH1 WILD-TYPE" "TTYH1 WILD-TYPE" "TTYH1 WILD-TYPE" 
     TCGA-XF-AAMW      TCGA-XF-AAMX      TCGA-XF-AAMY      TCGA-XF-AAMZ 
"TTYH1 WILD-TYPE" "TTYH1 WILD-TYPE" "TTYH1 WILD-TYPE" "TTYH1 WILD-TYPE" 
     TCGA-XF-AAN0      TCGA-XF-AAN1      TCGA-XF-AAN2      TCGA-XF-AAN3 
"TTYH1 WILD-TYPE" "TTYH1 WILD-TYPE" "TTYH1 WILD-TYPE" "TTYH1 WILD-TYPE" 
     TCGA-XF-AAN4      TCGA-XF-AAN5      TCGA-XF-AAN7      TCGA-XF-AAN8 
"TTYH1 WILD-TYPE" "TTYH1 WILD-TYPE" "TTYH1 WILD-TYPE" "TTYH1 WILD-TYPE" 
     TCGA-YF-AA3L      TCGA-YF-AA3M 
"TTYH1 WILD-TYPE" "TTYH1 WILD-TYPE" 
D87V9, continuous
D87V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TTYH1 MUTATED       0                         0     7
  TTYH1 WILD-TYPE    38                        21   294
D87V11, multiclass
                           clus
vv                          TTYH1 MUTATED TTYH1 WILD-TYPE
  ASIAN                                 0              38
  BLACK OR AFRICAN AMERICAN             0              21
  WHITE                                 7             294
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D87V12, binary
                 cls
clus                0   1
  TTYH1 MUTATED     0   7
  TTYH1 WILD-TYPE   8 331
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TTYH1 MUTATED      0    7
  TTYH1 WILD-TYPE    8  331
                        clus
vv                       TTYH1 MUTATED TTYH1 WILD-TYPE
  HISPANIC OR LATINO                 0               8
  NOT HISPANIC OR LATINO             7             331
[1] 2 2
[1] FALSE

Clustering(88) Variable = IL10RB MUTATION ANALYSIS
D88V1, survival
                  sevent
clus2                0   1
  IL10RB MUTATED     4   3
  IL10RB WILD-TYPE 215 148
  IL10RB MUTATED IL10RB WILD-TYPE 
               7              363 
  IL10RB MUTATED IL10RB WILD-TYPE 
               3              148 
$`IL10RB MUTATED`
TCGA-4Z-AA84 TCGA-BT-A20O TCGA-DK-A1A5 TCGA-DK-A2I4 TCGA-FD-A43P TCGA-G2-A3IE 
       15.12        12.16         2.14       123.85        27.35        20.12 
TCGA-ZF-AA4V 
       59.38 

$`IL10RB WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        91.63       103.50       105.70         8.35 
TCGA-4Z-AA7M TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7S 
       16.27        44.94        16.83        16.77        17.16        34.98 
TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 
       27.62        49.12         0.62        41.75        51.16        66.54 
TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J 
       10.22        47.80        33.83        40.08         7.33         2.66 
TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N 
        6.74        12.39         6.58        13.15        19.04        32.84 
TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20V 
       17.88        19.50         5.06        14.89        14.96         5.06 
TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH 
        8.35         8.25        17.16        16.18        20.48         4.67 
TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E TCGA-BT-A42F 
       12.82         9.96        17.56        28.70        24.26        28.41 
TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-C4-A0F6 TCGA-C4-A0F7 TCGA-CF-A1HR 
        8.98         1.94         2.93        23.01         2.04         0.46 
TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W 
        0.43         0.69        10.95        12.66        12.46        12.10 
TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A9FF 
       12.62        12.26        13.12        12.00        12.10        11.87 
TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3QU 
       13.08        12.92         4.90         7.20         5.46         5.19 
TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1A7 
       16.31         1.84        13.58        21.86        66.41        18.41 
TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF 
       19.00        16.70       130.88       112.44        16.14        17.62 
TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I6 TCGA-DK-A3IK 
       15.62         1.81        10.59         7.79        87.32         2.20 
TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT 
       13.58         7.82         8.22        17.72        50.27        21.30 
TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 
       23.21         9.67        20.81        10.55       140.81        48.00 
TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 
       17.98        64.18        41.56        76.60        67.36        15.68 
TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6S 
       41.06        30.67        38.24        15.02        13.58       166.03 
TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA74 
       12.36        10.49         8.65         7.53        13.64        43.50 
TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 
       12.03        10.62        43.59        15.35        38.83        24.66 
TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KE 
        0.10         0.49         2.24        16.70        17.39         0.56 
TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DU 
        0.66        14.56        13.97        12.99        14.33         0.92 
TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A97P TCGA-E7-A97Q 
        1.22        13.68        14.07        12.95        14.37         8.09 
TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 
       32.02        16.77         8.94        33.04         4.01        12.62 
TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM 
       22.52        27.98        60.66        24.30        23.41        17.98 
TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS 
       29.16         5.52        25.74        46.78        19.79        12.85 
TCGA-FD-A43N TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS 
       22.98        14.96        20.91         3.62        26.73        53.88 
TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ 
       11.01        19.33         5.36         5.69         8.25        27.45 
TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S 
       18.08        58.92         2.70         7.10         6.28        13.35 
TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF 
       62.86        18.81         6.15        12.69        12.36         2.27 
TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 
        3.06         4.31         9.67        10.85        31.07         7.13 
TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FJ-A871 TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EC 
       10.65        17.23         8.94         3.25         6.48        22.88 
TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES 
       61.94        30.61        15.95        26.93        35.24        33.01 
TCGA-G2-A3IB TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3D TCGA-G2-AA3F 
        7.23        17.62        66.02         6.94        64.44        19.46 
TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD 
       21.40         2.24        15.81         4.50        15.91        14.07 
TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP 
       17.75        24.92         8.94        13.91         7.73         2.10 
TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42Q 
        3.12        20.98         2.20         7.36        10.92        11.31 
TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 
       11.31         7.63        27.09        20.05         5.62         4.73 
TCGA-GU-AATO TCGA-GU-AATP TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX 
       10.65        32.98         7.00        14.27        21.34        19.10 
TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E 
       19.82        20.28         8.48        10.59        27.35         8.58 
TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF 
       19.07        22.72         1.51        19.40        38.60         3.06 
TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB 
        9.01         8.22        25.02         3.45        21.24         2.76 
TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ 
        9.14        27.68         9.07        11.70         1.74         1.81 
TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V 
       15.42         6.38        11.80        15.32        15.58        13.48 
TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 TCGA-SY-A9G0 
       12.23        16.67        14.24         1.84         3.75        12.43 
TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78N TCGA-UY-A78O 
       31.56        17.62        37.05        22.68        86.83        76.01 
TCGA-UY-A8OB TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF 
       65.75        35.24        29.56        17.82         4.54         1.64 
TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SJ 
        1.87        17.88        48.62        64.80        79.66         3.22 
TCGA-XF-A9SL TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ 
       66.41        12.76        11.90        23.64        21.04        28.24 
TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 
       26.27        18.90         2.24        16.27        66.64         2.10 
TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMG TCGA-XF-AAMH TCGA-XF-AAMJ 
       13.74        92.98        10.82       110.60        11.31        54.90 
TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX 
        7.63        71.57        91.73         2.96         8.32         6.77 
TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 
       98.99        44.32        56.48        30.94        61.45        86.30 
TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YC-A9TC 
       27.06        75.39        18.81         3.88         9.63         0.66 
TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R3 
       11.97        13.64        18.64         7.36        21.11        24.13 
TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RD 
       30.28        27.19        21.86        28.41        74.56        13.41 
TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-A9RN 
        3.48        52.73        52.60        82.49        47.84        20.22 
TCGA-ZF-AA4N TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4U TCGA-ZF-AA4W TCGA-ZF-AA4X 
        2.89        34.06        19.69         8.61        60.16        63.02 
TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 
       38.73        35.41        57.90        19.40         8.52        47.15 
TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-ZF-AA5P 
       19.17         5.52        10.13 

  IL10RB MUTATED IL10RB WILD-TYPE 
            2.14             0.10 
  IL10RB MUTATED IL10RB WILD-TYPE 
          123.85           166.03 
  IL10RB MUTATED IL10RB WILD-TYPE 
           20.12            15.62 
[1] "2.1 - 123.8 (20.1)" "0.1 - 166.0 (15.6)"
[1] "hr=" "1.2"
D88V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  IL10RB MUTATED         0        3         3        1
  IL10RB WILD-TYPE       4      114       119      127
D88V3, multiclass
           clus
vv          IL10RB MUTATED IL10RB WILD-TYPE
  STAGE I                0                4
  STAGE II               3              114
  STAGE III              3              119
  STAGE IV               1              127
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1+T2  T3  T4
  IL10RB MUTATED          2   4   0
  IL10RB WILD-TYPE      112 175  52
D88V4, multiclass
          clus
vv         IL10RB MUTATED IL10RB WILD-TYPE
  T0+T1+T2              2              112
  T3                    4              175
  T4                    0               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"
                  vv
clus                N0  N1  N2  N3
  IL10RB MUTATED     5   0   1   0
  IL10RB WILD-TYPE 208  41  74   8
D88V5, multiclass
    clus
vv   IL10RB MUTATED IL10RB WILD-TYPE
  N0              5              208
  N1              0               41
  N2              1               74
  N3              0                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"
D88V6, binary
                  cls
clus                 0   1
  IL10RB MUTATED     3   1
  IL10RB WILD-TYPE 179   9
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IL10RB MUTATED      3    1
  IL10RB WILD-TYPE  179    9
   clus
vv  IL10RB MUTATED IL10RB WILD-TYPE
  0              3              179
  1              1                9
[1] 2 2
[1] FALSE
D88V7, binary
                  cls
clus                 0   1
  IL10RB MUTATED     0   7
  IL10RB WILD-TYPE  96 273
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IL10RB MUTATED      0    7
  IL10RB WILD-TYPE   96  273
        clus
vv       IL10RB MUTATED IL10RB WILD-TYPE
  FEMALE              0               96
  MALE                7              273
[1] 2 2
[1] FALSE
D88V8, continuous
[1] "Remove cluster labels:" "IL10RB MUTATED"        
clus
  IL10RB MUTATED IL10RB WILD-TYPE 
               1              119 
      TCGA-2F-A9KO       TCGA-2F-A9KP       TCGA-2F-A9KQ       TCGA-2F-A9KR 
"IL10RB WILD-TYPE" "IL10RB WILD-TYPE" "IL10RB WILD-TYPE" "IL10RB WILD-TYPE" 
      TCGA-2F-A9KT       TCGA-2F-A9KW       TCGA-CF-A1HS       TCGA-CF-A27C 
"IL10RB WILD-TYPE" "IL10RB WILD-TYPE" "IL10RB WILD-TYPE" "IL10RB WILD-TYPE" 
      TCGA-CF-A3MF       TCGA-CF-A3MG       TCGA-CF-A3MH       TCGA-CF-A3MI 
"IL10RB WILD-TYPE" "IL10RB WILD-TYPE" "IL10RB WILD-TYPE" "IL10RB WILD-TYPE" 
      TCGA-CF-A47S       TCGA-CF-A47T       TCGA-CF-A47V       TCGA-CF-A47W 
"IL10RB WILD-TYPE" "IL10RB WILD-TYPE" "IL10RB WILD-TYPE" "IL10RB WILD-TYPE" 
      TCGA-CF-A47X       TCGA-CF-A47Y       TCGA-CF-A5U8       TCGA-CF-A5UA 
"IL10RB WILD-TYPE" "IL10RB WILD-TYPE" "IL10RB WILD-TYPE" "IL10RB WILD-TYPE" 
      TCGA-CF-A7I0       TCGA-DK-A2HX       TCGA-DK-A3IN       TCGA-DK-A3IV 
"IL10RB WILD-TYPE" "IL10RB WILD-TYPE" "IL10RB WILD-TYPE" "IL10RB WILD-TYPE" 
      TCGA-DK-A3WX       TCGA-DK-A3X2       TCGA-DK-A6B2       TCGA-DK-A6B5 
"IL10RB WILD-TYPE" "IL10RB WILD-TYPE" "IL10RB WILD-TYPE" "IL10RB WILD-TYPE" 
      TCGA-DK-A6B6       TCGA-DK-AA6P       TCGA-DK-AA6S       TCGA-DK-AA6U 
"IL10RB WILD-TYPE" "IL10RB WILD-TYPE" "IL10RB WILD-TYPE" "IL10RB WILD-TYPE" 
      TCGA-DK-AA6W       TCGA-DK-AA76       TCGA-E5-A2PC       TCGA-E5-A4TZ 
"IL10RB WILD-TYPE" "IL10RB WILD-TYPE" "IL10RB WILD-TYPE" "IL10RB WILD-TYPE" 
      TCGA-E5-A4U1       TCGA-E7-A519       TCGA-E7-A541       TCGA-E7-A7DU 
"IL10RB WILD-TYPE" "IL10RB WILD-TYPE" "IL10RB WILD-TYPE" "IL10RB WILD-TYPE" 
      TCGA-E7-A7DV       TCGA-FT-A61P       TCGA-G2-A2EC       TCGA-G2-A2EF 
"IL10RB WILD-TYPE" "IL10RB WILD-TYPE" "IL10RB WILD-TYPE" "IL10RB WILD-TYPE" 
      TCGA-G2-A2EJ       TCGA-G2-A2EK       TCGA-G2-A2EL       TCGA-G2-A2EO 
"IL10RB WILD-TYPE" "IL10RB WILD-TYPE" "IL10RB WILD-TYPE" "IL10RB WILD-TYPE" 
      TCGA-G2-A2ES       TCGA-G2-A3IB       TCGA-G2-A3VY       TCGA-GC-A3BM 
"IL10RB WILD-TYPE" "IL10RB WILD-TYPE" "IL10RB WILD-TYPE" "IL10RB WILD-TYPE" 
      TCGA-GC-A3I6       TCGA-GC-A3OO       TCGA-GC-A3RC       TCGA-GC-A3RD 
"IL10RB WILD-TYPE" "IL10RB WILD-TYPE" "IL10RB WILD-TYPE" "IL10RB WILD-TYPE" 
      TCGA-GC-A3YS       TCGA-GC-A6I1       TCGA-GC-A6I3       TCGA-GD-A3OS 
"IL10RB WILD-TYPE" "IL10RB WILD-TYPE" "IL10RB WILD-TYPE" "IL10RB WILD-TYPE" 
      TCGA-GD-A6C6       TCGA-GV-A3JV       TCGA-GV-A3JW       TCGA-GV-A3JX 
"IL10RB WILD-TYPE" "IL10RB WILD-TYPE" "IL10RB WILD-TYPE" "IL10RB WILD-TYPE" 
      TCGA-GV-A3JZ       TCGA-GV-A3QF       TCGA-GV-A3QH       TCGA-GV-A3QI 
"IL10RB WILD-TYPE" "IL10RB WILD-TYPE" "IL10RB WILD-TYPE" "IL10RB WILD-TYPE" 
      TCGA-GV-A3QK       TCGA-GV-A40E       TCGA-GV-A40G       TCGA-GV-A6ZA 
"IL10RB WILD-TYPE" "IL10RB WILD-TYPE" "IL10RB WILD-TYPE" "IL10RB WILD-TYPE" 
      TCGA-SY-A9G0       TCGA-SY-A9G5       TCGA-UY-A78L       TCGA-UY-A78M 
"IL10RB WILD-TYPE" "IL10RB WILD-TYPE" "IL10RB WILD-TYPE" "IL10RB WILD-TYPE" 
      TCGA-UY-A78N       TCGA-XF-A8HH       TCGA-XF-A8HI       TCGA-XF-A9SG 
"IL10RB WILD-TYPE" "IL10RB WILD-TYPE" "IL10RB WILD-TYPE" "IL10RB WILD-TYPE" 
      TCGA-XF-A9SH       TCGA-XF-A9SI       TCGA-XF-A9SJ       TCGA-XF-A9SL 
"IL10RB WILD-TYPE" "IL10RB WILD-TYPE" "IL10RB WILD-TYPE" "IL10RB WILD-TYPE" 
      TCGA-XF-A9SV       TCGA-XF-A9SW       TCGA-XF-A9SX       TCGA-XF-A9SY 
"IL10RB WILD-TYPE" "IL10RB WILD-TYPE" "IL10RB WILD-TYPE" "IL10RB WILD-TYPE" 
      TCGA-XF-A9SZ       TCGA-XF-A9T0       TCGA-XF-A9T2       TCGA-XF-A9T3 
"IL10RB WILD-TYPE" "IL10RB WILD-TYPE" "IL10RB WILD-TYPE" "IL10RB WILD-TYPE" 
      TCGA-XF-A9T4       TCGA-XF-A9T5       TCGA-XF-A9T6       TCGA-XF-A9T8 
"IL10RB WILD-TYPE" "IL10RB WILD-TYPE" "IL10RB WILD-TYPE" "IL10RB WILD-TYPE" 
      TCGA-XF-AAME       TCGA-XF-AAMF       TCGA-XF-AAMG       TCGA-XF-AAMH 
"IL10RB WILD-TYPE" "IL10RB WILD-TYPE" "IL10RB WILD-TYPE" "IL10RB WILD-TYPE" 
      TCGA-XF-AAMJ       TCGA-XF-AAML       TCGA-XF-AAMQ       TCGA-XF-AAMR 
"IL10RB WILD-TYPE" "IL10RB WILD-TYPE" "IL10RB WILD-TYPE" "IL10RB WILD-TYPE" 
      TCGA-XF-AAMT       TCGA-XF-AAMW       TCGA-XF-AAMX       TCGA-XF-AAMY 
"IL10RB WILD-TYPE" "IL10RB WILD-TYPE" "IL10RB WILD-TYPE" "IL10RB WILD-TYPE" 
      TCGA-XF-AAMZ       TCGA-XF-AAN0       TCGA-XF-AAN1       TCGA-XF-AAN2 
"IL10RB WILD-TYPE" "IL10RB WILD-TYPE" "IL10RB WILD-TYPE" "IL10RB WILD-TYPE" 
      TCGA-XF-AAN3       TCGA-XF-AAN4       TCGA-XF-AAN5       TCGA-XF-AAN7 
"IL10RB WILD-TYPE" "IL10RB WILD-TYPE" "IL10RB WILD-TYPE" "IL10RB WILD-TYPE" 
      TCGA-XF-AAN8       TCGA-YF-AA3L       TCGA-YF-AA3M 
"IL10RB WILD-TYPE" "IL10RB WILD-TYPE" "IL10RB WILD-TYPE" 
D88V9, continuous
D88V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  IL10RB MUTATED       0                         1     6
  IL10RB WILD-TYPE    38                        20   295
D88V11, multiclass
                           clus
vv                          IL10RB MUTATED IL10RB WILD-TYPE
  ASIAN                                  0               38
  BLACK OR AFRICAN AMERICAN              1               20
  WHITE                                  6              295
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D88V12, binary
                  cls
clus                 0   1
  IL10RB MUTATED     0   6
  IL10RB WILD-TYPE   8 332
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IL10RB MUTATED      0    6
  IL10RB WILD-TYPE    8  332
                        clus
vv                       IL10RB MUTATED IL10RB WILD-TYPE
  HISPANIC OR LATINO                  0                8
  NOT HISPANIC OR LATINO              6              332
[1] 2 2
[1] FALSE

Clustering(89) Variable = THSD4 MUTATION ANALYSIS
D89V1, survival
                 sevent
clus2               0   1
  THSD4 MUTATED     6   3
  THSD4 WILD-TYPE 213 148
  THSD4 MUTATED THSD4 WILD-TYPE 
              9             361 
  THSD4 MUTATED THSD4 WILD-TYPE 
              3             148 
$`THSD4 MUTATED`
TCGA-BT-A0S7 TCGA-DK-A6AW TCGA-E7-A541 TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-G2-A2EJ 
        6.58        41.56        17.39        10.85         7.13        30.61 
TCGA-GU-A767 TCGA-GV-A3QH TCGA-GV-A3QK 
        4.73         8.48        27.35 

$`THSD4 WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        91.63       103.50       105.70         8.35 
TCGA-4Z-AA7M TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7S 
       16.27        44.94        16.83        16.77        17.16        34.98 
TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 
       27.62        49.12         0.62        41.75        51.16        66.54 
TCGA-4Z-AA84 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BL-A13I 
       15.12        10.22        47.80        33.83        40.08         7.33 
TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N 
        2.66         6.74        12.39        13.15        19.04        32.84 
TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U 
       12.16        17.88        19.50         5.06        14.89        14.96 
TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A2LD 
        5.06         8.35         8.25        17.16        16.18        20.48 
TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E 
        4.67        12.82         9.96        17.56        28.70        24.26 
TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-C4-A0F6 TCGA-C4-A0F7 
       28.41         8.98         1.94         2.93        23.01         2.04 
TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V 
        0.46         0.43         0.69        10.95        12.66        12.46 
TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 
       12.10        12.62        12.26        13.12        12.00        12.10 
TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ 
       11.87        13.08        12.92         4.90         7.20         5.46 
TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 
        5.19        16.31         1.84        13.58        21.86         2.14 
TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD 
       66.41        18.41        19.00        16.70       130.88       112.44 
TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 
       16.14        17.62        15.62         1.81        10.59         7.79 
TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN 
      123.85        87.32         2.20        13.58         7.82         8.22 
TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW 
       17.72        50.27        21.30        23.21         9.67        20.81 
TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6B0 
       10.55       140.81        48.00        17.98        64.18        76.60 
TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6P 
       67.36        15.68        41.06        30.67        38.24        15.02 
TCGA-DK-AA6Q TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA6X 
       13.58       166.03        12.36        10.49         8.65         7.53 
TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A2PC TCGA-E5-A4TZ 
       13.64        43.50        12.03        10.62        43.59        15.35 
TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 
       38.83        24.66         0.10         0.49         2.24        16.70 
TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF 
        0.56         0.66        14.56        13.97        12.99        14.33 
TCGA-E7-A7DU TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A97P 
        0.92         1.22        13.68        14.07        12.95        14.37 
TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 
        8.09        32.02        16.77         8.94        33.04         4.01 
TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL 
       12.62        22.52        27.98        60.66        24.30        23.41 
TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR 
       17.98        29.16         5.52        25.74        46.78        19.79 
TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X 
       12.85        22.98        27.35        14.96        20.91         3.62 
TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX 
       26.73        53.88        11.01        19.33         5.36         5.69 
TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O 
        8.25        27.45        18.08        58.92         2.70         7.10 
TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD 
        6.28        13.35        62.86        18.81         6.15        12.69 
TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3Z7 
       12.36         2.27         3.06         4.31         9.67        31.07 
TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FJ-A871 TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EC 
       10.65        17.23         8.94         3.25         6.48        22.88 
TCGA-G2-A2EF TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB 
       61.94        15.95        26.93        35.24        33.01         7.23 
TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3D TCGA-G2-AA3F 
       20.12        17.62        66.02         6.94        64.44        19.46 
TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD 
       21.40         2.24        15.81         4.50        15.91        14.07 
TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP 
       17.75        24.92         8.94        13.91         7.73         2.10 
TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42Q 
        3.12        20.98         2.20         7.36        10.92        11.31 
TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-AATO 
       11.31         7.63        27.09        20.05         5.62        10.65 
TCGA-GU-AATP TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ 
       32.98         7.00        14.27        21.34        19.10        19.82 
TCGA-GV-A3QF TCGA-GV-A3QI TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO 
       20.28        10.59         8.58        19.07        22.72         1.51 
TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS 
       19.40        38.60         3.06         9.01         8.22        25.02 
TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RH 
        3.45        21.24         2.76         9.14        27.68         9.07 
TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO 
       11.70         1.74         1.81        15.42         6.38        11.80 
TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X 
       15.32        15.58        13.48        12.23        16.67        14.24 
TCGA-S5-A6DX TCGA-S5-AA26 TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L 
        1.84         3.75        12.43        31.56        17.62        37.05 
TCGA-UY-A78M TCGA-UY-A78N TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A9PA TCGA-UY-A9PB 
       22.68        86.83        76.01        65.75        35.24        29.56 
TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG 
       17.82         4.54         1.64         1.87        17.88        48.62 
TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SL TCGA-XF-A9SV TCGA-XF-A9SW 
       64.80        79.66         3.22        66.41        12.76        11.90 
TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 
       23.64        21.04        28.24        26.27        18.90         2.24 
TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMF 
       16.27        66.64         2.10        13.74        92.98        10.82 
TCGA-XF-AAMG TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR 
      110.60        11.31        54.90         7.63        71.57        91.73 
TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN0 
        2.96         8.32         6.77        98.99        44.32        56.48 
TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN7 
       30.94        61.45        86.30        27.06        75.39        18.81 
TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R0 
        3.88         9.63         0.66        11.97        13.64        18.64 
TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R7 
        7.36        21.11        24.13        30.28        27.19        21.86 
TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RG 
       28.41        74.56        13.41         3.48        52.73        52.60 
TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4R TCGA-ZF-AA4T 
       82.49        47.84        20.22         2.89        34.06        19.69 
TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 
        8.61        59.38        60.16        63.02        38.73        35.41 
TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N 
       57.90        19.40         8.52        47.15        19.17         5.52 
TCGA-ZF-AA5P 
       10.13 

  THSD4 MUTATED THSD4 WILD-TYPE 
           4.73            0.10 
  THSD4 MUTATED THSD4 WILD-TYPE 
          41.56          166.03 
  THSD4 MUTATED THSD4 WILD-TYPE 
          10.85           15.68 
[1] "4.7 - 41.6 (10.8)"  "0.1 - 166.0 (15.7)"
[1] "hr=" "1"  
D89V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  THSD4 MUTATED         1        4         2        2
  THSD4 WILD-TYPE       3      113       120      126
D89V3, multiclass
           clus
vv          THSD4 MUTATED THSD4 WILD-TYPE
  STAGE I               1               3
  STAGE II              4             113
  STAGE III             2             120
  STAGE IV              2             126
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1+T2  T3  T4
  THSD4 MUTATED          3   2   2
  THSD4 WILD-TYPE      111 177  50
D89V4, multiclass
          clus
vv         THSD4 MUTATED THSD4 WILD-TYPE
  T0+T1+T2             3             111
  T3                   2             177
  T4                   2              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"
                 vv
clus               N0  N1  N2  N3
  THSD4 MUTATED     6   0   2   0
  THSD4 WILD-TYPE 207  41  73   8
D89V5, multiclass
    clus
vv   THSD4 MUTATED THSD4 WILD-TYPE
  N0             6             207
  N1             0              41
  N2             2              73
  N3             0               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"
D89V6, binary
                 cls
clus                0   1
  THSD4 MUTATED     4   0
  THSD4 WILD-TYPE 178  10
[1] "tbl2"
                 cls
clus              [,1] [,2]
  THSD4 MUTATED      4    0
  THSD4 WILD-TYPE  178   10
   clus
vv  THSD4 MUTATED THSD4 WILD-TYPE
  0             4             178
  1             0              10
[1] 2 2
[1] FALSE
D89V7, binary
                 cls
clus                0   1
  THSD4 MUTATED     2   7
  THSD4 WILD-TYPE  94 273
[1] "tbl2"
                 cls
clus              [,1] [,2]
  THSD4 MUTATED      2    7
  THSD4 WILD-TYPE   94  273
        clus
vv       THSD4 MUTATED THSD4 WILD-TYPE
  FEMALE             2              94
  MALE               7             273
[1] 2 2
[1] FALSE
D89V8, continuous
D89V9, continuous
D89V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  THSD4 MUTATED       0                         0     9
  THSD4 WILD-TYPE    38                        21   292
D89V11, multiclass
                           clus
vv                          THSD4 MUTATED THSD4 WILD-TYPE
  ASIAN                                 0              38
  BLACK OR AFRICAN AMERICAN             0              21
  WHITE                                 9             292
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D89V12, binary
                 cls
clus                0   1
  THSD4 MUTATED     0   9
  THSD4 WILD-TYPE   8 329
[1] "tbl2"
                 cls
clus              [,1] [,2]
  THSD4 MUTATED      0    9
  THSD4 WILD-TYPE    8  329
                        clus
vv                       THSD4 MUTATED THSD4 WILD-TYPE
  HISPANIC OR LATINO                 0               8
  NOT HISPANIC OR LATINO             9             329
[1] 2 2
[1] FALSE

Clustering(90) Variable = DDX3X MUTATION ANALYSIS
D90V1, survival
                 sevent
clus2               0   1
  DDX3X MUTATED     6   8
  DDX3X WILD-TYPE 213 143
  DDX3X MUTATED DDX3X WILD-TYPE 
             14             356 
  DDX3X MUTATED DDX3X WILD-TYPE 
              8             143 
$`DDX3X MUTATED`
TCGA-BL-A13I TCGA-DK-A2I4 TCGA-DK-AA6Q TCGA-DK-AA6U TCGA-E7-A3Y1 TCGA-G2-A3VY 
        7.33       123.85        13.58        10.49         0.10        17.62 
TCGA-UY-A78K TCGA-UY-A78N TCGA-XF-A9T2 TCGA-XF-A9T5 TCGA-XF-A9T8 TCGA-XF-AAMX 
       17.62        86.83        18.90        66.64        13.74         6.77 
TCGA-ZF-A9RD TCGA-ZF-AA51 
       13.41        38.73 

$`DDX3X WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        91.63       103.50       105.70         8.35 
TCGA-4Z-AA7M TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7S 
       16.27        44.94        16.83        16.77        17.16        34.98 
TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 
       27.62        49.12         0.62        41.75        51.16        66.54 
TCGA-4Z-AA84 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BL-A13J 
       15.12        10.22        47.80        33.83        40.08         2.66 
TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N 
        6.74        12.39         6.58        13.15        19.04        32.84 
TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U 
       12.16        17.88        19.50         5.06        14.89        14.96 
TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A2LD 
        5.06         8.35         8.25        17.16        16.18        20.48 
TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E 
        4.67        12.82         9.96        17.56        28.70        24.26 
TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-C4-A0F6 TCGA-C4-A0F7 
       28.41         8.98         1.94         2.93        23.01         2.04 
TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V 
        0.46         0.43         0.69        10.95        12.66        12.46 
TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 
       12.10        12.62        12.26        13.12        12.00        12.10 
TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ 
       11.87        13.08        12.92         4.90         7.20         5.46 
TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 
        5.19        16.31         1.84        13.58        21.86         2.14 
TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD 
       66.41        18.41        19.00        16.70       130.88       112.44 
TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 
       16.14        17.62        15.62         1.81        10.59         7.79 
TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ 
       87.32         2.20        13.58         7.82         8.22        17.72 
TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX 
       50.27        21.30        23.21         9.67        20.81        10.55 
TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 
      140.81        48.00        17.98        64.18        41.56        76.60 
TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6P 
       67.36        15.68        41.06        30.67        38.24        15.02 
TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA74 
      166.03        12.36         8.65         7.53        13.64        43.50 
TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 
       12.03        10.62        43.59        15.35        38.83        24.66 
TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF 
        0.49         2.24        16.70        17.39         0.56         0.66 
TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7DV 
       14.56        13.97        12.99        14.33         0.92         1.22 
TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B3 
       13.68        14.07        12.95        14.37         8.09        32.02 
TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 
       16.77         8.94        33.04         4.01        12.62        22.52 
TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN 
       27.98        60.66        24.30        23.41        17.98        29.16 
TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N 
        5.52        25.74        46.78        19.79        12.85        22.98 
TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS 
       27.35        14.96        20.91         3.62        26.73        53.88 
TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ 
       11.01        19.33         5.36         5.69         8.25        27.45 
TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S 
       18.08        58.92         2.70         7.10         6.28        13.35 
TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF 
       62.86        18.81         6.15        12.69        12.36         2.27 
TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 
        3.06         4.31         9.67        10.85        31.07         7.13 
TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FJ-A871 TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EC 
       10.65        17.23         8.94         3.25         6.48        22.88 
TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES 
       61.94        30.61        15.95        26.93        35.24        33.01 
TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3D TCGA-G2-AA3F 
        7.23        20.12        66.02         6.94        64.44        19.46 
TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD 
       21.40         2.24        15.81         4.50        15.91        14.07 
TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP 
       17.75        24.92         8.94        13.91         7.73         2.10 
TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42Q 
        3.12        20.98         2.20         7.36        10.92        11.31 
TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 
       11.31         7.63        27.09        20.05         5.62         4.73 
TCGA-GU-AATO TCGA-GU-AATP TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX 
       10.65        32.98         7.00        14.27        21.34        19.10 
TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E 
       19.82        20.28         8.48        10.59        27.35         8.58 
TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF 
       19.07        22.72         1.51        19.40        38.60         3.06 
TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB 
        9.01         8.22        25.02         3.45        21.24         2.76 
TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ 
        9.14        27.68         9.07        11.70         1.74         1.81 
TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V 
       15.42         6.38        11.80        15.32        15.58        13.48 
TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 TCGA-SY-A9G0 
       12.23        16.67        14.24         1.84         3.75        12.43 
TCGA-SY-A9G5 TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A9PA 
       31.56        37.05        22.68        76.01        65.75        35.24 
TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HH TCGA-XF-A8HI 
       29.56        17.82         4.54         1.64         1.87        17.88 
TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SL TCGA-XF-A9SV 
       48.62        64.80        79.66         3.22        66.41        12.76 
TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T3 
       11.90        23.64        21.04        28.24        26.27         2.24 
TCGA-XF-A9T4 TCGA-XF-A9T6 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMG TCGA-XF-AAMH 
       16.27         2.10        92.98        10.82       110.60        11.31 
TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMW 
       54.90         7.63        71.57        91.73         2.96         8.32 
TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 
       98.99        44.32        56.48        30.94        61.45        86.30 
TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YC-A9TC 
       27.06        75.39        18.81         3.88         9.63         0.66 
TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R3 
       11.97        13.64        18.64         7.36        21.11        24.13 
TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RE 
       30.28        27.19        21.86        28.41        74.56         3.48 
TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N 
       52.73        52.60        82.49        47.84        20.22         2.89 
TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA4X 
       34.06        19.69         8.61        59.38        60.16        63.02 
TCGA-ZF-AA52 TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H 
       35.41        57.90        19.40         8.52        47.15        19.17 
TCGA-ZF-AA5N TCGA-ZF-AA5P 
        5.52        10.13 

  DDX3X MUTATED DDX3X WILD-TYPE 
           0.10            0.43 
  DDX3X MUTATED DDX3X WILD-TYPE 
         123.85          166.03 
  DDX3X MUTATED DDX3X WILD-TYPE 
          15.68           15.65 
[1] "0.1 - 123.8 (15.7)" "0.4 - 166.0 (15.6)"
[1] "hr=" "1.2"
D90V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  DDX3X MUTATED         1        3         5        5
  DDX3X WILD-TYPE       3      114       117      123
D90V3, multiclass
           clus
vv          DDX3X MUTATED DDX3X WILD-TYPE
  STAGE I               1               3
  STAGE II              3             114
  STAGE III             5             117
  STAGE IV              5             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"
                 vv
clus              T0+T1+T2  T3  T4
  DDX3X MUTATED          2   8   0
  DDX3X WILD-TYPE      112 171  52
D90V4, multiclass
          clus
vv         DDX3X MUTATED DDX3X WILD-TYPE
  T0+T1+T2             2             112
  T3                   8             171
  T4                   0              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"
                 vv
clus               N0  N1  N2  N3
  DDX3X MUTATED     7   3   2   0
  DDX3X WILD-TYPE 206  38  73   8
D90V5, multiclass
    clus
vv   DDX3X MUTATED DDX3X WILD-TYPE
  N0             7             206
  N1             3              38
  N2             2              73
  N3             0               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"
D90V6, binary
                 cls
clus                0   1
  DDX3X MUTATED     6   0
  DDX3X WILD-TYPE 176  10
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX3X MUTATED      6    0
  DDX3X WILD-TYPE  176   10
   clus
vv  DDX3X MUTATED DDX3X WILD-TYPE
  0             6             176
  1             0              10
[1] 2 2
[1] FALSE
D90V7, binary
                 cls
clus                0   1
  DDX3X MUTATED     6   8
  DDX3X WILD-TYPE  90 272
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX3X MUTATED      6    8
  DDX3X WILD-TYPE   90  272
        clus
vv       DDX3X MUTATED DDX3X WILD-TYPE
  FEMALE             6              90
  MALE               8             272
[1] 2 2
[1] FALSE
D90V8, continuous
D90V9, continuous
D90V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DDX3X MUTATED       1                         1    12
  DDX3X WILD-TYPE    37                        20   289
D90V11, multiclass
                           clus
vv                          DDX3X MUTATED DDX3X WILD-TYPE
  ASIAN                                 1              37
  BLACK OR AFRICAN AMERICAN             1              20
  WHITE                                12             289
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D90V12, binary
                 cls
clus                0   1
  DDX3X MUTATED     0  14
  DDX3X WILD-TYPE   8 324
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX3X MUTATED      0   14
  DDX3X WILD-TYPE    8  324
                        clus
vv                       DDX3X MUTATED DDX3X WILD-TYPE
  HISPANIC OR LATINO                 0               8
  NOT HISPANIC OR LATINO            14             324
[1] 2 2
[1] FALSE

Clustering(91) Variable = DGKG MUTATION ANALYSIS
D91V1, survival
                sevent
clus2              0   1
  DGKG MUTATED     9   3
  DGKG WILD-TYPE 210 148
  DGKG MUTATED DGKG WILD-TYPE 
            12            358 
  DGKG MUTATED DGKG WILD-TYPE 
             3            148 
$`DGKG MUTATED`
TCGA-2F-A9KW TCGA-BT-A3PK TCGA-CU-A3KJ TCGA-DK-A6AW TCGA-FD-A62N TCGA-G2-A2EO 
        8.35         9.96         5.46        41.56         2.70        35.24 
TCGA-G2-AA3B TCGA-GV-A3JX TCGA-K4-A5RJ TCGA-UY-A78K TCGA-XF-A9T0 TCGA-ZF-AA4X 
       66.02        19.10         1.74        17.62        26.27        63.02 

$`DGKG WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-4Z-AA7M 
       22.29        11.97        91.63       103.50       105.70        16.27 
TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7W 
       44.94        16.83        16.77        17.16        34.98        27.62 
TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA84 
       49.12         0.62        41.75        51.16        66.54        15.12 
TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J 
       10.22        47.80        33.83        40.08         7.33         2.66 
TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N 
        6.74        12.39         6.58        13.15        19.04        32.84 
TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U 
       12.16        17.88        19.50         5.06        14.89        14.96 
TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A2LD 
        5.06         8.35         8.25        17.16        16.18        20.48 
TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E TCGA-BT-A42F 
        4.67        12.82        17.56        28.70        24.26        28.41 
TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-C4-A0F6 TCGA-C4-A0F7 TCGA-CF-A1HR 
        8.98         1.94         2.93        23.01         2.04         0.46 
TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W 
        0.43         0.69        10.95        12.66        12.46        12.10 
TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A9FF 
       12.62        12.26        13.12        12.00        12.10        11.87 
TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3QU TCGA-CU-A3YL 
       13.08        12.92         4.90         7.20         5.19        16.31 
TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 
        1.84        13.58        21.86         2.14        66.41        18.41 
TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF 
       19.00        16.70       130.88       112.44        16.14        17.62 
TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A2I6 
       15.62         1.81        10.59         7.79       123.85        87.32 
TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS 
        2.20        13.58         7.82         8.22        17.72        50.27 
TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY 
       21.30        23.21         9.67        20.81        10.55       140.81 
TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 
       48.00        17.98        64.18        76.60        67.36        15.68 
TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6S 
       41.06        30.67        38.24        15.02        13.58       166.03 
TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA74 
       12.36        10.49         8.65         7.53        13.64        43.50 
TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 
       12.03        10.62        43.59        15.35        38.83        24.66 
TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KE 
        0.10         0.49         2.24        16.70        17.39         0.56 
TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DU 
        0.66        14.56        13.97        12.99        14.33         0.92 
TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A97P TCGA-E7-A97Q 
        1.22        13.68        14.07        12.95        14.37         8.09 
TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 
       32.02        16.77         8.94        33.04         4.01        12.62 
TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM 
       22.52        27.98        60.66        24.30        23.41        17.98 
TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS 
       29.16         5.52        25.74        46.78        19.79        12.85 
TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BR 
       22.98        27.35        14.96        20.91         3.62        26.73 
TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY 
       53.88        11.01        19.33         5.36         5.69         8.25 
TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S 
       27.45        18.08        58.92         7.10         6.28        13.35 
TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF 
       62.86        18.81         6.15        12.69        12.36         2.27 
TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 
        3.06         4.31         9.67        10.85        31.07         7.13 
TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FJ-A871 TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EC 
       10.65        17.23         8.94         3.25         6.48        22.88 
TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2ES TCGA-G2-A3IB 
       61.94        30.61        15.95        26.93        33.01         7.23 
TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3C TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3BM 
       20.12        17.62         6.94        64.44        19.46        21.40 
TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC 
        2.24        15.81         4.50        15.91        14.07        17.75 
TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ 
       24.92         8.94        13.91         7.73         2.10         3.12 
TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R 
       20.98         2.20         7.36        10.92        11.31        11.31 
TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATO 
        7.63        27.09        20.05         5.62         4.73        10.65 
TCGA-GU-AATP TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JZ TCGA-GV-A3QF 
       32.98         7.00        14.27        21.34        19.82        20.28 
TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA 
        8.48        10.59        27.35         8.58        19.07        22.72 
TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE 
        1.51        19.40        38.60         3.06         9.01         8.22 
TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R 
       25.02         3.45        21.24         2.76         9.14        27.68 
TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO 
        9.07        11.70         1.81        15.42         6.38        11.80 
TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X 
       15.32        15.58        13.48        12.23        16.67        14.24 
TCGA-S5-A6DX TCGA-S5-AA26 TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78L TCGA-UY-A78M 
        1.84         3.75        12.43        31.56        37.05        22.68 
TCGA-UY-A78N TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD 
       86.83        76.01        65.75        35.24        29.56        17.82 
TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH 
        4.54         1.64         1.87        17.88        48.62        64.80 
TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SL TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SX 
       79.66         3.22        66.41        12.76        11.90        23.64 
TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T5 
       21.04        28.24        18.90         2.24        16.27        66.64 
TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMG TCGA-XF-AAMH 
        2.10        13.74        92.98        10.82       110.60        11.31 
TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMW 
       54.90         7.63        71.57        91.73         2.96         8.32 
TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN2 
        6.77        98.99        44.32        56.48        30.94        61.45 
TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 
       86.30        27.06        75.39        18.81         3.88         9.63 
TCGA-YC-A9TC TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R2 
        0.66        11.97        13.64        18.64         7.36        21.11 
TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RC 
       24.13        30.28        27.19        21.86        28.41        74.56 
TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-A9RM 
       13.41         3.48        52.73        52.60        82.49        47.84 
TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4U TCGA-ZF-AA4V 
       20.22         2.89        34.06        19.69         8.61        59.38 
TCGA-ZF-AA4W TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA56 
       60.16        38.73        35.41        57.90        19.40         8.52 
TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-ZF-AA5P 
       47.15        19.17         5.52        10.13 

  DGKG MUTATED DGKG WILD-TYPE 
          1.74           0.10 
  DGKG MUTATED DGKG WILD-TYPE 
         66.02         166.03 
  DGKG MUTATED DGKG WILD-TYPE 
         18.36          15.60 
[1] "1.7 - 66.0 (18.4)"  "0.1 - 166.0 (15.6)"
[1] "hr=" "1.8"
D91V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  DGKG MUTATED         0        5         6        1
  DGKG WILD-TYPE       4      112       116      127
D91V3, multiclass
           clus
vv          DGKG MUTATED DGKG WILD-TYPE
  STAGE I              0              4
  STAGE II             5            112
  STAGE III            6            116
  STAGE IV             1            127
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1+T2  T3  T4
  DGKG MUTATED          5   6   0
  DGKG WILD-TYPE      109 173  52
D91V4, multiclass
          clus
vv         DGKG MUTATED DGKG WILD-TYPE
  T0+T1+T2            5            109
  T3                  6            173
  T4                  0             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"
                vv
clus              N0  N1  N2  N3
  DGKG MUTATED    10   0   1   0
  DGKG WILD-TYPE 203  41  74   8
D91V5, multiclass
    clus
vv   DGKG MUTATED DGKG WILD-TYPE
  N0           10            203
  N1            0             41
  N2            1             74
  N3            0              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"
D91V6, binary
                cls
clus               0   1
  DGKG MUTATED     5   0
  DGKG WILD-TYPE 177  10
[1] "tbl2"
                cls
clus             [,1] [,2]
  DGKG MUTATED      5    0
  DGKG WILD-TYPE  177   10
   clus
vv  DGKG MUTATED DGKG WILD-TYPE
  0            5            177
  1            0             10
[1] 2 2
[1] FALSE
D91V7, binary
                cls
clus               0   1
  DGKG MUTATED     2  10
  DGKG WILD-TYPE  94 270
[1] "tbl2"
                cls
clus             [,1] [,2]
  DGKG MUTATED      2   10
  DGKG WILD-TYPE   94  270
        clus
vv       DGKG MUTATED DGKG WILD-TYPE
  FEMALE            2             94
  MALE             10            270
[1] 2 2
[1] FALSE
D91V8, continuous
D91V9, continuous
D91V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DGKG MUTATED       1                         0    11
  DGKG WILD-TYPE    37                        21   290
D91V11, multiclass
                           clus
vv                          DGKG MUTATED DGKG WILD-TYPE
  ASIAN                                1             37
  BLACK OR AFRICAN AMERICAN            0             21
  WHITE                               11            290
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D91V12, binary
                cls
clus               0   1
  DGKG MUTATED     0  12
  DGKG WILD-TYPE   8 326
[1] "tbl2"
                cls
clus             [,1] [,2]
  DGKG MUTATED      0   12
  DGKG WILD-TYPE    8  326
                        clus
vv                       DGKG MUTATED DGKG WILD-TYPE
  HISPANIC OR LATINO                0              8
  NOT HISPANIC OR LATINO           12            326
[1] 2 2
[1] FALSE

Clustering(92) Variable = TAS2R9 MUTATION ANALYSIS
D92V1, survival
                  sevent
clus2                0   1
  TAS2R9 MUTATED     4   1
  TAS2R9 WILD-TYPE 215 150
  TAS2R9 MUTATED TAS2R9 WILD-TYPE 
               5              365 
  TAS2R9 MUTATED TAS2R9 WILD-TYPE 
               1              150 
$`TAS2R9 MUTATED`
TCGA-DK-A1AF TCGA-FJ-A3ZE TCGA-GV-A3JX TCGA-UY-A9PB TCGA-ZF-AA4X 
       17.62        10.65        19.10        29.56        63.02 

$`TAS2R9 WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        91.63       103.50       105.70         8.35 
TCGA-4Z-AA7M TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7S 
       16.27        44.94        16.83        16.77        17.16        34.98 
TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 
       27.62        49.12         0.62        41.75        51.16        66.54 
TCGA-4Z-AA84 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BL-A13I 
       15.12        10.22        47.80        33.83        40.08         7.33 
TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J 
        2.66         6.74        12.39         6.58        13.15        19.04 
TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T 
       32.84        12.16        17.88        19.50         5.06        14.89 
TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB 
       14.96         5.06         8.35         8.25        17.16        16.18 
TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C 
       20.48         4.67        12.82         9.96        17.56        28.70 
TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-C4-A0F6 
       24.26        28.41         8.98         1.94         2.93        23.01 
TCGA-C4-A0F7 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T 
        2.04         0.46         0.43         0.69        10.95        12.66 
TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA 
       12.46        12.10        12.62        12.26        13.12        12.00 
TCGA-CF-A7I0 TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR 
       12.10        11.87        13.08        12.92         4.90         7.20 
TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 
        5.46         5.19        16.31         1.84        13.58        21.86 
TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC 
        2.14        66.41        18.41        19.00        16.70       130.88 
TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 
      112.44        16.14        15.62         1.81        10.59         7.79 
TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN 
      123.85        87.32         2.20        13.58         7.82         8.22 
TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW 
       17.72        50.27        21.30        23.21         9.67        20.81 
TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW 
       10.55       140.81        48.00        17.98        64.18        41.56 
TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L 
       76.60        67.36        15.68        41.06        30.67        38.24 
TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6W 
       15.02        13.58       166.03        12.36        10.49         8.65 
TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A2PC 
        7.53        13.64        43.50        12.03        10.62        43.59 
TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ 
       15.35        38.83        24.66         0.10         0.49         2.24 
TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 
       16.70        17.39         0.56         0.66        14.56        13.97 
TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A7XN 
       12.99        14.33         0.92         1.22        13.68        14.07 
TCGA-E7-A85H TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 
       12.95        14.37         8.09        32.02        16.77         8.94 
TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA 
       33.04         4.01        12.62        22.52        27.98        60.66 
TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP 
       24.30        23.41        17.98        29.16         5.52        25.74 
TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S 
       46.78        19.79        12.85        22.98        27.35        14.96 
TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU 
       20.91         3.62        26.73        53.88        11.01        19.33 
TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 
        5.36         5.69         8.25        27.45        18.08        58.92 
TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB 
        2.70         7.10         6.28        13.35        62.86        18.81 
TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH 
        6.15        12.69        12.36         2.27         3.06         4.31 
TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZF TCGA-FJ-A871 
        9.67        10.85        31.07         7.13        17.23         8.94 
TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EC TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK 
        3.25         6.48        22.88        61.94        30.61        15.95 
TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY 
       26.93        35.24        33.01         7.23        20.12        17.62 
TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 
       66.02         6.94        64.44        19.46        21.40         2.24 
TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS 
       15.81         4.50        15.91        14.07        17.75        24.92 
TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS 
        8.94        13.91         7.73         2.10         3.12        20.98 
TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 
        2.20         7.36        10.92        11.31        11.31         7.63 
TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATO TCGA-GU-AATP 
       27.09        20.05         5.62         4.73        10.65        32.98 
TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH 
        7.00        14.27        21.34        19.82        20.28         8.48 
TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO 
       10.59        27.35         8.58        19.07        22.72         1.51 
TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS 
       19.40        38.60         3.06         9.01         8.22        25.02 
TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RH 
        3.45        21.24         2.76         9.14        27.68         9.07 
TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO 
       11.70         1.74         1.81        15.42         6.38        11.80 
TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X 
       15.32        15.58        13.48        12.23        16.67        14.24 
TCGA-S5-A6DX TCGA-S5-AA26 TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L 
        1.84         3.75        12.43        31.56        17.62        37.05 
TCGA-UY-A78M TCGA-UY-A78N TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A9PA TCGA-UY-A9PD 
       22.68        86.83        76.01        65.75        35.24        17.82 
TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH 
        4.54         1.64         1.87        17.88        48.62        64.80 
TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SL TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SX 
       79.66         3.22        66.41        12.76        11.90        23.64 
TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 
       21.04        28.24        26.27        18.90         2.24        16.27 
TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMG 
       66.64         2.10        13.74        92.98        10.82       110.60 
TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMT 
       11.31        54.90         7.63        71.57        91.73         2.96 
TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN0 TCGA-XF-AAN1 
        8.32         6.77        98.99        44.32        56.48        30.94 
TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN7 TCGA-XF-AAN8 
       61.45        86.30        27.06        75.39        18.81         3.88 
TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R0 TCGA-ZF-A9R1 
        9.63         0.66        11.97        13.64        18.64         7.36 
TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 
       21.11        24.13        30.28        27.19        21.86        28.41 
TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RL 
       74.56        13.41         3.48        52.73        52.60        82.49 
TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4U 
       47.84        20.22         2.89        34.06        19.69         8.61 
TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA53 TCGA-ZF-AA54 
       59.38        60.16        38.73        35.41        57.90        19.40 
TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-ZF-AA5P 
        8.52        47.15        19.17         5.52        10.13 

  TAS2R9 MUTATED TAS2R9 WILD-TYPE 
           10.65             0.10 
  TAS2R9 MUTATED TAS2R9 WILD-TYPE 
           63.02           166.03 
  TAS2R9 MUTATED TAS2R9 WILD-TYPE 
           19.10            15.58 
[1] "10.7 - 63.0 (19.1)" "0.1 - 166.0 (15.6)"
[1] "hr=" "2.6"
D92V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  TAS2R9 MUTATED         0        1         2        2
  TAS2R9 WILD-TYPE       4      116       120      126
D92V3, multiclass
           clus
vv          TAS2R9 MUTATED TAS2R9 WILD-TYPE
  STAGE I                0                4
  STAGE II               1              116
  STAGE III              2              120
  STAGE IV               2              126
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1+T2  T3  T4
  TAS2R9 MUTATED          1   3   0
  TAS2R9 WILD-TYPE      113 176  52
D92V4, multiclass
          clus
vv         TAS2R9 MUTATED TAS2R9 WILD-TYPE
  T0+T1+T2              1              113
  T3                    3              176
  T4                    0               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"
                  vv
clus                N0  N1  N2  N3
  TAS2R9 MUTATED     2   0   1   1
  TAS2R9 WILD-TYPE 211  41  74   7
D92V5, multiclass
    clus
vv   TAS2R9 MUTATED TAS2R9 WILD-TYPE
  N0              2              211
  N1              0               41
  N2              1               74
  N3              1                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"
D92V6, binary
                  cls
clus                 0   1
  TAS2R9 MUTATED     2   1
  TAS2R9 WILD-TYPE 180   9
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TAS2R9 MUTATED      2    1
  TAS2R9 WILD-TYPE  180    9
   clus
vv  TAS2R9 MUTATED TAS2R9 WILD-TYPE
  0              2              180
  1              1                9
[1] 2 2
[1] FALSE
D92V7, binary
                  cls
clus                 0   1
  TAS2R9 MUTATED     1   4
  TAS2R9 WILD-TYPE  95 276
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TAS2R9 MUTATED      1    4
  TAS2R9 WILD-TYPE   95  276
        clus
vv       TAS2R9 MUTATED TAS2R9 WILD-TYPE
  FEMALE              1               95
  MALE                4              276
[1] 2 2
[1] FALSE
D92V8, continuous
[1] "Remove cluster labels:" "TAS2R9 MUTATED"        
clus
  TAS2R9 MUTATED TAS2R9 WILD-TYPE 
               1              119 
      TCGA-2F-A9KO       TCGA-2F-A9KP       TCGA-2F-A9KQ       TCGA-2F-A9KR 
"TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" 
      TCGA-2F-A9KT       TCGA-2F-A9KW       TCGA-CF-A1HS       TCGA-CF-A27C 
"TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" 
      TCGA-CF-A3MF       TCGA-CF-A3MG       TCGA-CF-A3MH       TCGA-CF-A3MI 
"TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" 
      TCGA-CF-A47S       TCGA-CF-A47T       TCGA-CF-A47V       TCGA-CF-A47W 
"TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" 
      TCGA-CF-A47X       TCGA-CF-A47Y       TCGA-CF-A5U8       TCGA-CF-A5UA 
"TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" 
      TCGA-CF-A7I0       TCGA-DK-A2HX       TCGA-DK-A3IN       TCGA-DK-A3IV 
"TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" 
      TCGA-DK-A3WX       TCGA-DK-A3X2       TCGA-DK-A6B2       TCGA-DK-A6B5 
"TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" 
      TCGA-DK-A6B6       TCGA-DK-AA6P       TCGA-DK-AA6S       TCGA-DK-AA6U 
"TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" 
      TCGA-DK-AA6W       TCGA-DK-AA76       TCGA-E5-A2PC       TCGA-E5-A4TZ 
"TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" 
      TCGA-E5-A4U1       TCGA-E7-A519       TCGA-E7-A541       TCGA-E7-A7DU 
"TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" 
      TCGA-E7-A7DV       TCGA-FT-A61P       TCGA-G2-A2EC       TCGA-G2-A2EF 
"TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" 
      TCGA-G2-A2EJ       TCGA-G2-A2EK       TCGA-G2-A2EL       TCGA-G2-A2EO 
"TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" 
      TCGA-G2-A2ES       TCGA-G2-A3IB       TCGA-G2-A3IE       TCGA-G2-A3VY 
"TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" 
      TCGA-GC-A3BM       TCGA-GC-A3I6       TCGA-GC-A3OO       TCGA-GC-A3RC 
"TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" 
      TCGA-GC-A3RD       TCGA-GC-A3YS       TCGA-GC-A6I1       TCGA-GC-A6I3 
"TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" 
      TCGA-GD-A3OS       TCGA-GD-A6C6       TCGA-GV-A3JV       TCGA-GV-A3JW 
"TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" 
      TCGA-GV-A3JZ       TCGA-GV-A3QF       TCGA-GV-A3QH       TCGA-GV-A3QI 
"TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" 
      TCGA-GV-A3QK       TCGA-GV-A40E       TCGA-GV-A40G       TCGA-GV-A6ZA 
"TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" 
      TCGA-SY-A9G0       TCGA-SY-A9G5       TCGA-UY-A78L       TCGA-UY-A78M 
"TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" 
      TCGA-UY-A78N       TCGA-XF-A8HH       TCGA-XF-A8HI       TCGA-XF-A9SG 
"TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" 
      TCGA-XF-A9SH       TCGA-XF-A9SI       TCGA-XF-A9SJ       TCGA-XF-A9SL 
"TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" 
      TCGA-XF-A9SV       TCGA-XF-A9SW       TCGA-XF-A9SX       TCGA-XF-A9SY 
"TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" 
      TCGA-XF-A9SZ       TCGA-XF-A9T0       TCGA-XF-A9T2       TCGA-XF-A9T3 
"TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" 
      TCGA-XF-A9T4       TCGA-XF-A9T5       TCGA-XF-A9T6       TCGA-XF-A9T8 
"TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" 
      TCGA-XF-AAME       TCGA-XF-AAMF       TCGA-XF-AAMG       TCGA-XF-AAMH 
"TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" 
      TCGA-XF-AAMJ       TCGA-XF-AAML       TCGA-XF-AAMQ       TCGA-XF-AAMR 
"TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" 
      TCGA-XF-AAMT       TCGA-XF-AAMW       TCGA-XF-AAMX       TCGA-XF-AAMY 
"TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" 
      TCGA-XF-AAMZ       TCGA-XF-AAN0       TCGA-XF-AAN1       TCGA-XF-AAN2 
"TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" 
      TCGA-XF-AAN3       TCGA-XF-AAN4       TCGA-XF-AAN5       TCGA-XF-AAN7 
"TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" 
      TCGA-XF-AAN8       TCGA-YF-AA3L       TCGA-YF-AA3M 
"TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" 
D92V9, continuous
D92V10, continuous
[1] "Remove cluster labels:" "TAS2R9 MUTATED"        
clus
  TAS2R9 MUTATED TAS2R9 WILD-TYPE 
               2              273 
      TCGA-2F-A9KO       TCGA-2F-A9KP       TCGA-2F-A9KQ       TCGA-2F-A9KR 
"TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" 
      TCGA-2F-A9KT       TCGA-2F-A9KW       TCGA-4Z-AA7N       TCGA-4Z-AA7O 
"TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" 
      TCGA-4Z-AA7R       TCGA-4Z-AA7S       TCGA-4Z-AA7W       TCGA-4Z-AA7Y 
"TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" 
      TCGA-4Z-AA80       TCGA-4Z-AA81       TCGA-4Z-AA82       TCGA-4Z-AA84 
"TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" 
      TCGA-4Z-AA86       TCGA-4Z-AA87       TCGA-4Z-AA89       TCGA-BL-A0C8 
"TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" 
      TCGA-BL-A13I       TCGA-BL-A13J       TCGA-BL-A3JM       TCGA-BT-A0S7 
"TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" 
      TCGA-BT-A0YX       TCGA-BT-A20J       TCGA-BT-A20N       TCGA-BT-A20O 
"TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" 
      TCGA-BT-A20P       TCGA-BT-A20Q       TCGA-BT-A20T       TCGA-BT-A20V 
"TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" 
      TCGA-BT-A20W       TCGA-BT-A20X       TCGA-BT-A2LA       TCGA-BT-A2LB 
"TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" 
      TCGA-BT-A2LD       TCGA-BT-A3PH       TCGA-BT-A3PJ       TCGA-BT-A3PK 
"TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" 
      TCGA-BT-A42B       TCGA-BT-A42C       TCGA-BT-A42E       TCGA-BT-A42F 
"TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" 
      TCGA-CU-A0YN       TCGA-CU-A0YO       TCGA-CU-A0YR       TCGA-CU-A3KJ 
"TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" 
      TCGA-CU-A3QU       TCGA-CU-A3YL       TCGA-CU-A5W6       TCGA-CU-A72E 
"TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" 
      TCGA-DK-A1A3       TCGA-DK-A1A5       TCGA-DK-A1A6       TCGA-DK-A1A7 
"TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" 
      TCGA-DK-A1AA       TCGA-DK-A1AB       TCGA-DK-A1AC       TCGA-DK-A1AD 
"TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" 
      TCGA-DK-A1AE       TCGA-DK-A1AG       TCGA-DK-A2HX       TCGA-DK-A2I1 
"TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" 
      TCGA-DK-A2I2       TCGA-DK-A2I4       TCGA-DK-A2I6       TCGA-DK-A3IK 
"TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" 
      TCGA-DK-A3IL       TCGA-DK-A3IM       TCGA-DK-A3IN       TCGA-DK-A3IQ 
"TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" 
      TCGA-DK-A3IS       TCGA-DK-A3IT       TCGA-DK-A3IU       TCGA-DK-A3WW 
"TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" 
      TCGA-DK-A3WX       TCGA-DK-A3WY       TCGA-DK-A3X1       TCGA-DK-A3X2 
"TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" 
      TCGA-DK-A6AV       TCGA-DK-A6AW       TCGA-DK-A6B0       TCGA-DK-A6B1 
"TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" 
      TCGA-DK-A6B2       TCGA-DK-A6B5       TCGA-DK-AA6L       TCGA-DK-AA6Q 
"TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" 
      TCGA-DK-AA6S       TCGA-DK-AA71       TCGA-DK-AA77       TCGA-E5-A2PC 
"TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" 
      TCGA-E5-A4TZ       TCGA-E5-A4U1       TCGA-E7-A541       TCGA-E7-A7DU 
"TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" 
      TCGA-E7-A7DV       TCGA-E7-A85H       TCGA-E7-A97Q       TCGA-FD-A3B3 
"TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" 
      TCGA-FD-A3B4       TCGA-FD-A3B5       TCGA-FD-A3B6       TCGA-FD-A3B7 
"TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" 
      TCGA-FD-A3B8       TCGA-FD-A3N5       TCGA-FD-A3N6       TCGA-FD-A3NA 
"TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" 
      TCGA-FD-A3SJ       TCGA-FD-A3SL       TCGA-FD-A3SM       TCGA-FD-A3SN 
"TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" 
      TCGA-FD-A3SO       TCGA-FD-A3SP       TCGA-FD-A3SQ       TCGA-FD-A3SR 
"TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" 
      TCGA-FD-A3SS       TCGA-FD-A43N       TCGA-FD-A43P       TCGA-FD-A43S 
"TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" 
      TCGA-FD-A43U       TCGA-FD-A43X       TCGA-FD-A5BR       TCGA-FD-A5BS 
"TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" 
      TCGA-FD-A5BT       TCGA-FD-A5BU       TCGA-FD-A5BV       TCGA-FD-A5BX 
"TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" 
      TCGA-FD-A5BY       TCGA-FD-A5BZ       TCGA-FD-A5C0       TCGA-FD-A5C1 
"TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" 
      TCGA-FD-A62N       TCGA-FD-A62O       TCGA-FD-A62P       TCGA-FD-A62S 
"TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" 
      TCGA-FD-A6TA       TCGA-FD-A6TB       TCGA-FD-A6TC       TCGA-FD-A6TD 
"TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" 
      TCGA-FD-A6TE       TCGA-FD-A6TF       TCGA-FD-A6TG       TCGA-FD-A6TH 
"TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" 
      TCGA-FD-A6TI       TCGA-FD-A6TK       TCGA-FJ-A3Z7       TCGA-FJ-A3Z9 
"TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" 
      TCGA-FT-A3EE       TCGA-FT-A61P       TCGA-G2-AA3B       TCGA-G2-AA3C 
"TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" 
      TCGA-G2-AA3D       TCGA-G2-AA3F       TCGA-GC-A3BM       TCGA-GC-A3I6 
"TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" 
      TCGA-GC-A3OO       TCGA-GC-A3RB       TCGA-GC-A3RC       TCGA-GC-A3RD 
"TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" 
      TCGA-GC-A3WC       TCGA-GC-A3YS       TCGA-GC-A6I1       TCGA-GC-A6I3 
"TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" 
      TCGA-GD-A2C5       TCGA-GD-A3OP       TCGA-GD-A3OQ       TCGA-GD-A6C6 
"TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" 
      TCGA-GD-A76B       TCGA-GU-A42P       TCGA-GU-A42Q       TCGA-GU-A42R 
"TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" 
      TCGA-GU-A762       TCGA-GU-A763       TCGA-GU-A764       TCGA-GU-A766 
"TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" 
      TCGA-GU-A767       TCGA-GU-AATO       TCGA-GU-AATP       TCGA-GU-AATQ 
"TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" 
      TCGA-GV-A3JV       TCGA-GV-A3JZ       TCGA-GV-A3QF       TCGA-GV-A3QG 
"TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" 
      TCGA-GV-A3QI       TCGA-GV-A3QK       TCGA-GV-A40G       TCGA-H4-A2HO 
"TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" 
      TCGA-HQ-A2OF       TCGA-HQ-A5ND       TCGA-HQ-A5NE       TCGA-K4-A3WS 
"TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" 
      TCGA-K4-A3WV       TCGA-K4-A4AB       TCGA-K4-A4AC       TCGA-K4-A54R 
"TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" 
      TCGA-K4-A5RH       TCGA-K4-A5RI       TCGA-K4-A5RJ       TCGA-K4-A6FZ 
"TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" 
      TCGA-K4-A6MB       TCGA-K4-A83P       TCGA-LC-A66R       TCGA-MV-A51V 
"TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" 
      TCGA-PQ-A6FI       TCGA-PQ-A6FN       TCGA-R3-A69X       TCGA-S5-A6DX 
"TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" 
      TCGA-S5-AA26       TCGA-SY-A9G0       TCGA-SY-A9G5       TCGA-UY-A78K 
"TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" 
      TCGA-UY-A78L       TCGA-UY-A78N       TCGA-UY-A78O       TCGA-XF-A8HH 
"TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" 
      TCGA-XF-A8HI       TCGA-XF-A9SG       TCGA-XF-A9SH       TCGA-XF-A9SI 
"TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" 
      TCGA-XF-A9SJ       TCGA-XF-A9SL       TCGA-XF-A9SV       TCGA-XF-A9SW 
"TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" 
      TCGA-XF-A9SX       TCGA-XF-A9SY       TCGA-XF-A9SZ       TCGA-XF-A9T0 
"TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" 
      TCGA-XF-A9T2       TCGA-XF-A9T3       TCGA-XF-A9T4       TCGA-XF-A9T5 
"TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" 
      TCGA-XF-A9T6       TCGA-XF-A9T8       TCGA-XF-AAME       TCGA-XF-AAMF 
"TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" 
      TCGA-XF-AAMG       TCGA-XF-AAMH       TCGA-XF-AAMJ       TCGA-XF-AAML 
"TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" 
      TCGA-XF-AAMQ       TCGA-XF-AAMR       TCGA-XF-AAMT       TCGA-XF-AAMW 
"TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" 
      TCGA-XF-AAMX       TCGA-XF-AAMY       TCGA-XF-AAMZ       TCGA-XF-AAN0 
"TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" 
      TCGA-XF-AAN1       TCGA-XF-AAN2       TCGA-XF-AAN3       TCGA-XF-AAN4 
"TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" 
      TCGA-XF-AAN5       TCGA-XF-AAN7       TCGA-XF-AAN8       TCGA-YC-A8S6 
"TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" 
      TCGA-YF-AA3L       TCGA-ZF-A9R1       TCGA-ZF-A9R2       TCGA-ZF-A9R5 
"TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" 
      TCGA-ZF-A9R9       TCGA-ZF-A9RC       TCGA-ZF-A9RD       TCGA-ZF-A9RG 
"TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" 
      TCGA-ZF-A9RM       TCGA-ZF-AA4R       TCGA-ZF-AA4T       TCGA-ZF-AA4V 
"TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" 
      TCGA-ZF-AA4W       TCGA-ZF-AA56       TCGA-ZF-AA58       TCGA-ZF-AA5H 
"TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" "TAS2R9 WILD-TYPE" 
      TCGA-ZF-AA5P 
"TAS2R9 WILD-TYPE" 
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TAS2R9 MUTATED       0                         0     5
  TAS2R9 WILD-TYPE    38                        21   296
D92V11, multiclass
                           clus
vv                          TAS2R9 MUTATED TAS2R9 WILD-TYPE
  ASIAN                                  0               38
  BLACK OR AFRICAN AMERICAN              0               21
  WHITE                                  5              296
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D92V12, binary
                  cls
clus                 0   1
  TAS2R9 MUTATED     0   5
  TAS2R9 WILD-TYPE   8 333
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TAS2R9 MUTATED      0    5
  TAS2R9 WILD-TYPE    8  333
                        clus
vv                       TAS2R9 MUTATED TAS2R9 WILD-TYPE
  HISPANIC OR LATINO                  0                8
  NOT HISPANIC OR LATINO              5              333
[1] 2 2
[1] FALSE

Clustering(93) Variable = COL7A1 MUTATION ANALYSIS
D93V1, survival
                  sevent
clus2                0   1
  COL7A1 MUTATED    19  10
  COL7A1 WILD-TYPE 200 141
  COL7A1 MUTATED COL7A1 WILD-TYPE 
              29              341 
  COL7A1 MUTATED COL7A1 WILD-TYPE 
              10              141 
$`COL7A1 MUTATED`
TCGA-2F-A9KO TCGA-BT-A0YX TCGA-BT-A3PK TCGA-C4-A0F0 TCGA-CF-A1HR TCGA-DK-A1AC 
       22.29        13.15         9.96         1.94         0.46       130.88 
TCGA-DK-A3WW TCGA-DK-A6AW TCGA-E5-A2PC TCGA-E5-A4U1 TCGA-FD-A3N6 TCGA-FD-A3SM 
       20.81        41.56        43.59        38.83        27.98        17.98 
TCGA-FD-A3SR TCGA-FD-A5C0 TCGA-FD-A6TA TCGA-FD-A6TC TCGA-G2-A2EO TCGA-G2-A2ES 
       19.79        18.08        62.86         6.15        35.24        33.01 
TCGA-GV-A6ZA TCGA-H4-A2HQ TCGA-S5-AA26 TCGA-UY-A78M TCGA-UY-A8OB TCGA-UY-A9PD 
       22.72        19.40         3.75        22.68        65.75        17.82 
TCGA-XF-A9SY TCGA-XF-A9T8 TCGA-XF-AAMY TCGA-ZF-A9R7 TCGA-ZF-AA4T 
       21.04        13.74        98.99        21.86        19.69 

$`COL7A1 WILD-TYPE`
TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW TCGA-4Z-AA7M 
       11.97        91.63       103.50       105.70         8.35        16.27 
TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7W 
       44.94        16.83        16.77        17.16        34.98        27.62 
TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA84 
       49.12         0.62        41.75        51.16        66.54        15.12 
TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J 
       10.22        47.80        33.83        40.08         7.33         2.66 
TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O 
        6.74        12.39         6.58        19.04        32.84        12.16 
TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20V 
       17.88        19.50         5.06        14.89        14.96         5.06 
TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH 
        8.35         8.25        17.16        16.18        20.48         4.67 
TCGA-BT-A3PJ TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ 
       12.82        17.56        28.70        24.26        28.41         8.98 
TCGA-C4-A0F1 TCGA-C4-A0F6 TCGA-C4-A0F7 TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47S 
        2.93        23.01         2.04         0.43         0.69        10.95 
TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 
       12.66        12.46        12.10        12.62        12.26        13.12 
TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YO 
       12.00        12.10        11.87        13.08        12.92         4.90 
TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E 
        7.20         5.46         5.19        16.31         1.84        13.58 
TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB 
       21.86         2.14        66.41        18.41        19.00        16.70 
TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 
      112.44        16.14        17.62        15.62         1.81        10.59 
TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM 
        7.79       123.85        87.32         2.20        13.58         7.82 
TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV 
        8.22        17.72        50.27        21.30        23.21         9.67 
TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6B0 
       10.55       140.81        48.00        17.98        64.18        76.60 
TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6P 
       67.36        15.68        41.06        30.67        38.24        15.02 
TCGA-DK-AA6Q TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA6X 
       13.58       166.03        12.36        10.49         8.65         7.53 
TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A4TZ TCGA-E7-A3X6 
       13.64        43.50        12.03        10.62        15.35        24.66 
TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KE 
        0.10         0.49         2.24        16.70        17.39         0.56 
TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DU 
        0.66        14.56        13.97        12.99        14.33         0.92 
TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A97P TCGA-E7-A97Q 
        1.22        13.68        14.07        12.95        14.37         8.09 
TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 
       32.02        16.77         8.94        33.04         4.01        12.62 
TCGA-FD-A3N5 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SN TCGA-FD-A3SO 
       22.52        60.66        24.30        23.41        29.16         5.52 
TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S 
       25.74        46.78        12.85        22.98        27.35        14.96 
TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU 
       20.91         3.62        26.73        53.88        11.01        19.33 
TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C1 TCGA-FD-A62N 
        5.36         5.69         8.25        27.45        58.92         2.70 
TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TB TCGA-FD-A6TD TCGA-FD-A6TE 
        7.10         6.28        13.35        18.81        12.69        12.36 
TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z7 
        2.27         3.06         4.31         9.67        10.85        31.07 
TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FJ-A871 TCGA-FT-A3EE TCGA-FT-A61P 
        7.13        10.65        17.23         8.94         3.25         6.48 
TCGA-G2-A2EC TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A3IB 
       22.88        61.94        30.61        15.95        26.93         7.23 
TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3D TCGA-G2-AA3F 
       20.12        17.62        66.02         6.94        64.44        19.46 
TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD 
       21.40         2.24        15.81         4.50        15.91        14.07 
TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP 
       17.75        24.92         8.94        13.91         7.73         2.10 
TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42Q 
        3.12        20.98         2.20         7.36        10.92        11.31 
TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 
       11.31         7.63        27.09        20.05         5.62         4.73 
TCGA-GU-AATO TCGA-GU-AATP TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX 
       10.65        32.98         7.00        14.27        21.34        19.10 
TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E 
       19.82        20.28         8.48        10.59        27.35         8.58 
TCGA-GV-A40G TCGA-H4-A2HO TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE 
       19.07         1.51        38.60         3.06         9.01         8.22 
TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R 
       25.02         3.45        21.24         2.76         9.14        27.68 
TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P 
        9.07        11.70         1.74         1.81        15.42         6.38 
TCGA-K4-AAQO TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN 
       11.80        15.32        15.58        13.48        12.23        16.67 
TCGA-R3-A69X TCGA-S5-A6DX TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L 
       14.24         1.84        12.43        31.56        17.62        37.05 
TCGA-UY-A78N TCGA-UY-A78O TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PE TCGA-UY-A9PF 
       86.83        76.01        35.24        29.56         4.54         1.64 
TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SJ 
        1.87        17.88        48.62        64.80        79.66         3.22 
TCGA-XF-A9SL TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SZ TCGA-XF-A9T0 
       66.41        12.76        11.90        23.64        28.24        26.27 
TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-AAME 
       18.90         2.24        16.27        66.64         2.10        92.98 
TCGA-XF-AAMF TCGA-XF-AAMG TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ 
       10.82       110.60        11.31        54.90         7.63        71.57 
TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAMZ TCGA-XF-AAN0 
       91.73         2.96         8.32         6.77        44.32        56.48 
TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN7 
       30.94        61.45        86.30        27.06        75.39        18.81 
TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R0 
        3.88         9.63         0.66        11.97        13.64        18.64 
TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R9 
        7.36        21.11        24.13        30.28        27.19        28.41 
TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RL 
       74.56        13.41         3.48        52.73        52.60        82.49 
TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4R TCGA-ZF-AA4U TCGA-ZF-AA4V 
       47.84        20.22         2.89        34.06         8.61        59.38 
TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA53 TCGA-ZF-AA54 
       60.16        63.02        38.73        35.41        57.90        19.40 
TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-ZF-AA5P 
        8.52        47.15        19.17         5.52        10.13 

  COL7A1 MUTATED COL7A1 WILD-TYPE 
            0.46             0.10 
  COL7A1 MUTATED COL7A1 WILD-TYPE 
          130.88           166.03 
  COL7A1 MUTATED COL7A1 WILD-TYPE 
           21.04            14.96 
[1] "0.5 - 130.9 (21.0)" "0.1 - 166.0 (15.0)"
[1] "hr=" "1.6"
D93V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  COL7A1 MUTATED         0        9         9       11
  COL7A1 WILD-TYPE       4      108       113      117
D93V3, multiclass
           clus
vv          COL7A1 MUTATED COL7A1 WILD-TYPE
  STAGE I                0                4
  STAGE II               9              108
  STAGE III              9              113
  STAGE IV              11              117
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1+T2  T3  T4
  COL7A1 MUTATED          9  16   3
  COL7A1 WILD-TYPE      105 163  49
D93V4, multiclass
          clus
vv         COL7A1 MUTATED COL7A1 WILD-TYPE
  T0+T1+T2              9              105
  T3                   16              163
  T4                    3               49
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  COL7A1 MUTATED    18   3   7   0
  COL7A1 WILD-TYPE 195  38  68   8
D93V5, multiclass
    clus
vv   COL7A1 MUTATED COL7A1 WILD-TYPE
  N0             18              195
  N1              3               38
  N2              7               68
  N3              0                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"
D93V6, binary
                  cls
clus                 0   1
  COL7A1 MUTATED    12   2
  COL7A1 WILD-TYPE 170   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  COL7A1 MUTATED     12    2
  COL7A1 WILD-TYPE  170    8
   clus
vv  COL7A1 MUTATED COL7A1 WILD-TYPE
  0             12              170
  1              2                8
[1] 2 2
[1] FALSE
D93V7, binary
                  cls
clus                 0   1
  COL7A1 MUTATED     8  22
  COL7A1 WILD-TYPE  88 258
[1] "tbl2"
                  cls
clus               [,1] [,2]
  COL7A1 MUTATED      8   22
  COL7A1 WILD-TYPE   88  258
        clus
vv       COL7A1 MUTATED COL7A1 WILD-TYPE
  FEMALE              8               88
  MALE               22              258
[1] 2 2
[1] FALSE
D93V8, continuous
D93V9, continuous
D93V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  COL7A1 MUTATED       3                         3    22
  COL7A1 WILD-TYPE    35                        18   279
D93V11, multiclass
                           clus
vv                          COL7A1 MUTATED COL7A1 WILD-TYPE
  ASIAN                                  3               35
  BLACK OR AFRICAN AMERICAN              3               18
  WHITE                                 22              279
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D93V12, binary
                  cls
clus                 0   1
  COL7A1 MUTATED     1  27
  COL7A1 WILD-TYPE   7 311
[1] "tbl2"
                  cls
clus               [,1] [,2]
  COL7A1 MUTATED      1   27
  COL7A1 WILD-TYPE    7  311
                        clus
vv                       COL7A1 MUTATED COL7A1 WILD-TYPE
  HISPANIC OR LATINO                  1                7
  NOT HISPANIC OR LATINO             27              311
[1] 2 2
[1] FALSE

Clustering(94) Variable = ZNF513 MUTATION ANALYSIS
D94V1, survival
                  sevent
clus2                0   1
  ZNF513 MUTATED     6   5
  ZNF513 WILD-TYPE 213 146
  ZNF513 MUTATED ZNF513 WILD-TYPE 
              11              359 
  ZNF513 MUTATED ZNF513 WILD-TYPE 
               5              146 
$`ZNF513 MUTATED`
TCGA-4Z-AA87 TCGA-BT-A2LB TCGA-BT-A3PH TCGA-CU-A5W6 TCGA-DK-A2I6 TCGA-DK-A3IU 
       47.80        16.18         4.67         1.84        87.32        23.21 
TCGA-E5-A4U1 TCGA-FD-A5BX TCGA-G2-A2EO TCGA-G2-A3VY TCGA-GV-A3JW 
       38.83         5.69        35.24        17.62        21.34 

$`ZNF513 WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        91.63       103.50       105.70         8.35 
TCGA-4Z-AA7M TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7S 
       16.27        44.94        16.83        16.77        17.16        34.98 
TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 
       27.62        49.12         0.62        41.75        51.16        66.54 
TCGA-4Z-AA84 TCGA-4Z-AA86 TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J 
       15.12        10.22        33.83        40.08         7.33         2.66 
TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N 
        6.74        12.39         6.58        13.15        19.04        32.84 
TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U 
       12.16        17.88        19.50         5.06        14.89        14.96 
TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LD TCGA-BT-A3PJ 
        5.06         8.35         8.25        17.16        20.48        12.82 
TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ 
        9.96        17.56        28.70        24.26        28.41         8.98 
TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-C4-A0F6 TCGA-C4-A0F7 TCGA-CF-A1HR TCGA-CF-A1HS 
        1.94         2.93        23.01         2.04         0.46         0.43 
TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X 
        0.69        10.95        12.66        12.46        12.10        12.62 
TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A9FF TCGA-CF-A9FM 
       12.26        13.12        12.00        12.10        11.87        13.08 
TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL 
       12.92         4.90         7.20         5.46         5.19        16.31 
TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA 
       13.58        21.86         2.14        66.41        18.41        19.00 
TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG 
       16.70       130.88       112.44        16.14        17.62        15.62 
TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IK TCGA-DK-A3IL 
        1.81        10.59         7.79       123.85         2.20        13.58 
TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IV 
        7.82         8.22        17.72        50.27        21.30         9.67 
TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV 
       20.81        10.55       140.81        48.00        17.98        64.18 
TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 
       41.56        76.60        67.36        15.68        41.06        30.67 
TCGA-DK-AA6L TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6U 
       38.24        15.02        13.58       166.03        12.36        10.49 
TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA76 TCGA-DK-AA77 
        8.65         7.53        13.64        43.50        12.03        10.62 
TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ 
       43.59        15.35        24.66         0.10         0.49         2.24 
TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 
       16.70        17.39         0.56         0.66        14.56        13.97 
TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A7XN 
       12.99        14.33         0.92         1.22        13.68        14.07 
TCGA-E7-A85H TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 
       12.95        14.37         8.09        32.02        16.77         8.94 
TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA 
       33.04         4.01        12.62        22.52        27.98        60.66 
TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP 
       24.30        23.41        17.98        29.16         5.52        25.74 
TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S 
       46.78        19.79        12.85        22.98        27.35        14.96 
TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU 
       20.91         3.62        26.73        53.88        11.01        19.33 
TCGA-FD-A5BV TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N 
        5.36         8.25        27.45        18.08        58.92         2.70 
TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC 
        7.10         6.28        13.35        62.86        18.81         6.15 
TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI 
       12.69        12.36         2.27         3.06         4.31         9.67 
TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FJ-A871 
       10.85        31.07         7.13        10.65        17.23         8.94 
TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EC TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK 
        3.25         6.48        22.88        61.94        30.61        15.95 
TCGA-G2-A2EL TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3B TCGA-G2-AA3C 
       26.93        33.01         7.23        20.12        66.02         6.94 
TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB 
       64.44        19.46        21.40         2.24        15.81         4.50 
TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GC-A6I3 
       15.91        14.07        17.75        24.92         8.94        13.91 
TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GD-A76B 
        7.73         2.10         3.12        20.98         2.20         7.36 
TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A764 
       10.92        11.31        11.31         7.63        27.09        20.05 
TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATO TCGA-GU-AATP TCGA-GU-AATQ TCGA-GV-A3JV 
        5.62         4.73        10.65        32.98         7.00        14.27 
TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK 
       19.10        19.82        20.28         8.48        10.59        27.35 
TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE 
        8.58        19.07        22.72         1.51        19.40        38.60 
TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV 
        3.06         9.01         8.22        25.02         3.45        21.24 
TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ 
        2.76         9.14        27.68         9.07        11.70         1.74 
TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO TCGA-LC-A66R TCGA-LT-A5Z6 
        1.81        15.42         6.38        11.80        15.32        15.58 
TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 
       13.48        12.23        16.67        14.24         1.84         3.75 
TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78N 
       12.43        31.56        17.62        37.05        22.68        86.83 
TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE 
       76.01        65.75        35.24        29.56        17.82         4.54 
TCGA-UY-A9PF TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI 
        1.64         1.87        17.88        48.62        64.80        79.66 
TCGA-XF-A9SJ TCGA-XF-A9SL TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY 
        3.22        66.41        12.76        11.90        23.64        21.04 
TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T5 
       28.24        26.27        18.90         2.24        16.27        66.64 
TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMG TCGA-XF-AAMH 
        2.10        13.74        92.98        10.82       110.60        11.31 
TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMW 
       54.90         7.63        71.57        91.73         2.96         8.32 
TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN2 
        6.77        98.99        44.32        56.48        30.94        61.45 
TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 
       86.30        27.06        75.39        18.81         3.88         9.63 
TCGA-YC-A9TC TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R2 
        0.66        11.97        13.64        18.64         7.36        21.11 
TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RC 
       24.13        30.28        27.19        21.86        28.41        74.56 
TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-A9RM 
       13.41         3.48        52.73        52.60        82.49        47.84 
TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4U TCGA-ZF-AA4V 
       20.22         2.89        34.06        19.69         8.61        59.38 
TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA53 TCGA-ZF-AA54 
       60.16        63.02        38.73        35.41        57.90        19.40 
TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-ZF-AA5P 
        8.52        47.15        19.17         5.52        10.13 

  ZNF513 MUTATED ZNF513 WILD-TYPE 
            1.84             0.10 
  ZNF513 MUTATED ZNF513 WILD-TYPE 
           87.32           166.03 
  ZNF513 MUTATED ZNF513 WILD-TYPE 
           21.34            15.42 
[1] "1.8 - 87.3 (21.3)"  "0.1 - 166.0 (15.4)"
[1] "hr=" "1.1"
D94V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  ZNF513 MUTATED         0        4         4        3
  ZNF513 WILD-TYPE       4      113       118      125
D94V3, multiclass
           clus
vv          ZNF513 MUTATED ZNF513 WILD-TYPE
  STAGE I                0                4
  STAGE II               4              113
  STAGE III              4              118
  STAGE IV               3              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"
                  vv
clus               T0+T1+T2  T3  T4
  ZNF513 MUTATED          4   4   2
  ZNF513 WILD-TYPE      110 175  50
D94V4, multiclass
          clus
vv         ZNF513 MUTATED ZNF513 WILD-TYPE
  T0+T1+T2              4              110
  T3                    4              175
  T4                    2               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"
                  vv
clus                N0  N1  N2  N3
  ZNF513 MUTATED     6   2   1   0
  ZNF513 WILD-TYPE 207  39  74   8
D94V5, multiclass
    clus
vv   ZNF513 MUTATED ZNF513 WILD-TYPE
  N0              6              207
  N1              2               39
  N2              1               74
  N3              0                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"
D94V6, binary
                  cls
clus                 0   1
  ZNF513 MUTATED     7   0
  ZNF513 WILD-TYPE 175  10
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF513 MUTATED      7    0
  ZNF513 WILD-TYPE  175   10
   clus
vv  ZNF513 MUTATED ZNF513 WILD-TYPE
  0              7              175
  1              0               10
[1] 2 2
[1] FALSE
D94V7, binary
                  cls
clus                 0   1
  ZNF513 MUTATED     1  10
  ZNF513 WILD-TYPE  95 270
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF513 MUTATED      1   10
  ZNF513 WILD-TYPE   95  270
        clus
vv       ZNF513 MUTATED ZNF513 WILD-TYPE
  FEMALE              1               95
  MALE               10              270
[1] 2 2
[1] FALSE
D94V8, continuous
D94V9, continuous
D94V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ZNF513 MUTATED       1                         1     8
  ZNF513 WILD-TYPE    37                        20   293
D94V11, multiclass
                           clus
vv                          ZNF513 MUTATED ZNF513 WILD-TYPE
  ASIAN                                  1               37
  BLACK OR AFRICAN AMERICAN              1               20
  WHITE                                  8              293
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D94V12, binary
                  cls
clus                 0   1
  ZNF513 MUTATED     0  10
  ZNF513 WILD-TYPE   8 328
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF513 MUTATED      0   10
  ZNF513 WILD-TYPE    8  328
                        clus
vv                       ZNF513 MUTATED ZNF513 WILD-TYPE
  HISPANIC OR LATINO                  0                8
  NOT HISPANIC OR LATINO             10              328
[1] 2 2
[1] FALSE

Clustering(95) Variable = ACSL5 MUTATION ANALYSIS
D95V1, survival
                 sevent
clus2               0   1
  ACSL5 MUTATED     6   0
  ACSL5 WILD-TYPE 213 151
  ACSL5 MUTATED ACSL5 WILD-TYPE 
              6             364 
  ACSL5 MUTATED ACSL5 WILD-TYPE 
              0             151 
$`ACSL5 MUTATED`
TCGA-DK-A1AC TCGA-DK-AA71 TCGA-DK-AA76 TCGA-DK-AA77 TCGA-FD-A43X TCGA-FD-A6TC 
      130.88        13.64        12.03        10.62         3.62         6.15 

$`ACSL5 WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        91.63       103.50       105.70         8.35 
TCGA-4Z-AA7M TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7S 
       16.27        44.94        16.83        16.77        17.16        34.98 
TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 
       27.62        49.12         0.62        41.75        51.16        66.54 
TCGA-4Z-AA84 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BL-A13I 
       15.12        10.22        47.80        33.83        40.08         7.33 
TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J 
        2.66         6.74        12.39         6.58        13.15        19.04 
TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T 
       32.84        12.16        17.88        19.50         5.06        14.89 
TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB 
       14.96         5.06         8.35         8.25        17.16        16.18 
TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C 
       20.48         4.67        12.82         9.96        17.56        28.70 
TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-C4-A0F6 
       24.26        28.41         8.98         1.94         2.93        23.01 
TCGA-C4-A0F7 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T 
        2.04         0.46         0.43         0.69        10.95        12.66 
TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA 
       12.46        12.10        12.62        12.26        13.12        12.00 
TCGA-CF-A7I0 TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR 
       12.10        11.87        13.08        12.92         4.90         7.20 
TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 
        5.46         5.19        16.31         1.84        13.58        21.86 
TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AD 
        2.14        66.41        18.41        19.00        16.70       112.44 
TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 
       16.14        17.62        15.62         1.81        10.59         7.79 
TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN 
      123.85        87.32         2.20        13.58         7.82         8.22 
TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW 
       17.72        50.27        21.30        23.21         9.67        20.81 
TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW 
       10.55       140.81        48.00        17.98        64.18        41.56 
TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L 
       76.60        67.36        15.68        41.06        30.67        38.24 
TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6W 
       15.02        13.58       166.03        12.36        10.49         8.65 
TCGA-DK-AA6X TCGA-DK-AA74 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 
        7.53        43.50        43.59        15.35        38.83        24.66 
TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KE 
        0.10         0.49         2.24        16.70        17.39         0.56 
TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DU 
        0.66        14.56        13.97        12.99        14.33         0.92 
TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A97P TCGA-E7-A97Q 
        1.22        13.68        14.07        12.95        14.37         8.09 
TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 
       32.02        16.77         8.94        33.04         4.01        12.62 
TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM 
       22.52        27.98        60.66        24.30        23.41        17.98 
TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS 
       29.16         5.52        25.74        46.78        19.79        12.85 
TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A5BR TCGA-FD-A5BS 
       22.98        27.35        14.96        20.91        26.73        53.88 
TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ 
       11.01        19.33         5.36         5.69         8.25        27.45 
TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S 
       18.08        58.92         2.70         7.10         6.28        13.35 
TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TG 
       62.86        18.81        12.69        12.36         2.27         3.06 
TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE 
        4.31         9.67        10.85        31.07         7.13        10.65 
TCGA-FJ-A3ZF TCGA-FJ-A871 TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EC TCGA-G2-A2EF 
       17.23         8.94         3.25         6.48        22.88        61.94 
TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB 
       30.61        15.95        26.93        35.24        33.01         7.23 
TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3D TCGA-G2-AA3F 
       20.12        17.62        66.02         6.94        64.44        19.46 
TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD 
       21.40         2.24        15.81         4.50        15.91        14.07 
TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP 
       17.75        24.92         8.94        13.91         7.73         2.10 
TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42Q 
        3.12        20.98         2.20         7.36        10.92        11.31 
TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 
       11.31         7.63        27.09        20.05         5.62         4.73 
TCGA-GU-AATO TCGA-GU-AATP TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX 
       10.65        32.98         7.00        14.27        21.34        19.10 
TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E 
       19.82        20.28         8.48        10.59        27.35         8.58 
TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF 
       19.07        22.72         1.51        19.40        38.60         3.06 
TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB 
        9.01         8.22        25.02         3.45        21.24         2.76 
TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ 
        9.14        27.68         9.07        11.70         1.74         1.81 
TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V 
       15.42         6.38        11.80        15.32        15.58        13.48 
TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 TCGA-SY-A9G0 
       12.23        16.67        14.24         1.84         3.75        12.43 
TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78N TCGA-UY-A78O 
       31.56        17.62        37.05        22.68        86.83        76.01 
TCGA-UY-A8OB TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF 
       65.75        35.24        29.56        17.82         4.54         1.64 
TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SJ 
        1.87        17.88        48.62        64.80        79.66         3.22 
TCGA-XF-A9SL TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ 
       66.41        12.76        11.90        23.64        21.04        28.24 
TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 
       26.27        18.90         2.24        16.27        66.64         2.10 
TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMG TCGA-XF-AAMH TCGA-XF-AAMJ 
       13.74        92.98        10.82       110.60        11.31        54.90 
TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX 
        7.63        71.57        91.73         2.96         8.32         6.77 
TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 
       98.99        44.32        56.48        30.94        61.45        86.30 
TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YC-A9TC 
       27.06        75.39        18.81         3.88         9.63         0.66 
TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R3 
       11.97        13.64        18.64         7.36        21.11        24.13 
TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RD 
       30.28        27.19        21.86        28.41        74.56        13.41 
TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-A9RN 
        3.48        52.73        52.60        82.49        47.84        20.22 
TCGA-ZF-AA4N TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W 
        2.89        34.06        19.69         8.61        59.38        60.16 
TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA56 
       63.02        38.73        35.41        57.90        19.40         8.52 
TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-ZF-AA5P 
       47.15        19.17         5.52        10.13 

  ACSL5 MUTATED ACSL5 WILD-TYPE 
           3.62            0.10 
  ACSL5 MUTATED ACSL5 WILD-TYPE 
         130.88          166.03 
  ACSL5 MUTATED ACSL5 WILD-TYPE 
         11.325          15.860 
[1] "3.6 - 130.9 (11.3)" "0.1 - 166.0 (15.9)"
[1] "hr="     "9200000"
D95V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  ACSL5 MUTATED         0        4         2        0
  ACSL5 WILD-TYPE       4      113       120      128
D95V3, multiclass
           clus
vv          ACSL5 MUTATED ACSL5 WILD-TYPE
  STAGE I               0               4
  STAGE II              4             113
  STAGE III             2             120
  STAGE IV              0             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"
                 vv
clus              T0+T1+T2  T3  T4
  ACSL5 MUTATED          3   1   1
  ACSL5 WILD-TYPE      111 178  51
D95V4, multiclass
          clus
vv         ACSL5 MUTATED ACSL5 WILD-TYPE
  T0+T1+T2             3             111
  T3                   1             178
  T4                   1              51
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  ACSL5 MUTATED     6   0   0   0
  ACSL5 WILD-TYPE 207  41  75   8
D95V5, multiclass
    clus
vv   ACSL5 MUTATED ACSL5 WILD-TYPE
  N0             6             207
  N1             0              41
  N2             0              75
  N3             0               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"
D95V6, binary
                 cls
clus                0   1
  ACSL5 MUTATED     4   0
  ACSL5 WILD-TYPE 178  10
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ACSL5 MUTATED      4    0
  ACSL5 WILD-TYPE  178   10
   clus
vv  ACSL5 MUTATED ACSL5 WILD-TYPE
  0             4             178
  1             0              10
[1] 2 2
[1] FALSE
D95V7, binary
                 cls
clus                0   1
  ACSL5 MUTATED     2   4
  ACSL5 WILD-TYPE  94 276
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ACSL5 MUTATED      2    4
  ACSL5 WILD-TYPE   94  276
        clus
vv       ACSL5 MUTATED ACSL5 WILD-TYPE
  FEMALE             2              94
  MALE               4             276
[1] 2 2
[1] FALSE
D95V8, continuous
[1] "Remove cluster labels:" "ACSL5 MUTATED"         
clus
  ACSL5 MUTATED ACSL5 WILD-TYPE 
              1             119 
     TCGA-2F-A9KO      TCGA-2F-A9KP      TCGA-2F-A9KQ      TCGA-2F-A9KR 
"ACSL5 WILD-TYPE" "ACSL5 WILD-TYPE" "ACSL5 WILD-TYPE" "ACSL5 WILD-TYPE" 
     TCGA-2F-A9KT      TCGA-2F-A9KW      TCGA-CF-A1HS      TCGA-CF-A27C 
"ACSL5 WILD-TYPE" "ACSL5 WILD-TYPE" "ACSL5 WILD-TYPE" "ACSL5 WILD-TYPE" 
     TCGA-CF-A3MF      TCGA-CF-A3MG      TCGA-CF-A3MH      TCGA-CF-A3MI 
"ACSL5 WILD-TYPE" "ACSL5 WILD-TYPE" "ACSL5 WILD-TYPE" "ACSL5 WILD-TYPE" 
     TCGA-CF-A47S      TCGA-CF-A47T      TCGA-CF-A47V      TCGA-CF-A47W 
"ACSL5 WILD-TYPE" "ACSL5 WILD-TYPE" "ACSL5 WILD-TYPE" "ACSL5 WILD-TYPE" 
     TCGA-CF-A47X      TCGA-CF-A47Y      TCGA-CF-A5U8      TCGA-CF-A5UA 
"ACSL5 WILD-TYPE" "ACSL5 WILD-TYPE" "ACSL5 WILD-TYPE" "ACSL5 WILD-TYPE" 
     TCGA-CF-A7I0      TCGA-DK-A2HX      TCGA-DK-A3IN      TCGA-DK-A3IV 
"ACSL5 WILD-TYPE" "ACSL5 WILD-TYPE" "ACSL5 WILD-TYPE" "ACSL5 WILD-TYPE" 
     TCGA-DK-A3WX      TCGA-DK-A3X2      TCGA-DK-A6B2      TCGA-DK-A6B5 
"ACSL5 WILD-TYPE" "ACSL5 WILD-TYPE" "ACSL5 WILD-TYPE" "ACSL5 WILD-TYPE" 
     TCGA-DK-A6B6      TCGA-DK-AA6P      TCGA-DK-AA6S      TCGA-DK-AA6U 
"ACSL5 WILD-TYPE" "ACSL5 WILD-TYPE" "ACSL5 WILD-TYPE" "ACSL5 WILD-TYPE" 
     TCGA-DK-AA6W      TCGA-E5-A2PC      TCGA-E5-A4TZ      TCGA-E5-A4U1 
"ACSL5 WILD-TYPE" "ACSL5 WILD-TYPE" "ACSL5 WILD-TYPE" "ACSL5 WILD-TYPE" 
     TCGA-E7-A519      TCGA-E7-A541      TCGA-E7-A7DU      TCGA-E7-A7DV 
"ACSL5 WILD-TYPE" "ACSL5 WILD-TYPE" "ACSL5 WILD-TYPE" "ACSL5 WILD-TYPE" 
     TCGA-FT-A61P      TCGA-G2-A2EC      TCGA-G2-A2EF      TCGA-G2-A2EJ 
"ACSL5 WILD-TYPE" "ACSL5 WILD-TYPE" "ACSL5 WILD-TYPE" "ACSL5 WILD-TYPE" 
     TCGA-G2-A2EK      TCGA-G2-A2EL      TCGA-G2-A2EO      TCGA-G2-A2ES 
"ACSL5 WILD-TYPE" "ACSL5 WILD-TYPE" "ACSL5 WILD-TYPE" "ACSL5 WILD-TYPE" 
     TCGA-G2-A3IB      TCGA-G2-A3IE      TCGA-G2-A3VY      TCGA-GC-A3BM 
"ACSL5 WILD-TYPE" "ACSL5 WILD-TYPE" "ACSL5 WILD-TYPE" "ACSL5 WILD-TYPE" 
     TCGA-GC-A3I6      TCGA-GC-A3OO      TCGA-GC-A3RC      TCGA-GC-A3RD 
"ACSL5 WILD-TYPE" "ACSL5 WILD-TYPE" "ACSL5 WILD-TYPE" "ACSL5 WILD-TYPE" 
     TCGA-GC-A3YS      TCGA-GC-A6I1      TCGA-GC-A6I3      TCGA-GD-A3OS 
"ACSL5 WILD-TYPE" "ACSL5 WILD-TYPE" "ACSL5 WILD-TYPE" "ACSL5 WILD-TYPE" 
     TCGA-GD-A6C6      TCGA-GV-A3JV      TCGA-GV-A3JW      TCGA-GV-A3JX 
"ACSL5 WILD-TYPE" "ACSL5 WILD-TYPE" "ACSL5 WILD-TYPE" "ACSL5 WILD-TYPE" 
     TCGA-GV-A3JZ      TCGA-GV-A3QF      TCGA-GV-A3QH      TCGA-GV-A3QI 
"ACSL5 WILD-TYPE" "ACSL5 WILD-TYPE" "ACSL5 WILD-TYPE" "ACSL5 WILD-TYPE" 
     TCGA-GV-A3QK      TCGA-GV-A40E      TCGA-GV-A40G      TCGA-GV-A6ZA 
"ACSL5 WILD-TYPE" "ACSL5 WILD-TYPE" "ACSL5 WILD-TYPE" "ACSL5 WILD-TYPE" 
     TCGA-SY-A9G0      TCGA-SY-A9G5      TCGA-UY-A78L      TCGA-UY-A78M 
"ACSL5 WILD-TYPE" "ACSL5 WILD-TYPE" "ACSL5 WILD-TYPE" "ACSL5 WILD-TYPE" 
     TCGA-UY-A78N      TCGA-XF-A8HH      TCGA-XF-A8HI      TCGA-XF-A9SG 
"ACSL5 WILD-TYPE" "ACSL5 WILD-TYPE" "ACSL5 WILD-TYPE" "ACSL5 WILD-TYPE" 
     TCGA-XF-A9SH      TCGA-XF-A9SI      TCGA-XF-A9SJ      TCGA-XF-A9SL 
"ACSL5 WILD-TYPE" "ACSL5 WILD-TYPE" "ACSL5 WILD-TYPE" "ACSL5 WILD-TYPE" 
     TCGA-XF-A9SV      TCGA-XF-A9SW      TCGA-XF-A9SX      TCGA-XF-A9SY 
"ACSL5 WILD-TYPE" "ACSL5 WILD-TYPE" "ACSL5 WILD-TYPE" "ACSL5 WILD-TYPE" 
     TCGA-XF-A9SZ      TCGA-XF-A9T0      TCGA-XF-A9T2      TCGA-XF-A9T3 
"ACSL5 WILD-TYPE" "ACSL5 WILD-TYPE" "ACSL5 WILD-TYPE" "ACSL5 WILD-TYPE" 
     TCGA-XF-A9T4      TCGA-XF-A9T5      TCGA-XF-A9T6      TCGA-XF-A9T8 
"ACSL5 WILD-TYPE" "ACSL5 WILD-TYPE" "ACSL5 WILD-TYPE" "ACSL5 WILD-TYPE" 
     TCGA-XF-AAME      TCGA-XF-AAMF      TCGA-XF-AAMG      TCGA-XF-AAMH 
"ACSL5 WILD-TYPE" "ACSL5 WILD-TYPE" "ACSL5 WILD-TYPE" "ACSL5 WILD-TYPE" 
     TCGA-XF-AAMJ      TCGA-XF-AAML      TCGA-XF-AAMQ      TCGA-XF-AAMR 
"ACSL5 WILD-TYPE" "ACSL5 WILD-TYPE" "ACSL5 WILD-TYPE" "ACSL5 WILD-TYPE" 
     TCGA-XF-AAMT      TCGA-XF-AAMW      TCGA-XF-AAMX      TCGA-XF-AAMY 
"ACSL5 WILD-TYPE" "ACSL5 WILD-TYPE" "ACSL5 WILD-TYPE" "ACSL5 WILD-TYPE" 
     TCGA-XF-AAMZ      TCGA-XF-AAN0      TCGA-XF-AAN1      TCGA-XF-AAN2 
"ACSL5 WILD-TYPE" "ACSL5 WILD-TYPE" "ACSL5 WILD-TYPE" "ACSL5 WILD-TYPE" 
     TCGA-XF-AAN3      TCGA-XF-AAN4      TCGA-XF-AAN5      TCGA-XF-AAN7 
"ACSL5 WILD-TYPE" "ACSL5 WILD-TYPE" "ACSL5 WILD-TYPE" "ACSL5 WILD-TYPE" 
     TCGA-XF-AAN8      TCGA-YF-AA3L      TCGA-YF-AA3M 
"ACSL5 WILD-TYPE" "ACSL5 WILD-TYPE" "ACSL5 WILD-TYPE" 
D95V9, continuous
D95V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ACSL5 MUTATED       0                         0     6
  ACSL5 WILD-TYPE    38                        21   295
D95V11, multiclass
                           clus
vv                          ACSL5 MUTATED ACSL5 WILD-TYPE
  ASIAN                                 0              38
  BLACK OR AFRICAN AMERICAN             0              21
  WHITE                                 6             295
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D95V12, binary
                 cls
clus                0   1
  ACSL5 MUTATED     0   5
  ACSL5 WILD-TYPE   8 333
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ACSL5 MUTATED      0    5
  ACSL5 WILD-TYPE    8  333
                        clus
vv                       ACSL5 MUTATED ACSL5 WILD-TYPE
  HISPANIC OR LATINO                 0               8
  NOT HISPANIC OR LATINO             5             333
[1] 2 2
[1] FALSE

Clustering(96) Variable = C18ORF8 MUTATION ANALYSIS
D96V1, survival
                   sevent
clus2                 0   1
  C18ORF8 MUTATED     2   4
  C18ORF8 WILD-TYPE 217 147
  C18ORF8 MUTATED C18ORF8 WILD-TYPE 
                6               364 
  C18ORF8 MUTATED C18ORF8 WILD-TYPE 
                4               147 
$`C18ORF8 MUTATED`
TCGA-BT-A2LB TCGA-CU-A0YO TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-S5-A6DX TCGA-ZF-AA4X 
       16.18         4.90        43.59        15.35         1.84        63.02 

$`C18ORF8 WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        91.63       103.50       105.70         8.35 
TCGA-4Z-AA7M TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7S 
       16.27        44.94        16.83        16.77        17.16        34.98 
TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 
       27.62        49.12         0.62        41.75        51.16        66.54 
TCGA-4Z-AA84 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BL-A13I 
       15.12        10.22        47.80        33.83        40.08         7.33 
TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J 
        2.66         6.74        12.39         6.58        13.15        19.04 
TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T 
       32.84        12.16        17.88        19.50         5.06        14.89 
TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LD 
       14.96         5.06         8.35         8.25        17.16        20.48 
TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E 
        4.67        12.82         9.96        17.56        28.70        24.26 
TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-C4-A0F6 TCGA-C4-A0F7 
       28.41         8.98         1.94         2.93        23.01         2.04 
TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V 
        0.46         0.43         0.69        10.95        12.66        12.46 
TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 
       12.10        12.62        12.26        13.12        12.00        12.10 
TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3QU 
       11.87        13.08        12.92         7.20         5.46         5.19 
TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 
       16.31         1.84        13.58        21.86         2.14        66.41 
TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE 
       18.41        19.00        16.70       130.88       112.44        16.14 
TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 
       17.62        15.62         1.81        10.59         7.79       123.85 
TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ 
       87.32         2.20        13.58         7.82         8.22        17.72 
TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX 
       50.27        21.30        23.21         9.67        20.81        10.55 
TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 
      140.81        48.00        17.98        64.18        41.56        76.60 
TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6P 
       67.36        15.68        41.06        30.67        38.24        15.02 
TCGA-DK-AA6Q TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA6X 
       13.58       166.03        12.36        10.49         8.65         7.53 
TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A4U1 TCGA-E7-A3X6 
       13.64        43.50        12.03        10.62        38.83        24.66 
TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KE 
        0.10         0.49         2.24        16.70        17.39         0.56 
TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DU 
        0.66        14.56        13.97        12.99        14.33         0.92 
TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A97P TCGA-E7-A97Q 
        1.22        13.68        14.07        12.95        14.37         8.09 
TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 
       32.02        16.77         8.94        33.04         4.01        12.62 
TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM 
       22.52        27.98        60.66        24.30        23.41        17.98 
TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS 
       29.16         5.52        25.74        46.78        19.79        12.85 
TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BR 
       22.98        27.35        14.96        20.91         3.62        26.73 
TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY 
       53.88        11.01        19.33         5.36         5.69         8.25 
TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P 
       27.45        18.08        58.92         2.70         7.10         6.28 
TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE 
       13.35        62.86        18.81         6.15        12.69        12.36 
TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z7 
        2.27         3.06         4.31         9.67        10.85        31.07 
TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FJ-A871 TCGA-FT-A3EE TCGA-FT-A61P 
        7.13        10.65        17.23         8.94         3.25         6.48 
TCGA-G2-A2EC TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO 
       22.88        61.94        30.61        15.95        26.93        35.24 
TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3C 
       33.01         7.23        20.12        17.62        66.02         6.94 
TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB 
       64.44        19.46        21.40         2.24        15.81         4.50 
TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GC-A6I3 
       15.91        14.07        17.75        24.92         8.94        13.91 
TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GD-A76B 
        7.73         2.10         3.12        20.98         2.20         7.36 
TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A764 
       10.92        11.31        11.31         7.63        27.09        20.05 
TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATO TCGA-GU-AATP TCGA-GU-AATQ TCGA-GV-A3JV 
        5.62         4.73        10.65        32.98         7.00        14.27 
TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI 
       21.34        19.10        19.82        20.28         8.48        10.59 
TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-H4-A2HQ 
       27.35         8.58        19.07        22.72         1.51        19.40 
TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU 
       38.60         3.06         9.01         8.22        25.02         3.45 
TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RH TCGA-K4-A5RI 
       21.24         2.76         9.14        27.68         9.07        11.70 
TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO TCGA-LC-A66R 
        1.74         1.81        15.42         6.38        11.80        15.32 
TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-AA26 
       15.58        13.48        12.23        16.67        14.24         3.75 
TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78N 
       12.43        31.56        17.62        37.05        22.68        86.83 
TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE 
       76.01        65.75        35.24        29.56        17.82         4.54 
TCGA-UY-A9PF TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI 
        1.64         1.87        17.88        48.62        64.80        79.66 
TCGA-XF-A9SJ TCGA-XF-A9SL TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY 
        3.22        66.41        12.76        11.90        23.64        21.04 
TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T5 
       28.24        26.27        18.90         2.24        16.27        66.64 
TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMG TCGA-XF-AAMH 
        2.10        13.74        92.98        10.82       110.60        11.31 
TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMW 
       54.90         7.63        71.57        91.73         2.96         8.32 
TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN2 
        6.77        98.99        44.32        56.48        30.94        61.45 
TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 
       86.30        27.06        75.39        18.81         3.88         9.63 
TCGA-YC-A9TC TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R2 
        0.66        11.97        13.64        18.64         7.36        21.11 
TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RC 
       24.13        30.28        27.19        21.86        28.41        74.56 
TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-A9RM 
       13.41         3.48        52.73        52.60        82.49        47.84 
TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4U TCGA-ZF-AA4V 
       20.22         2.89        34.06        19.69         8.61        59.38 
TCGA-ZF-AA4W TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA56 
       60.16        38.73        35.41        57.90        19.40         8.52 
TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-ZF-AA5P 
       47.15        19.17         5.52        10.13 

  C18ORF8 MUTATED C18ORF8 WILD-TYPE 
             1.84              0.10 
  C18ORF8 MUTATED C18ORF8 WILD-TYPE 
            63.02            166.03 
  C18ORF8 MUTATED C18ORF8 WILD-TYPE 
           15.765            15.650 
[1] "1.8 - 63.0 (15.8)"  "0.1 - 166.0 (15.6)"
[1] "hr=" "1.7"
D96V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  C18ORF8 MUTATED         0        1         1        4
  C18ORF8 WILD-TYPE       4      116       121      124
D96V3, multiclass
           clus
vv          C18ORF8 MUTATED C18ORF8 WILD-TYPE
  STAGE I                 0                 4
  STAGE II                1               116
  STAGE III               1               121
  STAGE IV                4               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"
                   vv
clus                T0+T1+T2  T3  T4
  C18ORF8 MUTATED          2   2   2
  C18ORF8 WILD-TYPE      112 177  50
D96V4, multiclass
          clus
vv         C18ORF8 MUTATED C18ORF8 WILD-TYPE
  T0+T1+T2               2               112
  T3                     2               177
  T4                     2                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"
                   vv
clus                 N0  N1  N2  N3
  C18ORF8 MUTATED     1   1   3   0
  C18ORF8 WILD-TYPE 212  40  72   8
D96V5, multiclass
    clus
vv   C18ORF8 MUTATED C18ORF8 WILD-TYPE
  N0               1               212
  N1               1                40
  N2               3                72
  N3               0                 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"
D96V6, binary
                   cls
clus                  0   1
  C18ORF8 MUTATED     2   0
  C18ORF8 WILD-TYPE 180  10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C18ORF8 MUTATED      2    0
  C18ORF8 WILD-TYPE  180   10
   clus
vv  C18ORF8 MUTATED C18ORF8 WILD-TYPE
  0               2               180
  1               0                10
[1] 2 2
[1] FALSE
D96V7, binary
                   cls
clus                  0   1
  C18ORF8 MUTATED     2   4
  C18ORF8 WILD-TYPE  94 276
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C18ORF8 MUTATED      2    4
  C18ORF8 WILD-TYPE   94  276
        clus
vv       C18ORF8 MUTATED C18ORF8 WILD-TYPE
  FEMALE               2                94
  MALE                 4               276
[1] 2 2
[1] FALSE
D96V8, continuous
[1] "Remove cluster labels:" "C18ORF8 MUTATED"       
clus
  C18ORF8 MUTATED C18ORF8 WILD-TYPE 
                2               118 
       TCGA-2F-A9KO        TCGA-2F-A9KP        TCGA-2F-A9KQ        TCGA-2F-A9KR 
"C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" 
       TCGA-2F-A9KT        TCGA-2F-A9KW        TCGA-CF-A1HS        TCGA-CF-A27C 
"C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" 
       TCGA-CF-A3MF        TCGA-CF-A3MG        TCGA-CF-A3MH        TCGA-CF-A3MI 
"C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" 
       TCGA-CF-A47S        TCGA-CF-A47T        TCGA-CF-A47V        TCGA-CF-A47W 
"C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" 
       TCGA-CF-A47X        TCGA-CF-A47Y        TCGA-CF-A5U8        TCGA-CF-A5UA 
"C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" 
       TCGA-CF-A7I0        TCGA-DK-A2HX        TCGA-DK-A3IN        TCGA-DK-A3IV 
"C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" 
       TCGA-DK-A3WX        TCGA-DK-A3X2        TCGA-DK-A6B2        TCGA-DK-A6B5 
"C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" 
       TCGA-DK-A6B6        TCGA-DK-AA6P        TCGA-DK-AA6S        TCGA-DK-AA6U 
"C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" 
       TCGA-DK-AA6W        TCGA-DK-AA76        TCGA-E5-A4U1        TCGA-E7-A519 
"C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" 
       TCGA-E7-A541        TCGA-E7-A7DU        TCGA-E7-A7DV        TCGA-FT-A61P 
"C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" 
       TCGA-G2-A2EC        TCGA-G2-A2EF        TCGA-G2-A2EJ        TCGA-G2-A2EK 
"C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" 
       TCGA-G2-A2EL        TCGA-G2-A2EO        TCGA-G2-A2ES        TCGA-G2-A3IB 
"C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" 
       TCGA-G2-A3IE        TCGA-G2-A3VY        TCGA-GC-A3BM        TCGA-GC-A3I6 
"C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" 
       TCGA-GC-A3OO        TCGA-GC-A3RC        TCGA-GC-A3RD        TCGA-GC-A3YS 
"C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" 
       TCGA-GC-A6I1        TCGA-GC-A6I3        TCGA-GD-A3OS        TCGA-GD-A6C6 
"C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" 
       TCGA-GV-A3JV        TCGA-GV-A3JW        TCGA-GV-A3JX        TCGA-GV-A3JZ 
"C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" 
       TCGA-GV-A3QF        TCGA-GV-A3QH        TCGA-GV-A3QI        TCGA-GV-A3QK 
"C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" 
       TCGA-GV-A40E        TCGA-GV-A40G        TCGA-GV-A6ZA        TCGA-SY-A9G0 
"C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" 
       TCGA-SY-A9G5        TCGA-UY-A78L        TCGA-UY-A78M        TCGA-UY-A78N 
"C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" 
       TCGA-XF-A8HH        TCGA-XF-A8HI        TCGA-XF-A9SG        TCGA-XF-A9SH 
"C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" 
       TCGA-XF-A9SI        TCGA-XF-A9SJ        TCGA-XF-A9SL        TCGA-XF-A9SV 
"C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" 
       TCGA-XF-A9SW        TCGA-XF-A9SX        TCGA-XF-A9SY        TCGA-XF-A9SZ 
"C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" 
       TCGA-XF-A9T0        TCGA-XF-A9T2        TCGA-XF-A9T3        TCGA-XF-A9T4 
"C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" 
       TCGA-XF-A9T5        TCGA-XF-A9T6        TCGA-XF-A9T8        TCGA-XF-AAME 
"C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" 
       TCGA-XF-AAMF        TCGA-XF-AAMG        TCGA-XF-AAMH        TCGA-XF-AAMJ 
"C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" 
       TCGA-XF-AAML        TCGA-XF-AAMQ        TCGA-XF-AAMR        TCGA-XF-AAMT 
"C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" 
       TCGA-XF-AAMW        TCGA-XF-AAMX        TCGA-XF-AAMY        TCGA-XF-AAMZ 
"C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" 
       TCGA-XF-AAN0        TCGA-XF-AAN1        TCGA-XF-AAN2        TCGA-XF-AAN3 
"C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" 
       TCGA-XF-AAN4        TCGA-XF-AAN5        TCGA-XF-AAN7        TCGA-XF-AAN8 
"C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" 
       TCGA-YF-AA3L        TCGA-YF-AA3M 
"C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" 
D96V9, continuous
[1] "Remove cluster labels:" "C18ORF8 MUTATED"       
clus
  C18ORF8 MUTATED C18ORF8 WILD-TYPE 
                2               203 
       TCGA-2F-A9KO        TCGA-2F-A9KP        TCGA-2F-A9KR        TCGA-4Z-AA7M 
"C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" 
       TCGA-4Z-AA89        TCGA-BL-A0C8        TCGA-BL-A13I        TCGA-BL-A13J 
"C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" 
       TCGA-BL-A3JM        TCGA-BL-A5ZZ        TCGA-BT-A20J        TCGA-BT-A20N 
"C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" 
       TCGA-BT-A2LA        TCGA-BT-A42B        TCGA-BT-A42C        TCGA-BT-A42E 
"C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" 
       TCGA-C4-A0EZ        TCGA-C4-A0F0        TCGA-C4-A0F1        TCGA-C4-A0F6 
"C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" 
       TCGA-CF-A3MH        TCGA-CF-A3MI        TCGA-CF-A47W        TCGA-CF-A47X 
"C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" 
       TCGA-CF-A5UA        TCGA-CF-A9FH        TCGA-CU-A0YN        TCGA-CU-A0YR 
"C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" 
       TCGA-CU-A3KJ        TCGA-CU-A3QU        TCGA-CU-A3YL        TCGA-CU-A5W6 
"C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" 
       TCGA-CU-A72E        TCGA-DK-A1A3        TCGA-DK-A1A5        TCGA-DK-A1A6 
"C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" 
       TCGA-DK-A1AA        TCGA-DK-A1AC        TCGA-DK-A1AE        TCGA-DK-A2HX 
"C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" 
       TCGA-DK-A2I6        TCGA-DK-A3IL        TCGA-DK-A3IM        TCGA-DK-A3IN 
"C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" 
       TCGA-DK-A3IQ        TCGA-DK-A3IU        TCGA-DK-A3IV        TCGA-DK-A3WX 
"C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" 
       TCGA-DK-A3X1        TCGA-DK-A3X2        TCGA-DK-A6AV        TCGA-DK-A6AW 
"C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" 
       TCGA-DK-A6B0        TCGA-DK-A6B2        TCGA-DK-A6B6        TCGA-DK-AA6L 
"C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" 
       TCGA-DK-AA6P        TCGA-DK-AA6T        TCGA-DK-AA6U        TCGA-DK-AA74 
"C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" 
       TCGA-DK-AA76        TCGA-E7-A4XJ        TCGA-E7-A519        TCGA-E7-A5KF 
"C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" 
       TCGA-E7-A678        TCGA-E7-A6ME        TCGA-E7-A6MF        TCGA-E7-A7PW 
"C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" 
       TCGA-E7-A7XN        TCGA-E7-A85H        TCGA-E7-A97Q        TCGA-FD-A3B3 
"C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" 
       TCGA-FD-A3B4        TCGA-FD-A3B5        TCGA-FD-A3B6        TCGA-FD-A3B7 
"C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" 
       TCGA-FD-A3B8        TCGA-FD-A3N5        TCGA-FD-A3N6        TCGA-FD-A3NA 
"C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" 
       TCGA-FD-A3SJ        TCGA-FD-A3SM        TCGA-FD-A3SN        TCGA-FD-A3SO 
"C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" 
       TCGA-FD-A3SP        TCGA-FD-A3SQ        TCGA-FD-A3SR        TCGA-FD-A3SS 
"C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" 
       TCGA-FD-A43N        TCGA-FD-A43P        TCGA-FD-A43S        TCGA-FD-A43U 
"C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" 
       TCGA-FD-A43X        TCGA-FD-A5BT        TCGA-FD-A5BU        TCGA-FD-A5BV 
"C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" 
       TCGA-FD-A5BX        TCGA-FD-A5C0        TCGA-FD-A62N        TCGA-FD-A6TB 
"C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" 
       TCGA-FD-A6TC        TCGA-FD-A6TE        TCGA-FD-A6TG        TCGA-FD-A6TH 
"C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" 
       TCGA-FD-A6TK        TCGA-FJ-A3Z9        TCGA-FJ-A3ZE        TCGA-FJ-A3ZF 
"C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" 
       TCGA-FJ-A871        TCGA-FT-A61P        TCGA-G2-A2EF        TCGA-G2-A2EJ 
"C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" 
       TCGA-G2-A2EL        TCGA-G2-A2ES        TCGA-G2-A3IE        TCGA-G2-AA3B 
"C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" 
       TCGA-G2-AA3C        TCGA-G2-AA3D        TCGA-G2-AA3F        TCGA-GC-A3BM 
"C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" 
       TCGA-GC-A3RB        TCGA-GC-A3WC        TCGA-GC-A3YS        TCGA-GD-A2C5 
"C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" 
       TCGA-GD-A3OQ        TCGA-GD-A3OS        TCGA-GD-A6C6        TCGA-GU-A42P 
"C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" 
       TCGA-GU-A42Q        TCGA-GU-A42R        TCGA-GU-A763        TCGA-GU-A764 
"C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" 
       TCGA-GU-AATO        TCGA-GU-AATP        TCGA-GU-AATQ        TCGA-GV-A3JV 
"C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" 
       TCGA-GV-A3JX        TCGA-GV-A3JZ        TCGA-GV-A3QF        TCGA-GV-A3QG 
"C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" 
       TCGA-GV-A3QH        TCGA-GV-A3QI        TCGA-GV-A3QK        TCGA-GV-A40E 
"C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" 
       TCGA-GV-A40G        TCGA-H4-A2HO        TCGA-H4-A2HQ        TCGA-HQ-A5ND 
"C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" 
       TCGA-HQ-A5NE        TCGA-K4-A3WS        TCGA-K4-A3WV        TCGA-K4-A5RH 
"C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" 
       TCGA-K4-A5RI        TCGA-K4-A83P        TCGA-K4-AAQO        TCGA-PQ-A6FI 
"C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" 
       TCGA-PQ-A6FN        TCGA-R3-A69X        TCGA-SY-A9G0        TCGA-UY-A78N 
"C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" 
       TCGA-UY-A8OB        TCGA-UY-A9PB        TCGA-UY-A9PE        TCGA-UY-A9PF 
"C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" 
       TCGA-XF-A9SJ        TCGA-XF-A9SL        TCGA-XF-A9SV        TCGA-XF-A9SX 
"C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" 
       TCGA-XF-A9SY        TCGA-XF-A9SZ        TCGA-XF-A9T3        TCGA-XF-A9T8 
"C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" 
       TCGA-XF-AAMF        TCGA-XF-AAMH        TCGA-XF-AAMQ        TCGA-XF-AAMT 
"C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" 
       TCGA-XF-AAN0        TCGA-XF-AAN1        TCGA-XF-AAN2        TCGA-XF-AAN4 
"C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" 
       TCGA-XF-AAN5        TCGA-XF-AAN7        TCGA-XF-AAN8        TCGA-YF-AA3L 
"C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" 
       TCGA-YF-AA3M        TCGA-ZF-A9R0        TCGA-ZF-A9R2        TCGA-ZF-A9R3 
"C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" 
       TCGA-ZF-A9R5        TCGA-ZF-A9R7        TCGA-ZF-A9R9        TCGA-ZF-A9RD 
"C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" 
       TCGA-ZF-A9RF        TCGA-ZF-A9RL        TCGA-ZF-A9RM        TCGA-ZF-AA4U 
"C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" 
       TCGA-ZF-AA4V        TCGA-ZF-AA51        TCGA-ZF-AA52        TCGA-ZF-AA58 
"C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" 
       TCGA-ZF-AA5H        TCGA-ZF-AA5N        TCGA-ZF-AA5P 
"C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" "C18ORF8 WILD-TYPE" 
D96V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  C18ORF8 MUTATED       0                         0     6
  C18ORF8 WILD-TYPE    38                        21   295
D96V11, multiclass
                           clus
vv                          C18ORF8 MUTATED C18ORF8 WILD-TYPE
  ASIAN                                   0                38
  BLACK OR AFRICAN AMERICAN               0                21
  WHITE                                   6               295
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D96V12, binary
                   cls
clus                  0   1
  C18ORF8 MUTATED     0   6
  C18ORF8 WILD-TYPE   8 332
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C18ORF8 MUTATED      0    6
  C18ORF8 WILD-TYPE    8  332
                        clus
vv                       C18ORF8 MUTATED C18ORF8 WILD-TYPE
  HISPANIC OR LATINO                   0                 8
  NOT HISPANIC OR LATINO               6               332
[1] 2 2
[1] FALSE

Clustering(97) Variable = PRB2 MUTATION ANALYSIS
D97V1, survival
                sevent
clus2              0   1
  PRB2 MUTATED     2   5
  PRB2 WILD-TYPE 217 146
  PRB2 MUTATED PRB2 WILD-TYPE 
             7            363 
  PRB2 MUTATED PRB2 WILD-TYPE 
             5            146 
$`PRB2 MUTATED`
TCGA-BT-A2LB TCGA-FD-A62P TCGA-G2-A3IE TCGA-G2-AA3B TCGA-GC-A3I6 TCGA-UY-A78K 
       16.18         6.28        20.12        66.02         2.24        17.62 
TCGA-XF-AAML 
        7.63 

$`PRB2 WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        91.63       103.50       105.70         8.35 
TCGA-4Z-AA7M TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7S 
       16.27        44.94        16.83        16.77        17.16        34.98 
TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 
       27.62        49.12         0.62        41.75        51.16        66.54 
TCGA-4Z-AA84 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BL-A13I 
       15.12        10.22        47.80        33.83        40.08         7.33 
TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J 
        2.66         6.74        12.39         6.58        13.15        19.04 
TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T 
       32.84        12.16        17.88        19.50         5.06        14.89 
TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LD 
       14.96         5.06         8.35         8.25        17.16        20.48 
TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E 
        4.67        12.82         9.96        17.56        28.70        24.26 
TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-C4-A0F6 TCGA-C4-A0F7 
       28.41         8.98         1.94         2.93        23.01         2.04 
TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V 
        0.46         0.43         0.69        10.95        12.66        12.46 
TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 
       12.10        12.62        12.26        13.12        12.00        12.10 
TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ 
       11.87        13.08        12.92         4.90         7.20         5.46 
TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 
        5.19        16.31         1.84        13.58        21.86         2.14 
TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD 
       66.41        18.41        19.00        16.70       130.88       112.44 
TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 
       16.14        17.62        15.62         1.81        10.59         7.79 
TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN 
      123.85        87.32         2.20        13.58         7.82         8.22 
TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW 
       17.72        50.27        21.30        23.21         9.67        20.81 
TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW 
       10.55       140.81        48.00        17.98        64.18        41.56 
TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L 
       76.60        67.36        15.68        41.06        30.67        38.24 
TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6W 
       15.02        13.58       166.03        12.36        10.49         8.65 
TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A2PC 
        7.53        13.64        43.50        12.03        10.62        43.59 
TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ 
       15.35        38.83        24.66         0.10         0.49         2.24 
TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 
       16.70        17.39         0.56         0.66        14.56        13.97 
TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A7XN 
       12.99        14.33         0.92         1.22        13.68        14.07 
TCGA-E7-A85H TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 
       12.95        14.37         8.09        32.02        16.77         8.94 
TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA 
       33.04         4.01        12.62        22.52        27.98        60.66 
TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP 
       24.30        23.41        17.98        29.16         5.52        25.74 
TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S 
       46.78        19.79        12.85        22.98        27.35        14.96 
TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU 
       20.91         3.62        26.73        53.88        11.01        19.33 
TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 
        5.36         5.69         8.25        27.45        18.08        58.92 
TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC 
        2.70         7.10        13.35        62.86        18.81         6.15 
TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI 
       12.69        12.36         2.27         3.06         4.31         9.67 
TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FJ-A871 
       10.85        31.07         7.13        10.65        17.23         8.94 
TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EC TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK 
        3.25         6.48        22.88        61.94        30.61        15.95 
TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3VY TCGA-G2-AA3C 
       26.93        35.24        33.01         7.23        17.62         6.94 
TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC 
       64.44        19.46        21.40        15.81         4.50        15.91 
TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 
       14.07        17.75        24.92         8.94        13.91         7.73 
TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42P 
        2.10         3.12        20.98         2.20         7.36        10.92 
TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 
       11.31        11.31         7.63        27.09        20.05         5.62 
TCGA-GU-A767 TCGA-GU-AATO TCGA-GU-AATP TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW 
        4.73        10.65        32.98         7.00        14.27        21.34 
TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK 
       19.10        19.82        20.28         8.48        10.59        27.35 
TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE 
        8.58        19.07        22.72         1.51        19.40        38.60 
TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV 
        3.06         9.01         8.22        25.02         3.45        21.24 
TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ 
        2.76         9.14        27.68         9.07        11.70         1.74 
TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO TCGA-LC-A66R TCGA-LT-A5Z6 
        1.81        15.42         6.38        11.80        15.32        15.58 
TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 
       13.48        12.23        16.67        14.24         1.84         3.75 
TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78N TCGA-UY-A78O 
       12.43        31.56        37.05        22.68        86.83        76.01 
TCGA-UY-A8OB TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF 
       65.75        35.24        29.56        17.82         4.54         1.64 
TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SJ 
        1.87        17.88        48.62        64.80        79.66         3.22 
TCGA-XF-A9SL TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ 
       66.41        12.76        11.90        23.64        21.04        28.24 
TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 
       26.27        18.90         2.24        16.27        66.64         2.10 
TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMG TCGA-XF-AAMH TCGA-XF-AAMJ 
       13.74        92.98        10.82       110.60        11.31        54.90 
TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAMY 
       71.57        91.73         2.96         8.32         6.77        98.99 
TCGA-XF-AAMZ TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN4 
       44.32        56.48        30.94        61.45        86.30        27.06 
TCGA-XF-AAN5 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L 
       75.39        18.81         3.88         9.63         0.66        11.97 
TCGA-YF-AA3M TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R4 
       13.64        18.64         7.36        21.11        24.13        30.28 
TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RE 
       27.19        21.86        28.41        74.56        13.41         3.48 
TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N 
       52.73        52.60        82.49        47.84        20.22         2.89 
TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA4X 
       34.06        19.69         8.61        59.38        60.16        63.02 
TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 
       38.73        35.41        57.90        19.40         8.52        47.15 
TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-ZF-AA5P 
       19.17         5.52        10.13 

  PRB2 MUTATED PRB2 WILD-TYPE 
          2.24           0.10 
  PRB2 MUTATED PRB2 WILD-TYPE 
         66.02         166.03 
  PRB2 MUTATED PRB2 WILD-TYPE 
         16.18          15.62 
[1] "2.2 - 66.0 (16.2)"  "0.1 - 166.0 (15.6)"
[1] "hr=" "2.1"
D97V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  PRB2 MUTATED         0        4         2        1
  PRB2 WILD-TYPE       4      113       120      127
D97V3, multiclass
           clus
vv          PRB2 MUTATED PRB2 WILD-TYPE
  STAGE I              0              4
  STAGE II             4            113
  STAGE III            2            120
  STAGE IV             1            127
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1+T2  T3  T4
  PRB2 MUTATED          3   2   0
  PRB2 WILD-TYPE      111 177  52
D97V4, multiclass
          clus
vv         PRB2 MUTATED PRB2 WILD-TYPE
  T0+T1+T2            3            111
  T3                  2            177
  T4                  0             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"
                vv
clus              N0  N1  N2  N3
  PRB2 MUTATED     5   0   1   0
  PRB2 WILD-TYPE 208  41  74   8
D97V5, multiclass
    clus
vv   PRB2 MUTATED PRB2 WILD-TYPE
  N0            5            208
  N1            0             41
  N2            1             74
  N3            0              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"
D97V6, binary
                cls
clus               0   1
  PRB2 MUTATED     3   0
  PRB2 WILD-TYPE 179  10
[1] "tbl2"
                cls
clus             [,1] [,2]
  PRB2 MUTATED      3    0
  PRB2 WILD-TYPE  179   10
   clus
vv  PRB2 MUTATED PRB2 WILD-TYPE
  0            3            179
  1            0             10
[1] 2 2
[1] FALSE
D97V7, binary
                cls
clus               0   1
  PRB2 MUTATED     2   5
  PRB2 WILD-TYPE  94 275
[1] "tbl2"
                cls
clus             [,1] [,2]
  PRB2 MUTATED      2    5
  PRB2 WILD-TYPE   94  275
        clus
vv       PRB2 MUTATED PRB2 WILD-TYPE
  FEMALE            2             94
  MALE              5            275
[1] 2 2
[1] FALSE
D97V8, continuous
D97V9, continuous
[1] "Remove cluster labels:" "PRB2 MUTATED"          
clus
  PRB2 MUTATED PRB2 WILD-TYPE 
             2            203 
    TCGA-2F-A9KO     TCGA-2F-A9KP     TCGA-2F-A9KR     TCGA-4Z-AA7M 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-4Z-AA89     TCGA-BL-A0C8     TCGA-BL-A13I     TCGA-BL-A13J 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-BL-A3JM     TCGA-BL-A5ZZ     TCGA-BT-A20J     TCGA-BT-A20N 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-BT-A2LA     TCGA-BT-A42B     TCGA-BT-A42C     TCGA-BT-A42E 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-C4-A0EZ     TCGA-C4-A0F0     TCGA-C4-A0F1     TCGA-C4-A0F6 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-CF-A3MH     TCGA-CF-A3MI     TCGA-CF-A47W     TCGA-CF-A47X 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-CF-A5UA     TCGA-CF-A9FH     TCGA-CU-A0YN     TCGA-CU-A0YR 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-CU-A3KJ     TCGA-CU-A3QU     TCGA-CU-A3YL     TCGA-CU-A5W6 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-CU-A72E     TCGA-DK-A1A3     TCGA-DK-A1A5     TCGA-DK-A1A6 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-DK-A1AA     TCGA-DK-A1AC     TCGA-DK-A1AE     TCGA-DK-A2HX 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-DK-A2I6     TCGA-DK-A3IL     TCGA-DK-A3IM     TCGA-DK-A3IN 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-DK-A3IQ     TCGA-DK-A3IU     TCGA-DK-A3IV     TCGA-DK-A3WX 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-DK-A3X1     TCGA-DK-A3X2     TCGA-DK-A6AV     TCGA-DK-A6AW 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-DK-A6B0     TCGA-DK-A6B2     TCGA-DK-A6B6     TCGA-DK-AA6L 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-DK-AA6P     TCGA-DK-AA6T     TCGA-DK-AA6U     TCGA-DK-AA74 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-DK-AA76     TCGA-E5-A4TZ     TCGA-E7-A4XJ     TCGA-E7-A519 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-E7-A5KF     TCGA-E7-A678     TCGA-E7-A6ME     TCGA-E7-A6MF 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-E7-A7PW     TCGA-E7-A7XN     TCGA-E7-A85H     TCGA-E7-A97Q 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-FD-A3B3     TCGA-FD-A3B4     TCGA-FD-A3B5     TCGA-FD-A3B6 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-FD-A3B7     TCGA-FD-A3B8     TCGA-FD-A3N5     TCGA-FD-A3N6 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-FD-A3NA     TCGA-FD-A3SJ     TCGA-FD-A3SM     TCGA-FD-A3SN 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-FD-A3SO     TCGA-FD-A3SP     TCGA-FD-A3SQ     TCGA-FD-A3SR 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-FD-A3SS     TCGA-FD-A43N     TCGA-FD-A43P     TCGA-FD-A43S 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-FD-A43U     TCGA-FD-A43X     TCGA-FD-A5BT     TCGA-FD-A5BU 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-FD-A5BV     TCGA-FD-A5BX     TCGA-FD-A5C0     TCGA-FD-A62N 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-FD-A6TB     TCGA-FD-A6TC     TCGA-FD-A6TE     TCGA-FD-A6TG 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-FD-A6TH     TCGA-FD-A6TK     TCGA-FJ-A3Z9     TCGA-FJ-A3ZE 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-FJ-A3ZF     TCGA-FJ-A871     TCGA-FT-A61P     TCGA-G2-A2EF 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-G2-A2EJ     TCGA-G2-A2EL     TCGA-G2-A2ES     TCGA-G2-AA3C 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-G2-AA3D     TCGA-G2-AA3F     TCGA-GC-A3BM     TCGA-GC-A3RB 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-GC-A3WC     TCGA-GC-A3YS     TCGA-GD-A2C5     TCGA-GD-A3OQ 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-GD-A3OS     TCGA-GD-A6C6     TCGA-GU-A42P     TCGA-GU-A42Q 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-GU-A42R     TCGA-GU-A763     TCGA-GU-A764     TCGA-GU-AATO 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-GU-AATP     TCGA-GU-AATQ     TCGA-GV-A3JV     TCGA-GV-A3JX 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-GV-A3JZ     TCGA-GV-A3QF     TCGA-GV-A3QG     TCGA-GV-A3QH 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-GV-A3QI     TCGA-GV-A3QK     TCGA-GV-A40E     TCGA-GV-A40G 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-H4-A2HO     TCGA-H4-A2HQ     TCGA-HQ-A5ND     TCGA-HQ-A5NE 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-K4-A3WS     TCGA-K4-A3WV     TCGA-K4-A5RH     TCGA-K4-A5RI 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-K4-A83P     TCGA-K4-AAQO     TCGA-PQ-A6FI     TCGA-PQ-A6FN 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-R3-A69X     TCGA-S5-A6DX     TCGA-SY-A9G0     TCGA-UY-A78N 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-UY-A8OB     TCGA-UY-A9PB     TCGA-UY-A9PE     TCGA-UY-A9PF 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-XF-A9SJ     TCGA-XF-A9SL     TCGA-XF-A9SV     TCGA-XF-A9SX 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-XF-A9SY     TCGA-XF-A9SZ     TCGA-XF-A9T3     TCGA-XF-A9T8 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-XF-AAMF     TCGA-XF-AAMH     TCGA-XF-AAMQ     TCGA-XF-AAMT 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-XF-AAN0     TCGA-XF-AAN1     TCGA-XF-AAN2     TCGA-XF-AAN4 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-XF-AAN5     TCGA-XF-AAN7     TCGA-XF-AAN8     TCGA-YF-AA3L 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-YF-AA3M     TCGA-ZF-A9R0     TCGA-ZF-A9R2     TCGA-ZF-A9R3 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-ZF-A9R5     TCGA-ZF-A9R7     TCGA-ZF-A9R9     TCGA-ZF-A9RD 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-ZF-A9RF     TCGA-ZF-A9RL     TCGA-ZF-A9RM     TCGA-ZF-AA4U 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-ZF-AA4V     TCGA-ZF-AA51     TCGA-ZF-AA52     TCGA-ZF-AA58 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-ZF-AA5H     TCGA-ZF-AA5N     TCGA-ZF-AA5P 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
D97V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PRB2 MUTATED       0                         0     7
  PRB2 WILD-TYPE    38                        21   294
D97V11, multiclass
                           clus
vv                          PRB2 MUTATED PRB2 WILD-TYPE
  ASIAN                                0             38
  BLACK OR AFRICAN AMERICAN            0             21
  WHITE                                7            294
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D97V12, binary
                cls
clus               0   1
  PRB2 MUTATED     0   7
  PRB2 WILD-TYPE   8 331
[1] "tbl2"
                cls
clus             [,1] [,2]
  PRB2 MUTATED      0    7
  PRB2 WILD-TYPE    8  331
                        clus
vv                       PRB2 MUTATED PRB2 WILD-TYPE
  HISPANIC OR LATINO                0              8
  NOT HISPANIC OR LATINO            7            331
[1] 2 2
[1] FALSE

Clustering(98) Variable = POU3F1 MUTATION ANALYSIS
D98V1, survival
                  sevent
clus2                0   1
  POU3F1 MUTATED     1   2
  POU3F1 WILD-TYPE 218 149
  POU3F1 MUTATED POU3F1 WILD-TYPE 
               3              367 
  POU3F1 MUTATED POU3F1 WILD-TYPE 
               2              149 
$`POU3F1 MUTATED`
TCGA-E5-A2PC TCGA-FD-A6TH TCGA-GU-AATO 
       43.59         4.31        10.65 

$`POU3F1 WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        91.63       103.50       105.70         8.35 
TCGA-4Z-AA7M TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7S 
       16.27        44.94        16.83        16.77        17.16        34.98 
TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 
       27.62        49.12         0.62        41.75        51.16        66.54 
TCGA-4Z-AA84 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BL-A13I 
       15.12        10.22        47.80        33.83        40.08         7.33 
TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J 
        2.66         6.74        12.39         6.58        13.15        19.04 
TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T 
       32.84        12.16        17.88        19.50         5.06        14.89 
TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB 
       14.96         5.06         8.35         8.25        17.16        16.18 
TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C 
       20.48         4.67        12.82         9.96        17.56        28.70 
TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-C4-A0F6 
       24.26        28.41         8.98         1.94         2.93        23.01 
TCGA-C4-A0F7 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T 
        2.04         0.46         0.43         0.69        10.95        12.66 
TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA 
       12.46        12.10        12.62        12.26        13.12        12.00 
TCGA-CF-A7I0 TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR 
       12.10        11.87        13.08        12.92         4.90         7.20 
TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 
        5.46         5.19        16.31         1.84        13.58        21.86 
TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC 
        2.14        66.41        18.41        19.00        16.70       130.88 
TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 
      112.44        16.14        17.62        15.62         1.81        10.59 
TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM 
        7.79       123.85        87.32         2.20        13.58         7.82 
TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV 
        8.22        17.72        50.27        21.30        23.21         9.67 
TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV 
       20.81        10.55       140.81        48.00        17.98        64.18 
TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 
       41.56        76.60        67.36        15.68        41.06        30.67 
TCGA-DK-AA6L TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6U 
       38.24        15.02        13.58       166.03        12.36        10.49 
TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA76 TCGA-DK-AA77 
        8.65         7.53        13.64        43.50        12.03        10.62 
TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ 
       15.35        38.83        24.66         0.10         0.49         2.24 
TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 
       16.70        17.39         0.56         0.66        14.56        13.97 
TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A7XN 
       12.99        14.33         0.92         1.22        13.68        14.07 
TCGA-E7-A85H TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 
       12.95        14.37         8.09        32.02        16.77         8.94 
TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA 
       33.04         4.01        12.62        22.52        27.98        60.66 
TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP 
       24.30        23.41        17.98        29.16         5.52        25.74 
TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S 
       46.78        19.79        12.85        22.98        27.35        14.96 
TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU 
       20.91         3.62        26.73        53.88        11.01        19.33 
TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 
        5.36         5.69         8.25        27.45        18.08        58.92 
TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB 
        2.70         7.10         6.28        13.35        62.86        18.81 
TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TI 
        6.15        12.69        12.36         2.27         3.06         9.67 
TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FJ-A871 
       10.85        31.07         7.13        10.65        17.23         8.94 
TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EC TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK 
        3.25         6.48        22.88        61.94        30.61        15.95 
TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY 
       26.93        35.24        33.01         7.23        20.12        17.62 
TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 
       66.02         6.94        64.44        19.46        21.40         2.24 
TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS 
       15.81         4.50        15.91        14.07        17.75        24.92 
TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS 
        8.94        13.91         7.73         2.10         3.12        20.98 
TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 
        2.20         7.36        10.92        11.31        11.31         7.63 
TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATP TCGA-GU-AATQ 
       27.09        20.05         5.62         4.73        32.98         7.00 
TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH 
       14.27        21.34        19.10        19.82        20.28         8.48 
TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO 
       10.59        27.35         8.58        19.07        22.72         1.51 
TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS 
       19.40        38.60         3.06         9.01         8.22        25.02 
TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RH 
        3.45        21.24         2.76         9.14        27.68         9.07 
TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO 
       11.70         1.74         1.81        15.42         6.38        11.80 
TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X 
       15.32        15.58        13.48        12.23        16.67        14.24 
TCGA-S5-A6DX TCGA-S5-AA26 TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L 
        1.84         3.75        12.43        31.56        17.62        37.05 
TCGA-UY-A78M TCGA-UY-A78N TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A9PA TCGA-UY-A9PB 
       22.68        86.83        76.01        65.75        35.24        29.56 
TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG 
       17.82         4.54         1.64         1.87        17.88        48.62 
TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SL TCGA-XF-A9SV TCGA-XF-A9SW 
       64.80        79.66         3.22        66.41        12.76        11.90 
TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 
       23.64        21.04        28.24        26.27        18.90         2.24 
TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMF 
       16.27        66.64         2.10        13.74        92.98        10.82 
TCGA-XF-AAMG TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR 
      110.60        11.31        54.90         7.63        71.57        91.73 
TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN0 
        2.96         8.32         6.77        98.99        44.32        56.48 
TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN7 
       30.94        61.45        86.30        27.06        75.39        18.81 
TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R0 
        3.88         9.63         0.66        11.97        13.64        18.64 
TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R7 
        7.36        21.11        24.13        30.28        27.19        21.86 
TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RG 
       28.41        74.56        13.41         3.48        52.73        52.60 
TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4R TCGA-ZF-AA4T 
       82.49        47.84        20.22         2.89        34.06        19.69 
TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 
        8.61        59.38        60.16        63.02        38.73        35.41 
TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N 
       57.90        19.40         8.52        47.15        19.17         5.52 
TCGA-ZF-AA5P 
       10.13 

  POU3F1 MUTATED POU3F1 WILD-TYPE 
            4.31             0.10 
  POU3F1 MUTATED POU3F1 WILD-TYPE 
           43.59           166.03 
  POU3F1 MUTATED POU3F1 WILD-TYPE 
           10.65            15.68 
[1] "4.3 - 43.6 (10.7)"  "0.1 - 166.0 (15.7)"
[1] "hr=" "2"  
D98V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  POU3F1 MUTATED         0        0         0        3
  POU3F1 WILD-TYPE       4      117       122      125
D98V3, multiclass
           clus
vv          POU3F1 MUTATED POU3F1 WILD-TYPE
  STAGE I                0                4
  STAGE II               0              117
  STAGE III              0              122
  STAGE IV               3              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"
                  vv
clus               T0+T1+T2  T3  T4
  POU3F1 MUTATED          1   1   1
  POU3F1 WILD-TYPE      113 178  51
D98V4, multiclass
          clus
vv         POU3F1 MUTATED POU3F1 WILD-TYPE
  T0+T1+T2              1              113
  T3                    1              178
  T4                    1               51
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  POU3F1 MUTATED     0   1   2   0
  POU3F1 WILD-TYPE 213  40  73   8
D98V5, multiclass
    clus
vv   POU3F1 MUTATED POU3F1 WILD-TYPE
  N0              0              213
  N1              1               40
  N2              2               73
  N3              0                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"
D98V6, binary
                  cls
clus                 0   1
  POU3F1 MUTATED     0   0
  POU3F1 WILD-TYPE 182  10
[1] "tbl2"
                  cls
clus               [,1] [,2]
  POU3F1 MUTATED      0    0
  POU3F1 WILD-TYPE  182   10
D98V7, binary
                  cls
clus                 0   1
  POU3F1 MUTATED     1   2
  POU3F1 WILD-TYPE  95 278
[1] "tbl2"
                  cls
clus               [,1] [,2]
  POU3F1 MUTATED      1    2
  POU3F1 WILD-TYPE   95  278
        clus
vv       POU3F1 MUTATED POU3F1 WILD-TYPE
  FEMALE              1               95
  MALE                2              278
[1] 2 2
[1] FALSE
D98V8, continuous
[1] "Remove cluster labels:" "POU3F1 MUTATED"        
clus
  POU3F1 MUTATED POU3F1 WILD-TYPE 
               1              119 
      TCGA-2F-A9KO       TCGA-2F-A9KP       TCGA-2F-A9KQ       TCGA-2F-A9KR 
"POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" 
      TCGA-2F-A9KT       TCGA-2F-A9KW       TCGA-CF-A1HS       TCGA-CF-A27C 
"POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" 
      TCGA-CF-A3MF       TCGA-CF-A3MG       TCGA-CF-A3MH       TCGA-CF-A3MI 
"POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" 
      TCGA-CF-A47S       TCGA-CF-A47T       TCGA-CF-A47V       TCGA-CF-A47W 
"POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" 
      TCGA-CF-A47X       TCGA-CF-A47Y       TCGA-CF-A5U8       TCGA-CF-A5UA 
"POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" 
      TCGA-CF-A7I0       TCGA-DK-A2HX       TCGA-DK-A3IN       TCGA-DK-A3IV 
"POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" 
      TCGA-DK-A3WX       TCGA-DK-A3X2       TCGA-DK-A6B2       TCGA-DK-A6B5 
"POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" 
      TCGA-DK-A6B6       TCGA-DK-AA6P       TCGA-DK-AA6S       TCGA-DK-AA6U 
"POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" 
      TCGA-DK-AA6W       TCGA-DK-AA76       TCGA-E5-A4TZ       TCGA-E5-A4U1 
"POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" 
      TCGA-E7-A519       TCGA-E7-A541       TCGA-E7-A7DU       TCGA-E7-A7DV 
"POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" 
      TCGA-FT-A61P       TCGA-G2-A2EC       TCGA-G2-A2EF       TCGA-G2-A2EJ 
"POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" 
      TCGA-G2-A2EK       TCGA-G2-A2EL       TCGA-G2-A2EO       TCGA-G2-A2ES 
"POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" 
      TCGA-G2-A3IB       TCGA-G2-A3IE       TCGA-G2-A3VY       TCGA-GC-A3BM 
"POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" 
      TCGA-GC-A3I6       TCGA-GC-A3OO       TCGA-GC-A3RC       TCGA-GC-A3RD 
"POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" 
      TCGA-GC-A3YS       TCGA-GC-A6I1       TCGA-GC-A6I3       TCGA-GD-A3OS 
"POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" 
      TCGA-GD-A6C6       TCGA-GV-A3JV       TCGA-GV-A3JW       TCGA-GV-A3JX 
"POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" 
      TCGA-GV-A3JZ       TCGA-GV-A3QF       TCGA-GV-A3QH       TCGA-GV-A3QI 
"POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" 
      TCGA-GV-A3QK       TCGA-GV-A40E       TCGA-GV-A40G       TCGA-GV-A6ZA 
"POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" 
      TCGA-SY-A9G0       TCGA-SY-A9G5       TCGA-UY-A78L       TCGA-UY-A78M 
"POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" 
      TCGA-UY-A78N       TCGA-XF-A8HH       TCGA-XF-A8HI       TCGA-XF-A9SG 
"POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" 
      TCGA-XF-A9SH       TCGA-XF-A9SI       TCGA-XF-A9SJ       TCGA-XF-A9SL 
"POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" 
      TCGA-XF-A9SV       TCGA-XF-A9SW       TCGA-XF-A9SX       TCGA-XF-A9SY 
"POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" 
      TCGA-XF-A9SZ       TCGA-XF-A9T0       TCGA-XF-A9T2       TCGA-XF-A9T3 
"POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" 
      TCGA-XF-A9T4       TCGA-XF-A9T5       TCGA-XF-A9T6       TCGA-XF-A9T8 
"POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" 
      TCGA-XF-AAME       TCGA-XF-AAMF       TCGA-XF-AAMG       TCGA-XF-AAMH 
"POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" 
      TCGA-XF-AAMJ       TCGA-XF-AAML       TCGA-XF-AAMQ       TCGA-XF-AAMR 
"POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" 
      TCGA-XF-AAMT       TCGA-XF-AAMW       TCGA-XF-AAMX       TCGA-XF-AAMY 
"POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" 
      TCGA-XF-AAMZ       TCGA-XF-AAN0       TCGA-XF-AAN1       TCGA-XF-AAN2 
"POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" 
      TCGA-XF-AAN3       TCGA-XF-AAN4       TCGA-XF-AAN5       TCGA-XF-AAN7 
"POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" 
      TCGA-XF-AAN8       TCGA-YF-AA3L       TCGA-YF-AA3M 
"POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" 
D98V9, continuous
[1] "Remove cluster labels:" "POU3F1 MUTATED"        
clus
  POU3F1 MUTATED POU3F1 WILD-TYPE 
               2              203 
      TCGA-2F-A9KO       TCGA-2F-A9KP       TCGA-2F-A9KR       TCGA-4Z-AA7M 
"POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" 
      TCGA-4Z-AA89       TCGA-BL-A0C8       TCGA-BL-A13I       TCGA-BL-A13J 
"POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" 
      TCGA-BL-A3JM       TCGA-BL-A5ZZ       TCGA-BT-A20J       TCGA-BT-A20N 
"POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" 
      TCGA-BT-A2LA       TCGA-BT-A42B       TCGA-BT-A42C       TCGA-BT-A42E 
"POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" 
      TCGA-C4-A0EZ       TCGA-C4-A0F0       TCGA-C4-A0F1       TCGA-C4-A0F6 
"POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" 
      TCGA-CF-A3MH       TCGA-CF-A3MI       TCGA-CF-A47W       TCGA-CF-A47X 
"POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" 
      TCGA-CF-A5UA       TCGA-CF-A9FH       TCGA-CU-A0YN       TCGA-CU-A0YR 
"POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" 
      TCGA-CU-A3KJ       TCGA-CU-A3QU       TCGA-CU-A3YL       TCGA-CU-A5W6 
"POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" 
      TCGA-CU-A72E       TCGA-DK-A1A3       TCGA-DK-A1A5       TCGA-DK-A1A6 
"POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" 
      TCGA-DK-A1AA       TCGA-DK-A1AC       TCGA-DK-A1AE       TCGA-DK-A2HX 
"POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" 
      TCGA-DK-A2I6       TCGA-DK-A3IL       TCGA-DK-A3IM       TCGA-DK-A3IN 
"POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" 
      TCGA-DK-A3IQ       TCGA-DK-A3IU       TCGA-DK-A3IV       TCGA-DK-A3WX 
"POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" 
      TCGA-DK-A3X1       TCGA-DK-A3X2       TCGA-DK-A6AV       TCGA-DK-A6AW 
"POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" 
      TCGA-DK-A6B0       TCGA-DK-A6B2       TCGA-DK-A6B6       TCGA-DK-AA6L 
"POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" 
      TCGA-DK-AA6P       TCGA-DK-AA6T       TCGA-DK-AA6U       TCGA-DK-AA74 
"POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" 
      TCGA-DK-AA76       TCGA-E5-A4TZ       TCGA-E7-A4XJ       TCGA-E7-A519 
"POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" 
      TCGA-E7-A5KF       TCGA-E7-A678       TCGA-E7-A6ME       TCGA-E7-A6MF 
"POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" 
      TCGA-E7-A7PW       TCGA-E7-A7XN       TCGA-E7-A85H       TCGA-E7-A97Q 
"POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" 
      TCGA-FD-A3B3       TCGA-FD-A3B4       TCGA-FD-A3B5       TCGA-FD-A3B6 
"POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" 
      TCGA-FD-A3B7       TCGA-FD-A3B8       TCGA-FD-A3N5       TCGA-FD-A3N6 
"POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" 
      TCGA-FD-A3NA       TCGA-FD-A3SJ       TCGA-FD-A3SM       TCGA-FD-A3SN 
"POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" 
      TCGA-FD-A3SO       TCGA-FD-A3SP       TCGA-FD-A3SQ       TCGA-FD-A3SR 
"POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" 
      TCGA-FD-A3SS       TCGA-FD-A43N       TCGA-FD-A43P       TCGA-FD-A43S 
"POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" 
      TCGA-FD-A43U       TCGA-FD-A43X       TCGA-FD-A5BT       TCGA-FD-A5BU 
"POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" 
      TCGA-FD-A5BV       TCGA-FD-A5BX       TCGA-FD-A5C0       TCGA-FD-A62N 
"POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" 
      TCGA-FD-A6TB       TCGA-FD-A6TC       TCGA-FD-A6TE       TCGA-FD-A6TG 
"POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" 
      TCGA-FD-A6TK       TCGA-FJ-A3Z9       TCGA-FJ-A3ZE       TCGA-FJ-A3ZF 
"POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" 
      TCGA-FJ-A871       TCGA-FT-A61P       TCGA-G2-A2EF       TCGA-G2-A2EJ 
"POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" 
      TCGA-G2-A2EL       TCGA-G2-A2ES       TCGA-G2-A3IE       TCGA-G2-AA3B 
"POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" 
      TCGA-G2-AA3C       TCGA-G2-AA3D       TCGA-G2-AA3F       TCGA-GC-A3BM 
"POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" 
      TCGA-GC-A3RB       TCGA-GC-A3WC       TCGA-GC-A3YS       TCGA-GD-A2C5 
"POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" 
      TCGA-GD-A3OQ       TCGA-GD-A3OS       TCGA-GD-A6C6       TCGA-GU-A42P 
"POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" 
      TCGA-GU-A42Q       TCGA-GU-A42R       TCGA-GU-A763       TCGA-GU-A764 
"POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" 
      TCGA-GU-AATP       TCGA-GU-AATQ       TCGA-GV-A3JV       TCGA-GV-A3JX 
"POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" 
      TCGA-GV-A3JZ       TCGA-GV-A3QF       TCGA-GV-A3QG       TCGA-GV-A3QH 
"POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" 
      TCGA-GV-A3QI       TCGA-GV-A3QK       TCGA-GV-A40E       TCGA-GV-A40G 
"POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" 
      TCGA-H4-A2HO       TCGA-H4-A2HQ       TCGA-HQ-A5ND       TCGA-HQ-A5NE 
"POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" 
      TCGA-K4-A3WS       TCGA-K4-A3WV       TCGA-K4-A5RH       TCGA-K4-A5RI 
"POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" 
      TCGA-K4-A83P       TCGA-K4-AAQO       TCGA-PQ-A6FI       TCGA-PQ-A6FN 
"POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" 
      TCGA-R3-A69X       TCGA-S5-A6DX       TCGA-SY-A9G0       TCGA-UY-A78N 
"POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" 
      TCGA-UY-A8OB       TCGA-UY-A9PB       TCGA-UY-A9PE       TCGA-UY-A9PF 
"POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" 
      TCGA-XF-A9SJ       TCGA-XF-A9SL       TCGA-XF-A9SV       TCGA-XF-A9SX 
"POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" 
      TCGA-XF-A9SY       TCGA-XF-A9SZ       TCGA-XF-A9T3       TCGA-XF-A9T8 
"POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" 
      TCGA-XF-AAMF       TCGA-XF-AAMH       TCGA-XF-AAMQ       TCGA-XF-AAMT 
"POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" 
      TCGA-XF-AAN0       TCGA-XF-AAN1       TCGA-XF-AAN2       TCGA-XF-AAN4 
"POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" 
      TCGA-XF-AAN5       TCGA-XF-AAN7       TCGA-XF-AAN8       TCGA-YF-AA3L 
"POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" 
      TCGA-YF-AA3M       TCGA-ZF-A9R0       TCGA-ZF-A9R2       TCGA-ZF-A9R3 
"POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" 
      TCGA-ZF-A9R5       TCGA-ZF-A9R7       TCGA-ZF-A9R9       TCGA-ZF-A9RD 
"POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" 
      TCGA-ZF-A9RF       TCGA-ZF-A9RL       TCGA-ZF-A9RM       TCGA-ZF-AA4U 
"POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" 
      TCGA-ZF-AA4V       TCGA-ZF-AA51       TCGA-ZF-AA52       TCGA-ZF-AA58 
"POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" 
      TCGA-ZF-AA5H       TCGA-ZF-AA5N       TCGA-ZF-AA5P 
"POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" "POU3F1 WILD-TYPE" 
D98V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  POU3F1 MUTATED       0                         0     3
  POU3F1 WILD-TYPE    38                        21   298
D98V11, multiclass
                           clus
vv                          POU3F1 MUTATED POU3F1 WILD-TYPE
  ASIAN                                  0               38
  BLACK OR AFRICAN AMERICAN              0               21
  WHITE                                  3              298
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D98V12, binary
                  cls
clus                 0   1
  POU3F1 MUTATED     0   3
  POU3F1 WILD-TYPE   8 335
[1] "tbl2"
                  cls
clus               [,1] [,2]
  POU3F1 MUTATED      0    3
  POU3F1 WILD-TYPE    8  335
                        clus
vv                       POU3F1 MUTATED POU3F1 WILD-TYPE
  HISPANIC OR LATINO                  0                8
  NOT HISPANIC OR LATINO              3              335
[1] 2 2
[1] FALSE

Clustering(99) Variable = EZR MUTATION ANALYSIS
D99V1, survival
               sevent
clus2             0   1
  EZR MUTATED     9   2
  EZR WILD-TYPE 210 149
  EZR MUTATED EZR WILD-TYPE 
           11           359 
  EZR MUTATED EZR WILD-TYPE 
            2           149 
$`EZR MUTATED`
TCGA-DK-A1AC TCGA-DK-A1AF TCGA-DK-A2I4 TCGA-DK-A6AW TCGA-FD-A3N5 TCGA-FD-A6TB 
      130.88        17.62       123.85        41.56        22.52        18.81 
TCGA-GV-A3QH TCGA-H4-A2HQ TCGA-XF-A9SI TCGA-XF-AAN5 TCGA-ZF-AA4X 
        8.48        19.40        79.66        75.39        63.02 

$`EZR WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        91.63       103.50       105.70         8.35 
TCGA-4Z-AA7M TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7S 
       16.27        44.94        16.83        16.77        17.16        34.98 
TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 
       27.62        49.12         0.62        41.75        51.16        66.54 
TCGA-4Z-AA84 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BL-A13I 
       15.12        10.22        47.80        33.83        40.08         7.33 
TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J 
        2.66         6.74        12.39         6.58        13.15        19.04 
TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T 
       32.84        12.16        17.88        19.50         5.06        14.89 
TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB 
       14.96         5.06         8.35         8.25        17.16        16.18 
TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C 
       20.48         4.67        12.82         9.96        17.56        28.70 
TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-C4-A0F6 
       24.26        28.41         8.98         1.94         2.93        23.01 
TCGA-C4-A0F7 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T 
        2.04         0.46         0.43         0.69        10.95        12.66 
TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA 
       12.46        12.10        12.62        12.26        13.12        12.00 
TCGA-CF-A7I0 TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR 
       12.10        11.87        13.08        12.92         4.90         7.20 
TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 
        5.46         5.19        16.31         1.84        13.58        21.86 
TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AD 
        2.14        66.41        18.41        19.00        16.70       112.44 
TCGA-DK-A1AE TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I6 
       16.14        15.62         1.81        10.59         7.79        87.32 
TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS 
        2.20        13.58         7.82         8.22        17.72        50.27 
TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY 
       21.30        23.21         9.67        20.81        10.55       140.81 
TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 
       48.00        17.98        64.18        76.60        67.36        15.68 
TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6S 
       41.06        30.67        38.24        15.02        13.58       166.03 
TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA74 
       12.36        10.49         8.65         7.53        13.64        43.50 
TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 
       12.03        10.62        43.59        15.35        38.83        24.66 
TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KE 
        0.10         0.49         2.24        16.70        17.39         0.56 
TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DU 
        0.66        14.56        13.97        12.99        14.33         0.92 
TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A97P TCGA-E7-A97Q 
        1.22        13.68        14.07        12.95        14.37         8.09 
TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 
       32.02        16.77         8.94        33.04         4.01        12.62 
TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN 
       27.98        60.66        24.30        23.41        17.98        29.16 
TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N 
        5.52        25.74        46.78        19.79        12.85        22.98 
TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS 
       27.35        14.96        20.91         3.62        26.73        53.88 
TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ 
       11.01        19.33         5.36         5.69         8.25        27.45 
TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S 
       18.08        58.92         2.70         7.10         6.28        13.35 
TCGA-FD-A6TA TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TG 
       62.86         6.15        12.69        12.36         2.27         3.06 
TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE 
        4.31         9.67        10.85        31.07         7.13        10.65 
TCGA-FJ-A3ZF TCGA-FJ-A871 TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EC TCGA-G2-A2EF 
       17.23         8.94         3.25         6.48        22.88        61.94 
TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB 
       30.61        15.95        26.93        35.24        33.01         7.23 
TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3D TCGA-G2-AA3F 
       20.12        17.62        66.02         6.94        64.44        19.46 
TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD 
       21.40         2.24        15.81         4.50        15.91        14.07 
TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP 
       17.75        24.92         8.94        13.91         7.73         2.10 
TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42Q 
        3.12        20.98         2.20         7.36        10.92        11.31 
TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 
       11.31         7.63        27.09        20.05         5.62         4.73 
TCGA-GU-AATO TCGA-GU-AATP TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX 
       10.65        32.98         7.00        14.27        21.34        19.10 
TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G 
       19.82        20.28        10.59        27.35         8.58        19.07 
TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE 
       22.72         1.51        38.60         3.06         9.01         8.22 
TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R 
       25.02         3.45        21.24         2.76         9.14        27.68 
TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P 
        9.07        11.70         1.74         1.81        15.42         6.38 
TCGA-K4-AAQO TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN 
       11.80        15.32        15.58        13.48        12.23        16.67 
TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78K 
       14.24         1.84         3.75        12.43        31.56        17.62 
TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78N TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A9PA 
       37.05        22.68        86.83        76.01        65.75        35.24 
TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HH TCGA-XF-A8HI 
       29.56        17.82         4.54         1.64         1.87        17.88 
TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SJ TCGA-XF-A9SL TCGA-XF-A9SV TCGA-XF-A9SW 
       48.62        64.80         3.22        66.41        12.76        11.90 
TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 
       23.64        21.04        28.24        26.27        18.90         2.24 
TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMF 
       16.27        66.64         2.10        13.74        92.98        10.82 
TCGA-XF-AAMG TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR 
      110.60        11.31        54.90         7.63        71.57        91.73 
TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN0 
        2.96         8.32         6.77        98.99        44.32        56.48 
TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN7 TCGA-XF-AAN8 
       30.94        61.45        86.30        27.06        18.81         3.88 
TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R0 TCGA-ZF-A9R1 
        9.63         0.66        11.97        13.64        18.64         7.36 
TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 
       21.11        24.13        30.28        27.19        21.86        28.41 
TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RL 
       74.56        13.41         3.48        52.73        52.60        82.49 
TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4U 
       47.84        20.22         2.89        34.06        19.69         8.61 
TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA53 TCGA-ZF-AA54 
       59.38        60.16        38.73        35.41        57.90        19.40 
TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-ZF-AA5P 
        8.52        47.15        19.17         5.52        10.13 

  EZR MUTATED EZR WILD-TYPE 
         8.48          0.10 
  EZR MUTATED EZR WILD-TYPE 
       130.88        166.03 
  EZR MUTATED EZR WILD-TYPE 
        41.56         15.32 
[1] "8.5 - 130.9 (41.6)" "0.1 - 166.0 (15.3)"
[1] "hr=" "4.2"
D99V2, continuous
               vv
clus            STAGE I STAGE II STAGE III STAGE IV
  EZR MUTATED         0        5         4        2
  EZR WILD-TYPE       4      112       118      126
D99V3, multiclass
           clus
vv          EZR MUTATED EZR WILD-TYPE
  STAGE I             0             4
  STAGE II            5           112
  STAGE III           4           118
  STAGE IV            2           126
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            T0+T1+T2  T3  T4
  EZR MUTATED          4   5   0
  EZR WILD-TYPE      110 174  52
D99V4, multiclass
          clus
vv         EZR MUTATED EZR WILD-TYPE
  T0+T1+T2           4           110
  T3                 5           174
  T4                 0            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"
               vv
clus             N0  N1  N2  N3
  EZR MUTATED     7   0   1   0
  EZR WILD-TYPE 206  41  74   8
D99V5, multiclass
    clus
vv   EZR MUTATED EZR WILD-TYPE
  N0           7           206
  N1           0            41
  N2           1            74
  N3           0             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"
D99V6, binary
               cls
clus              0   1
  EZR MUTATED     5   1
  EZR WILD-TYPE 177   9
[1] "tbl2"
               cls
clus            [,1] [,2]
  EZR MUTATED      5    1
  EZR WILD-TYPE  177    9
   clus
vv  EZR MUTATED EZR WILD-TYPE
  0           5           177
  1           1             9
[1] 2 2
[1] FALSE
D99V7, binary
               cls
clus              0   1
  EZR MUTATED     4   7
  EZR WILD-TYPE  92 273
[1] "tbl2"
               cls
clus            [,1] [,2]
  EZR MUTATED      4    7
  EZR WILD-TYPE   92  273
        clus
vv       EZR MUTATED EZR WILD-TYPE
  FEMALE           4            92
  MALE             7           273
[1] 2 2
[1] FALSE
D99V8, continuous
D99V9, continuous
D99V10, continuous
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  EZR MUTATED       1                         2     8
  EZR WILD-TYPE    37                        19   293
D99V11, multiclass
                           clus
vv                          EZR MUTATED EZR WILD-TYPE
  ASIAN                               1            37
  BLACK OR AFRICAN AMERICAN           2            19
  WHITE                               8           293
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D99V12, binary
               cls
clus              0   1
  EZR MUTATED     0  10
  EZR WILD-TYPE   8 328
[1] "tbl2"
               cls
clus            [,1] [,2]
  EZR MUTATED      0   10
  EZR WILD-TYPE    8  328
                        clus
vv                       EZR MUTATED EZR WILD-TYPE
  HISPANIC OR LATINO               0             8
  NOT HISPANIC OR LATINO          10           328
[1] 2 2
[1] FALSE

Clustering(100) Variable = ZEB2 MUTATION ANALYSIS
D100V1, survival
                sevent
clus2              0   1
  ZEB2 MUTATED     8   5
  ZEB2 WILD-TYPE 211 146
  ZEB2 MUTATED ZEB2 WILD-TYPE 
            13            357 
  ZEB2 MUTATED ZEB2 WILD-TYPE 
             5            146 
$`ZEB2 MUTATED`
TCGA-BL-A5ZZ TCGA-BT-A3PJ TCGA-CF-A1HR TCGA-CF-A47X TCGA-DK-AA76 TCGA-FD-A5BU 
       12.39        12.82         0.46        12.62        12.03        19.33 
TCGA-FD-A5BZ TCGA-FD-A6TG TCGA-XF-A9T0 TCGA-XF-A9T8 TCGA-ZF-A9RD TCGA-ZF-AA4N 
       27.45         3.06        26.27        13.74        13.41         2.89 
TCGA-ZF-AA51 
       38.73 

$`ZEB2 WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        91.63       103.50       105.70         8.35 
TCGA-4Z-AA7M TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7S 
       16.27        44.94        16.83        16.77        17.16        34.98 
TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 
       27.62        49.12         0.62        41.75        51.16        66.54 
TCGA-4Z-AA84 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BL-A13I 
       15.12        10.22        47.80        33.83        40.08         7.33 
TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N 
        2.66         6.74         6.58        13.15        19.04        32.84 
TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U 
       12.16        17.88        19.50         5.06        14.89        14.96 
TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A2LD 
        5.06         8.35         8.25        17.16        16.18        20.48 
TCGA-BT-A3PH TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E TCGA-BT-A42F 
        4.67         9.96        17.56        28.70        24.26        28.41 
TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-C4-A0F6 TCGA-C4-A0F7 TCGA-CF-A1HS 
        8.98         1.94         2.93        23.01         2.04         0.43 
TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47Y 
        0.69        10.95        12.66        12.46        12.10        12.26 
TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A0YN 
       13.12        12.00        12.10        11.87        13.08        12.92 
TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 
        4.90         7.20         5.46         5.19        16.31         1.84 
TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA 
       13.58        21.86         2.14        66.41        18.41        19.00 
TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG 
       16.70       130.88       112.44        16.14        17.62        15.62 
TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK 
        1.81        10.59         7.79       123.85        87.32         2.20 
TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT 
       13.58         7.82         8.22        17.72        50.27        21.30 
TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 
       23.21         9.67        20.81        10.55       140.81        48.00 
TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 
       17.98        64.18        41.56        76.60        67.36        15.68 
TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6S 
       41.06        30.67        38.24        15.02        13.58       166.03 
TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA74 
       12.36        10.49         8.65         7.53        13.64        43.50 
TCGA-DK-AA77 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 
       10.62        43.59        15.35        38.83        24.66         0.10 
TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF 
        0.49         2.24        16.70        17.39         0.56         0.66 
TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7DV 
       14.56        13.97        12.99        14.33         0.92         1.22 
TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B3 
       13.68        14.07        12.95        14.37         8.09        32.02 
TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 
       16.77         8.94        33.04         4.01        12.62        22.52 
TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN 
       27.98        60.66        24.30        23.41        17.98        29.16 
TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N 
        5.52        25.74        46.78        19.79        12.85        22.98 
TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS 
       27.35        14.96        20.91         3.62        26.73        53.88 
TCGA-FD-A5BT TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5C0 TCGA-FD-A5C1 
       11.01         5.36         5.69         8.25        18.08        58.92 
TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB 
        2.70         7.10         6.28        13.35        62.86        18.81 
TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TH TCGA-FD-A6TI 
        6.15        12.69        12.36         2.27         4.31         9.67 
TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FJ-A871 
       10.85        31.07         7.13        10.65        17.23         8.94 
TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EC TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK 
        3.25         6.48        22.88        61.94        30.61        15.95 
TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY 
       26.93        35.24        33.01         7.23        20.12        17.62 
TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 
       66.02         6.94        64.44        19.46        21.40         2.24 
TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS 
       15.81         4.50        15.91        14.07        17.75        24.92 
TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS 
        8.94        13.91         7.73         2.10         3.12        20.98 
TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 
        2.20         7.36        10.92        11.31        11.31         7.63 
TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATO TCGA-GU-AATP 
       27.09        20.05         5.62         4.73        10.65        32.98 
TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF 
        7.00        14.27        21.34        19.10        19.82        20.28 
TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA 
        8.48        10.59        27.35         8.58        19.07        22.72 
TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE 
        1.51        19.40        38.60         3.06         9.01         8.22 
TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R 
       25.02         3.45        21.24         2.76         9.14        27.68 
TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P 
        9.07        11.70         1.74         1.81        15.42         6.38 
TCGA-K4-AAQO TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN 
       11.80        15.32        15.58        13.48        12.23        16.67 
TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78K 
       14.24         1.84         3.75        12.43        31.56        17.62 
TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78N TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A9PA 
       37.05        22.68        86.83        76.01        65.75        35.24 
TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HH TCGA-XF-A8HI 
       29.56        17.82         4.54         1.64         1.87        17.88 
TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SL TCGA-XF-A9SV 
       48.62        64.80        79.66         3.22        66.41        12.76 
TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T2 TCGA-XF-A9T3 
       11.90        23.64        21.04        28.24        18.90         2.24 
TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMG 
       16.27        66.64         2.10        92.98        10.82       110.60 
TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMT 
       11.31        54.90         7.63        71.57        91.73         2.96 
TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN0 TCGA-XF-AAN1 
        8.32         6.77        98.99        44.32        56.48        30.94 
TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN7 TCGA-XF-AAN8 
       61.45        86.30        27.06        75.39        18.81         3.88 
TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R0 TCGA-ZF-A9R1 
        9.63         0.66        11.97        13.64        18.64         7.36 
TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 
       21.11        24.13        30.28        27.19        21.86        28.41 
TCGA-ZF-A9RC TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-A9RM 
       74.56         3.48        52.73        52.60        82.49        47.84 
TCGA-ZF-A9RN TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W 
       20.22        34.06        19.69         8.61        59.38        60.16 
TCGA-ZF-AA4X TCGA-ZF-AA52 TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 
       63.02        35.41        57.90        19.40         8.52        47.15 
TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-ZF-AA5P 
       19.17         5.52        10.13 

  ZEB2 MUTATED ZEB2 WILD-TYPE 
          0.46           0.10 
  ZEB2 MUTATED ZEB2 WILD-TYPE 
         38.73         166.03 
  ZEB2 MUTATED ZEB2 WILD-TYPE 
         12.82          15.91 
[1] "0.5 - 38.7 (12.8)"  "0.1 - 166.0 (15.9)"
[1] "hr=" "1.3"
D100V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  ZEB2 MUTATED         0        5         4        3
  ZEB2 WILD-TYPE       4      112       118      125
D100V3, multiclass
           clus
vv          ZEB2 MUTATED ZEB2 WILD-TYPE
  STAGE I              0              4
  STAGE II             5            112
  STAGE III            4            118
  STAGE IV             3            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"
                vv
clus             T0+T1+T2  T3  T4
  ZEB2 MUTATED          3   7   1
  ZEB2 WILD-TYPE      111 172  51
D100V4, multiclass
          clus
vv         ZEB2 MUTATED ZEB2 WILD-TYPE
  T0+T1+T2            3            111
  T3                  7            172
  T4                  1             51
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  ZEB2 MUTATED     7   1   2   1
  ZEB2 WILD-TYPE 206  40  73   7
D100V5, multiclass
    clus
vv   ZEB2 MUTATED ZEB2 WILD-TYPE
  N0            7            206
  N1            1             40
  N2            2             73
  N3            1              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"
D100V6, binary
                cls
clus               0   1
  ZEB2 MUTATED     5   0
  ZEB2 WILD-TYPE 177  10
[1] "tbl2"
                cls
clus             [,1] [,2]
  ZEB2 MUTATED      5    0
  ZEB2 WILD-TYPE  177   10
   clus
vv  ZEB2 MUTATED ZEB2 WILD-TYPE
  0            5            177
  1            0             10
[1] 2 2
[1] FALSE
D100V7, binary
                cls
clus               0   1
  ZEB2 MUTATED     6   7
  ZEB2 WILD-TYPE  90 273
[1] "tbl2"
                cls
clus             [,1] [,2]
  ZEB2 MUTATED      6    7
  ZEB2 WILD-TYPE   90  273
        clus
vv       ZEB2 MUTATED ZEB2 WILD-TYPE
  FEMALE            6             90
  MALE              7            273
[1] 2 2
[1] FALSE
D100V8, continuous
D100V9, continuous
D100V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ZEB2 MUTATED       2                         1    10
  ZEB2 WILD-TYPE    36                        20   291
D100V11, multiclass
                           clus
vv                          ZEB2 MUTATED ZEB2 WILD-TYPE
  ASIAN                                2             36
  BLACK OR AFRICAN AMERICAN            1             20
  WHITE                               10            291
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D100V12, binary
                cls
clus               0   1
  ZEB2 MUTATED     0  13
  ZEB2 WILD-TYPE   8 325
[1] "tbl2"
                cls
clus             [,1] [,2]
  ZEB2 MUTATED      0   13
  ZEB2 WILD-TYPE    8  325
                        clus
vv                       ZEB2 MUTATED ZEB2 WILD-TYPE
  HISPANIC OR LATINO                0              8
  NOT HISPANIC OR LATINO           13            325
[1] 2 2
[1] FALSE

Clustering(101) Variable = C12ORF43 MUTATION ANALYSIS
D101V1, survival
                    sevent
clus2                  0   1
  C12ORF43 MUTATED     5   2
  C12ORF43 WILD-TYPE 214 149
  C12ORF43 MUTATED C12ORF43 WILD-TYPE 
                 7                363 
  C12ORF43 MUTATED C12ORF43 WILD-TYPE 
                 2                149 
$`C12ORF43 MUTATED`
TCGA-BT-A3PK TCGA-DK-A3X1 TCGA-G2-A2EF TCGA-GU-A42P TCGA-MV-A51V TCGA-SY-A9G5 
        9.96        48.00        61.94        10.92        13.48        31.56 
TCGA-ZF-A9RG 
       52.60 

$`C12ORF43 WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        91.63       103.50       105.70         8.35 
TCGA-4Z-AA7M TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7S 
       16.27        44.94        16.83        16.77        17.16        34.98 
TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 
       27.62        49.12         0.62        41.75        51.16        66.54 
TCGA-4Z-AA84 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BL-A13I 
       15.12        10.22        47.80        33.83        40.08         7.33 
TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J 
        2.66         6.74        12.39         6.58        13.15        19.04 
TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T 
       32.84        12.16        17.88        19.50         5.06        14.89 
TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB 
       14.96         5.06         8.35         8.25        17.16        16.18 
TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E 
       20.48         4.67        12.82        17.56        28.70        24.26 
TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-C4-A0F6 TCGA-C4-A0F7 
       28.41         8.98         1.94         2.93        23.01         2.04 
TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V 
        0.46         0.43         0.69        10.95        12.66        12.46 
TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 
       12.10        12.62        12.26        13.12        12.00        12.10 
TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ 
       11.87        13.08        12.92         4.90         7.20         5.46 
TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 
        5.19        16.31         1.84        13.58        21.86         2.14 
TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD 
       66.41        18.41        19.00        16.70       130.88       112.44 
TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 
       16.14        17.62        15.62         1.81        10.59         7.79 
TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN 
      123.85        87.32         2.20        13.58         7.82         8.22 
TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW 
       17.72        50.27        21.30        23.21         9.67        20.81 
TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 
       10.55       140.81        17.98        64.18        41.56        76.60 
TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6P 
       67.36        15.68        41.06        30.67        38.24        15.02 
TCGA-DK-AA6Q TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA6X 
       13.58       166.03        12.36        10.49         8.65         7.53 
TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A2PC TCGA-E5-A4TZ 
       13.64        43.50        12.03        10.62        43.59        15.35 
TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 
       38.83        24.66         0.10         0.49         2.24        16.70 
TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME 
       17.39         0.56         0.66        14.56        13.97        12.99 
TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H 
       14.33         0.92         1.22        13.68        14.07        12.95 
TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 
       14.37         8.09        32.02        16.77         8.94        33.04 
TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ 
        4.01        12.62        22.52        27.98        60.66        24.30 
TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ 
       23.41        17.98        29.16         5.52        25.74        46.78 
TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U 
       19.79        12.85        22.98        27.35        14.96        20.91 
TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV 
        3.62        26.73        53.88        11.01        19.33         5.36 
TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N 
        5.69         8.25        27.45        18.08        58.92         2.70 
TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC 
        7.10         6.28        13.35        62.86        18.81         6.15 
TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI 
       12.69        12.36         2.27         3.06         4.31         9.67 
TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FJ-A871 
       10.85        31.07         7.13        10.65        17.23         8.94 
TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EC TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL 
        3.25         6.48        22.88        30.61        15.95        26.93 
TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B 
       35.24        33.01         7.23        20.12        17.62        66.02 
TCGA-G2-AA3C TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO 
        6.94        64.44        19.46        21.40         2.24        15.81 
TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A6I1 
        4.50        15.91        14.07        17.75        24.92         8.94 
TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 
       13.91         7.73         2.10         3.12        20.98         2.20 
TCGA-GD-A76B TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A764 
        7.36        11.31        11.31         7.63        27.09        20.05 
TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATO TCGA-GU-AATP TCGA-GU-AATQ TCGA-GV-A3JV 
        5.62         4.73        10.65        32.98         7.00        14.27 
TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI 
       21.34        19.10        19.82        20.28         8.48        10.59 
TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-H4-A2HQ 
       27.35         8.58        19.07        22.72         1.51        19.40 
TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU 
       38.60         3.06         9.01         8.22        25.02         3.45 
TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RH TCGA-K4-A5RI 
       21.24         2.76         9.14        27.68         9.07        11.70 
TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO TCGA-LC-A66R 
        1.74         1.81        15.42         6.38        11.80        15.32 
TCGA-LT-A5Z6 TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 
       15.58        12.23        16.67        14.24         1.84         3.75 
TCGA-SY-A9G0 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78N TCGA-UY-A78O 
       12.43        17.62        37.05        22.68        86.83        76.01 
TCGA-UY-A8OB TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF 
       65.75        35.24        29.56        17.82         4.54         1.64 
TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SJ 
        1.87        17.88        48.62        64.80        79.66         3.22 
TCGA-XF-A9SL TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ 
       66.41        12.76        11.90        23.64        21.04        28.24 
TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 
       26.27        18.90         2.24        16.27        66.64         2.10 
TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMG TCGA-XF-AAMH TCGA-XF-AAMJ 
       13.74        92.98        10.82       110.60        11.31        54.90 
TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX 
        7.63        71.57        91.73         2.96         8.32         6.77 
TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 
       98.99        44.32        56.48        30.94        61.45        86.30 
TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YC-A9TC 
       27.06        75.39        18.81         3.88         9.63         0.66 
TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R3 
       11.97        13.64        18.64         7.36        21.11        24.13 
TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RD 
       30.28        27.19        21.86        28.41        74.56        13.41 
TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N 
        3.48        52.73        82.49        47.84        20.22         2.89 
TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA4X 
       34.06        19.69         8.61        59.38        60.16        63.02 
TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 
       38.73        35.41        57.90        19.40         8.52        47.15 
TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-ZF-AA5P 
       19.17         5.52        10.13 

  C12ORF43 MUTATED C12ORF43 WILD-TYPE 
              9.96               0.10 
  C12ORF43 MUTATED C12ORF43 WILD-TYPE 
             61.94             166.03 
  C12ORF43 MUTATED C12ORF43 WILD-TYPE 
             31.56              15.62 
[1] "10.0 - 61.9 (31.6)" "0.1 - 166.0 (15.6)"
[1] "hr=" "2"  
D101V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  C12ORF43 MUTATED         0        2         4        1
  C12ORF43 WILD-TYPE       4      115       118      127
D101V3, multiclass
           clus
vv          C12ORF43 MUTATED C12ORF43 WILD-TYPE
  STAGE I                  0                  4
  STAGE II                 2                115
  STAGE III                4                118
  STAGE IV                 1                127
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1+T2  T3  T4
  C12ORF43 MUTATED          1   4   1
  C12ORF43 WILD-TYPE      113 175  51
D101V4, multiclass
          clus
vv         C12ORF43 MUTATED C12ORF43 WILD-TYPE
  T0+T1+T2                1                113
  T3                      4                175
  T4                      1                 51
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  C12ORF43 MUTATED     6   1   0   0
  C12ORF43 WILD-TYPE 207  40  75   8
D101V5, multiclass
    clus
vv   C12ORF43 MUTATED C12ORF43 WILD-TYPE
  N0                6                207
  N1                1                 40
  N2                0                 75
  N3                0                  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"
D101V6, binary
                    cls
clus                   0   1
  C12ORF43 MUTATED     5   0
  C12ORF43 WILD-TYPE 177  10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C12ORF43 MUTATED      5    0
  C12ORF43 WILD-TYPE  177   10
   clus
vv  C12ORF43 MUTATED C12ORF43 WILD-TYPE
  0                5                177
  1                0                 10
[1] 2 2
[1] FALSE
D101V7, binary
                    cls
clus                   0   1
  C12ORF43 MUTATED     2   5
  C12ORF43 WILD-TYPE  94 275
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C12ORF43 MUTATED      2    5
  C12ORF43 WILD-TYPE   94  275
        clus
vv       C12ORF43 MUTATED C12ORF43 WILD-TYPE
  FEMALE                2                 94
  MALE                  5                275
[1] 2 2
[1] FALSE
D101V8, continuous
[1] "Remove cluster labels:" "C12ORF43 MUTATED"      
clus
  C12ORF43 MUTATED C12ORF43 WILD-TYPE 
                 2                118 
        TCGA-2F-A9KO         TCGA-2F-A9KP         TCGA-2F-A9KQ 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-2F-A9KR         TCGA-2F-A9KT         TCGA-2F-A9KW 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-CF-A1HS         TCGA-CF-A27C         TCGA-CF-A3MF 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-CF-A3MG         TCGA-CF-A3MH         TCGA-CF-A3MI 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-CF-A47S         TCGA-CF-A47T         TCGA-CF-A47V 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-CF-A47W         TCGA-CF-A47X         TCGA-CF-A47Y 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-CF-A5U8         TCGA-CF-A5UA         TCGA-CF-A7I0 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-DK-A2HX         TCGA-DK-A3IN         TCGA-DK-A3IV 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-DK-A3WX         TCGA-DK-A3X2         TCGA-DK-A6B2 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-DK-A6B5         TCGA-DK-A6B6         TCGA-DK-AA6P 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-DK-AA6S         TCGA-DK-AA6U         TCGA-DK-AA6W 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-DK-AA76         TCGA-E5-A2PC         TCGA-E5-A4TZ 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-E5-A4U1         TCGA-E7-A519         TCGA-E7-A541 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-E7-A7DU         TCGA-E7-A7DV         TCGA-FT-A61P 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-G2-A2EC         TCGA-G2-A2EJ         TCGA-G2-A2EK 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-G2-A2EL         TCGA-G2-A2EO         TCGA-G2-A2ES 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-G2-A3IB         TCGA-G2-A3IE         TCGA-G2-A3VY 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-GC-A3BM         TCGA-GC-A3I6         TCGA-GC-A3OO 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-GC-A3RC         TCGA-GC-A3RD         TCGA-GC-A3YS 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-GC-A6I1         TCGA-GC-A6I3         TCGA-GD-A3OS 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-GD-A6C6         TCGA-GV-A3JV         TCGA-GV-A3JW 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-GV-A3JX         TCGA-GV-A3JZ         TCGA-GV-A3QF 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-GV-A3QH         TCGA-GV-A3QI         TCGA-GV-A3QK 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-GV-A40E         TCGA-GV-A40G         TCGA-GV-A6ZA 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-SY-A9G0         TCGA-UY-A78L         TCGA-UY-A78M 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-UY-A78N         TCGA-XF-A8HH         TCGA-XF-A8HI 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-XF-A9SG         TCGA-XF-A9SH         TCGA-XF-A9SI 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-XF-A9SJ         TCGA-XF-A9SL         TCGA-XF-A9SV 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-XF-A9SW         TCGA-XF-A9SX         TCGA-XF-A9SY 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-XF-A9SZ         TCGA-XF-A9T0         TCGA-XF-A9T2 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-XF-A9T3         TCGA-XF-A9T4         TCGA-XF-A9T5 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-XF-A9T6         TCGA-XF-A9T8         TCGA-XF-AAME 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-XF-AAMF         TCGA-XF-AAMG         TCGA-XF-AAMH 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-XF-AAMJ         TCGA-XF-AAML         TCGA-XF-AAMQ 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-XF-AAMR         TCGA-XF-AAMT         TCGA-XF-AAMW 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-XF-AAMX         TCGA-XF-AAMY         TCGA-XF-AAMZ 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-XF-AAN0         TCGA-XF-AAN1         TCGA-XF-AAN2 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-XF-AAN3         TCGA-XF-AAN4         TCGA-XF-AAN5 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-XF-AAN7         TCGA-XF-AAN8         TCGA-YF-AA3L 
"C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" "C12ORF43 WILD-TYPE" 
        TCGA-YF-AA3M 
"C12ORF43 WILD-TYPE" 
D101V9, continuous
D101V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  C12ORF43 MUTATED       0                         0     7
  C12ORF43 WILD-TYPE    38                        21   294
D101V11, multiclass
                           clus
vv                          C12ORF43 MUTATED C12ORF43 WILD-TYPE
  ASIAN                                    0                 38
  BLACK OR AFRICAN AMERICAN                0                 21
  WHITE                                    7                294
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D101V12, binary
                    cls
clus                   0   1
  C12ORF43 MUTATED     0   7
  C12ORF43 WILD-TYPE   8 331
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C12ORF43 MUTATED      0    7
  C12ORF43 WILD-TYPE    8  331
                        clus
vv                       C12ORF43 MUTATED C12ORF43 WILD-TYPE
  HISPANIC OR LATINO                    0                  8
  NOT HISPANIC OR LATINO                7                331
[1] 2 2
[1] FALSE

Clustering(102) Variable = NAP1L1 MUTATION ANALYSIS
D102V1, survival
                  sevent
clus2                0   1
  NAP1L1 MUTATED     8   2
  NAP1L1 WILD-TYPE 211 149
  NAP1L1 MUTATED NAP1L1 WILD-TYPE 
              10              360 
  NAP1L1 MUTATED NAP1L1 WILD-TYPE 
               2              149 
$`NAP1L1 MUTATED`
TCGA-BT-A20R TCGA-BT-A42E TCGA-DK-A2I6 TCGA-DK-AA6X TCGA-E5-A4U1 TCGA-E7-A6ME 
        5.06        24.26        87.32         7.53        38.83        12.99 
TCGA-FD-A3B5 TCGA-FT-A61P TCGA-XF-A9SI TCGA-XF-AAN3 
        8.94         6.48        79.66        86.30 

$`NAP1L1 WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        91.63       103.50       105.70         8.35 
TCGA-4Z-AA7M TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7S 
       16.27        44.94        16.83        16.77        17.16        34.98 
TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 
       27.62        49.12         0.62        41.75        51.16        66.54 
TCGA-4Z-AA84 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BL-A13I 
       15.12        10.22        47.80        33.83        40.08         7.33 
TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J 
        2.66         6.74        12.39         6.58        13.15        19.04 
TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20T TCGA-BT-A20U 
       32.84        12.16        17.88        19.50        14.89        14.96 
TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A2LD 
        5.06         8.35         8.25        17.16        16.18        20.48 
TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42F 
        4.67        12.82         9.96        17.56        28.70        28.41 
TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-C4-A0F6 TCGA-C4-A0F7 TCGA-CF-A1HR 
        8.98         1.94         2.93        23.01         2.04         0.46 
TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W 
        0.43         0.69        10.95        12.66        12.46        12.10 
TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A9FF 
       12.62        12.26        13.12        12.00        12.10        11.87 
TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3QU 
       13.08        12.92         4.90         7.20         5.46         5.19 
TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 
       16.31         1.84        13.58        21.86         2.14        66.41 
TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE 
       18.41        19.00        16.70       130.88       112.44        16.14 
TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 
       17.62        15.62         1.81        10.59         7.79       123.85 
TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS 
        2.20        13.58         7.82         8.22        17.72        50.27 
TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY 
       21.30        23.21         9.67        20.81        10.55       140.81 
TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 
       48.00        17.98        64.18        41.56        76.60        67.36 
TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6P TCGA-DK-AA6Q 
       15.68        41.06        30.67        38.24        15.02        13.58 
TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA71 TCGA-DK-AA74 
      166.03        12.36        10.49         8.65        13.64        43.50 
TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E7-A3X6 TCGA-E7-A3Y1 
       12.03        10.62        43.59        15.35        24.66         0.10 
TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF 
        0.49         2.24        16.70        17.39         0.56         0.66 
TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7DV TCGA-E7-A7PW 
       14.56        13.97        14.33         0.92         1.22        13.68 
TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 
       14.07        12.95        14.37         8.09        32.02        16.77 
TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA 
       33.04         4.01        12.62        22.52        27.98        60.66 
TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP 
       24.30        23.41        17.98        29.16         5.52        25.74 
TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S 
       46.78        19.79        12.85        22.98        27.35        14.96 
TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU 
       20.91         3.62        26.73        53.88        11.01        19.33 
TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 
        5.36         5.69         8.25        27.45        18.08        58.92 
TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB 
        2.70         7.10         6.28        13.35        62.86        18.81 
TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH 
        6.15        12.69        12.36         2.27         3.06         4.31 
TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF 
        9.67        10.85        31.07         7.13        10.65        17.23 
TCGA-FJ-A871 TCGA-FT-A3EE TCGA-G2-A2EC TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK 
        8.94         3.25        22.88        61.94        30.61        15.95 
TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY 
       26.93        35.24        33.01         7.23        20.12        17.62 
TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 
       66.02         6.94        64.44        19.46        21.40         2.24 
TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS 
       15.81         4.50        15.91        14.07        17.75        24.92 
TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS 
        8.94        13.91         7.73         2.10         3.12        20.98 
TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 
        2.20         7.36        10.92        11.31        11.31         7.63 
TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATO TCGA-GU-AATP 
       27.09        20.05         5.62         4.73        10.65        32.98 
TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF 
        7.00        14.27        21.34        19.10        19.82        20.28 
TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA 
        8.48        10.59        27.35         8.58        19.07        22.72 
TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE 
        1.51        19.40        38.60         3.06         9.01         8.22 
TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R 
       25.02         3.45        21.24         2.76         9.14        27.68 
TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P 
        9.07        11.70         1.74         1.81        15.42         6.38 
TCGA-K4-AAQO TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN 
       11.80        15.32        15.58        13.48        12.23        16.67 
TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78K 
       14.24         1.84         3.75        12.43        31.56        17.62 
TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78N TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A9PA 
       37.05        22.68        86.83        76.01        65.75        35.24 
TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HH TCGA-XF-A8HI 
       29.56        17.82         4.54         1.64         1.87        17.88 
TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SJ TCGA-XF-A9SL TCGA-XF-A9SV TCGA-XF-A9SW 
       48.62        64.80         3.22        66.41        12.76        11.90 
TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 
       23.64        21.04        28.24        26.27        18.90         2.24 
TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMF 
       16.27        66.64         2.10        13.74        92.98        10.82 
TCGA-XF-AAMG TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR 
      110.60        11.31        54.90         7.63        71.57        91.73 
TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN0 
        2.96         8.32         6.77        98.99        44.32        56.48 
TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN7 TCGA-XF-AAN8 
       30.94        61.45        27.06        75.39        18.81         3.88 
TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R0 TCGA-ZF-A9R1 
        9.63         0.66        11.97        13.64        18.64         7.36 
TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 
       21.11        24.13        30.28        27.19        21.86        28.41 
TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RL 
       74.56        13.41         3.48        52.73        52.60        82.49 
TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4U 
       47.84        20.22         2.89        34.06        19.69         8.61 
TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA53 
       59.38        60.16        63.02        38.73        35.41        57.90 
TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-ZF-AA5P 
       19.40         8.52        47.15        19.17         5.52        10.13 

  NAP1L1 MUTATED NAP1L1 WILD-TYPE 
            5.06             0.10 
  NAP1L1 MUTATED NAP1L1 WILD-TYPE 
           87.32           166.03 
  NAP1L1 MUTATED NAP1L1 WILD-TYPE 
          18.625           15.650 
[1] "5.1 - 87.3 (18.6)"  "0.1 - 166.0 (15.6)"
[1] "hr=" "2.6"
D102V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  NAP1L1 MUTATED         0        4         1        5
  NAP1L1 WILD-TYPE       4      113       121      123
D102V3, multiclass
           clus
vv          NAP1L1 MUTATED NAP1L1 WILD-TYPE
  STAGE I                0                4
  STAGE II               4              113
  STAGE III              1              121
  STAGE IV               5              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"
                  vv
clus               T0+T1+T2  T3  T4
  NAP1L1 MUTATED          5   4   0
  NAP1L1 WILD-TYPE      109 175  52
D102V4, multiclass
          clus
vv         NAP1L1 MUTATED NAP1L1 WILD-TYPE
  T0+T1+T2              5              109
  T3                    4              175
  T4                    0               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"
                  vv
clus                N0  N1  N2  N3
  NAP1L1 MUTATED     4   3   2   0
  NAP1L1 WILD-TYPE 209  38  73   8
D102V5, multiclass
    clus
vv   NAP1L1 MUTATED NAP1L1 WILD-TYPE
  N0              4              209
  N1              3               38
  N2              2               73
  N3              0                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"
D102V6, binary
                  cls
clus                 0   1
  NAP1L1 MUTATED     6   0
  NAP1L1 WILD-TYPE 176  10
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NAP1L1 MUTATED      6    0
  NAP1L1 WILD-TYPE  176   10
   clus
vv  NAP1L1 MUTATED NAP1L1 WILD-TYPE
  0              6              176
  1              0               10
[1] 2 2
[1] FALSE
D102V7, binary
                  cls
clus                 0   1
  NAP1L1 MUTATED     2   8
  NAP1L1 WILD-TYPE  94 272
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NAP1L1 MUTATED      2    8
  NAP1L1 WILD-TYPE   94  272
        clus
vv       NAP1L1 MUTATED NAP1L1 WILD-TYPE
  FEMALE              2               94
  MALE                8              272
[1] 2 2
[1] FALSE
D102V8, continuous
D102V9, continuous
D102V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  NAP1L1 MUTATED       2                         1     6
  NAP1L1 WILD-TYPE    36                        20   295
D102V11, multiclass
                           clus
vv                          NAP1L1 MUTATED NAP1L1 WILD-TYPE
  ASIAN                                  2               36
  BLACK OR AFRICAN AMERICAN              1               20
  WHITE                                  6              295
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D102V12, binary
                  cls
clus                 0   1
  NAP1L1 MUTATED     0  10
  NAP1L1 WILD-TYPE   8 328
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NAP1L1 MUTATED      0   10
  NAP1L1 WILD-TYPE    8  328
                        clus
vv                       NAP1L1 MUTATED NAP1L1 WILD-TYPE
  HISPANIC OR LATINO                  0                8
  NOT HISPANIC OR LATINO             10              328
[1] 2 2
[1] FALSE

Clustering(103) Variable = NAALADL1 MUTATION ANALYSIS
D103V1, survival
                    sevent
clus2                  0   1
  NAALADL1 MUTATED     4   3
  NAALADL1 WILD-TYPE 215 148
  NAALADL1 MUTATED NAALADL1 WILD-TYPE 
                 7                363 
  NAALADL1 MUTATED NAALADL1 WILD-TYPE 
                 3                148 
$`NAALADL1 MUTATED`
TCGA-DK-A3WW TCGA-DK-A6AW TCGA-FD-A43P TCGA-FD-A6TH TCGA-K4-A4AC TCGA-ZF-AA4T 
       20.81        41.56        27.35         4.31         9.14        19.69 
TCGA-ZF-AA51 
       38.73 

$`NAALADL1 WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        91.63       103.50       105.70         8.35 
TCGA-4Z-AA7M TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7S 
       16.27        44.94        16.83        16.77        17.16        34.98 
TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 
       27.62        49.12         0.62        41.75        51.16        66.54 
TCGA-4Z-AA84 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BL-A13I 
       15.12        10.22        47.80        33.83        40.08         7.33 
TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J 
        2.66         6.74        12.39         6.58        13.15        19.04 
TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T 
       32.84        12.16        17.88        19.50         5.06        14.89 
TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB 
       14.96         5.06         8.35         8.25        17.16        16.18 
TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C 
       20.48         4.67        12.82         9.96        17.56        28.70 
TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-C4-A0F6 
       24.26        28.41         8.98         1.94         2.93        23.01 
TCGA-C4-A0F7 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T 
        2.04         0.46         0.43         0.69        10.95        12.66 
TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA 
       12.46        12.10        12.62        12.26        13.12        12.00 
TCGA-CF-A7I0 TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR 
       12.10        11.87        13.08        12.92         4.90         7.20 
TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 
        5.46         5.19        16.31         1.84        13.58        21.86 
TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC 
        2.14        66.41        18.41        19.00        16.70       130.88 
TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 
      112.44        16.14        17.62        15.62         1.81        10.59 
TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM 
        7.79       123.85        87.32         2.20        13.58         7.82 
TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV 
        8.22        17.72        50.27        21.30        23.21         9.67 
TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6B0 
       10.55       140.81        48.00        17.98        64.18        76.60 
TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6P 
       67.36        15.68        41.06        30.67        38.24        15.02 
TCGA-DK-AA6Q TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA6X 
       13.58       166.03        12.36        10.49         8.65         7.53 
TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A2PC TCGA-E5-A4TZ 
       13.64        43.50        12.03        10.62        43.59        15.35 
TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 
       38.83        24.66         0.10         0.49         2.24        16.70 
TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME 
       17.39         0.56         0.66        14.56        13.97        12.99 
TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H 
       14.33         0.92         1.22        13.68        14.07        12.95 
TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 
       14.37         8.09        32.02        16.77         8.94        33.04 
TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ 
        4.01        12.62        22.52        27.98        60.66        24.30 
TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ 
       23.41        17.98        29.16         5.52        25.74        46.78 
TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X 
       19.79        12.85        22.98        14.96        20.91         3.62 
TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX 
       26.73        53.88        11.01        19.33         5.36         5.69 
TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O 
        8.25        27.45        18.08        58.92         2.70         7.10 
TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD 
        6.28        13.35        62.86        18.81         6.15        12.69 
TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z7 
       12.36         2.27         3.06         9.67        10.85        31.07 
TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FJ-A871 TCGA-FT-A3EE TCGA-FT-A61P 
        7.13        10.65        17.23         8.94         3.25         6.48 
TCGA-G2-A2EC TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO 
       22.88        61.94        30.61        15.95        26.93        35.24 
TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3C 
       33.01         7.23        20.12        17.62        66.02         6.94 
TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB 
       64.44        19.46        21.40         2.24        15.81         4.50 
TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GC-A6I3 
       15.91        14.07        17.75        24.92         8.94        13.91 
TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GD-A76B 
        7.73         2.10         3.12        20.98         2.20         7.36 
TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A764 
       10.92        11.31        11.31         7.63        27.09        20.05 
TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATO TCGA-GU-AATP TCGA-GU-AATQ TCGA-GV-A3JV 
        5.62         4.73        10.65        32.98         7.00        14.27 
TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI 
       21.34        19.10        19.82        20.28         8.48        10.59 
TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-H4-A2HQ 
       27.35         8.58        19.07        22.72         1.51        19.40 
TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU 
       38.60         3.06         9.01         8.22        25.02         3.45 
TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A54R TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ 
       21.24         2.76        27.68         9.07        11.70         1.74 
TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO TCGA-LC-A66R TCGA-LT-A5Z6 
        1.81        15.42         6.38        11.80        15.32        15.58 
TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 
       13.48        12.23        16.67        14.24         1.84         3.75 
TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78N 
       12.43        31.56        17.62        37.05        22.68        86.83 
TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE 
       76.01        65.75        35.24        29.56        17.82         4.54 
TCGA-UY-A9PF TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI 
        1.64         1.87        17.88        48.62        64.80        79.66 
TCGA-XF-A9SJ TCGA-XF-A9SL TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY 
        3.22        66.41        12.76        11.90        23.64        21.04 
TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T5 
       28.24        26.27        18.90         2.24        16.27        66.64 
TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMG TCGA-XF-AAMH 
        2.10        13.74        92.98        10.82       110.60        11.31 
TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMW 
       54.90         7.63        71.57        91.73         2.96         8.32 
TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN2 
        6.77        98.99        44.32        56.48        30.94        61.45 
TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 
       86.30        27.06        75.39        18.81         3.88         9.63 
TCGA-YC-A9TC TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R2 
        0.66        11.97        13.64        18.64         7.36        21.11 
TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RC 
       24.13        30.28        27.19        21.86        28.41        74.56 
TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-A9RM 
       13.41         3.48        52.73        52.60        82.49        47.84 
TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4R TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W 
       20.22         2.89        34.06         8.61        59.38        60.16 
TCGA-ZF-AA4X TCGA-ZF-AA52 TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 
       63.02        35.41        57.90        19.40         8.52        47.15 
TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-ZF-AA5P 
       19.17         5.52        10.13 

  NAALADL1 MUTATED NAALADL1 WILD-TYPE 
              4.31               0.10 
  NAALADL1 MUTATED NAALADL1 WILD-TYPE 
             41.56             166.03 
  NAALADL1 MUTATED NAALADL1 WILD-TYPE 
             20.81              15.58 
[1] "4.3 - 41.6 (20.8)"  "0.1 - 166.0 (15.6)"
[1] "hr=" "1.1"
D103V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  NAALADL1 MUTATED         0        4         1        2
  NAALADL1 WILD-TYPE       4      113       121      126
D103V3, multiclass
           clus
vv          NAALADL1 MUTATED NAALADL1 WILD-TYPE
  STAGE I                  0                  4
  STAGE II                 4                113
  STAGE III                1                121
  STAGE IV                 2                126
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1+T2  T3  T4
  NAALADL1 MUTATED          4   2   1
  NAALADL1 WILD-TYPE      110 177  51
D103V4, multiclass
          clus
vv         NAALADL1 MUTATED NAALADL1 WILD-TYPE
  T0+T1+T2                4                110
  T3                      2                177
  T4                      1                 51
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  NAALADL1 MUTATED     4   0   2   0
  NAALADL1 WILD-TYPE 209  41  73   8
D103V5, multiclass
    clus
vv   NAALADL1 MUTATED NAALADL1 WILD-TYPE
  N0                4                209
  N1                0                 41
  N2                2                 73
  N3                0                  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"
D103V6, binary
                    cls
clus                   0   1
  NAALADL1 MUTATED     3   0
  NAALADL1 WILD-TYPE 179  10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  NAALADL1 MUTATED      3    0
  NAALADL1 WILD-TYPE  179   10
   clus
vv  NAALADL1 MUTATED NAALADL1 WILD-TYPE
  0                3                179
  1                0                 10
[1] 2 2
[1] FALSE
D103V7, binary
                    cls
clus                   0   1
  NAALADL1 MUTATED     1   6
  NAALADL1 WILD-TYPE  95 274
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  NAALADL1 MUTATED      1    6
  NAALADL1 WILD-TYPE   95  274
        clus
vv       NAALADL1 MUTATED NAALADL1 WILD-TYPE
  FEMALE                1                 95
  MALE                  6                274
[1] 2 2
[1] FALSE
D103V8, continuous
D103V9, continuous
D103V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  NAALADL1 MUTATED       0                         1     6
  NAALADL1 WILD-TYPE    38                        20   295
D103V11, multiclass
                           clus
vv                          NAALADL1 MUTATED NAALADL1 WILD-TYPE
  ASIAN                                    0                 38
  BLACK OR AFRICAN AMERICAN                1                 20
  WHITE                                    6                295
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D103V12, binary
                    cls
clus                   0   1
  NAALADL1 MUTATED     0   7
  NAALADL1 WILD-TYPE   8 331
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  NAALADL1 MUTATED      0    7
  NAALADL1 WILD-TYPE    8  331
                        clus
vv                       NAALADL1 MUTATED NAALADL1 WILD-TYPE
  HISPANIC OR LATINO                    0                  8
  NOT HISPANIC OR LATINO                7                331
[1] 2 2
[1] FALSE

Clustering(104) Variable = DENND5B MUTATION ANALYSIS
D104V1, survival
                   sevent
clus2                 0   1
  DENND5B MUTATED    12   7
  DENND5B WILD-TYPE 207 144
  DENND5B MUTATED DENND5B WILD-TYPE 
               19               351 
  DENND5B MUTATED DENND5B WILD-TYPE 
                7               144 
$`DENND5B MUTATED`
TCGA-4Z-AA7S TCGA-BT-A2LB TCGA-BT-A3PJ TCGA-CF-A47X TCGA-CU-A3YL TCGA-DK-A1A3 
       34.98        16.18        12.82        12.62        16.31        21.86 
TCGA-DK-A1A7 TCGA-DK-A2I1 TCGA-DK-A3IS TCGA-DK-AA6S TCGA-FD-A3SM TCGA-FD-A5BX 
       18.41        10.59        50.27       166.03        17.98         5.69 
TCGA-FD-A62P TCGA-FJ-A3ZF TCGA-GV-A40G TCGA-UY-A9PF TCGA-XF-A9SI TCGA-ZF-AA4W 
        6.28        17.23        19.07         1.64        79.66        60.16 
TCGA-ZF-AA58 
       47.15 

$`DENND5B WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        91.63       103.50       105.70         8.35 
TCGA-4Z-AA7M TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7W 
       16.27        44.94        16.83        16.77        17.16        27.62 
TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA84 
       49.12         0.62        41.75        51.16        66.54        15.12 
TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J 
       10.22        47.80        33.83        40.08         7.33         2.66 
TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N 
        6.74        12.39         6.58        13.15        19.04        32.84 
TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U 
       12.16        17.88        19.50         5.06        14.89        14.96 
TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LD TCGA-BT-A3PH 
        5.06         8.35         8.25        17.16        20.48         4.67 
TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ 
        9.96        17.56        28.70        24.26        28.41         8.98 
TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-C4-A0F6 TCGA-C4-A0F7 TCGA-CF-A1HR TCGA-CF-A1HS 
        1.94         2.93        23.01         2.04         0.46         0.43 
TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47Y 
        0.69        10.95        12.66        12.46        12.10        12.26 
TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A0YN 
       13.12        12.00        12.10        11.87        13.08        12.92 
TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A5W6 TCGA-CU-A72E 
        4.90         7.20         5.46         5.19         1.84        13.58 
TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD 
        2.14        66.41        19.00        16.70       130.88       112.44 
TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I2 TCGA-DK-A2I4 
       16.14        17.62        15.62         1.81         7.79       123.85 
TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ 
       87.32         2.20        13.58         7.82         8.22        17.72 
TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY 
       21.30        23.21         9.67        20.81        10.55       140.81 
TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 
       48.00        17.98        64.18        41.56        76.60        67.36 
TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6P TCGA-DK-AA6Q 
       15.68        41.06        30.67        38.24        15.02        13.58 
TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA74 
       12.36        10.49         8.65         7.53        13.64        43.50 
TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 
       12.03        10.62        43.59        15.35        38.83        24.66 
TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KE 
        0.10         0.49         2.24        16.70        17.39         0.56 
TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DU 
        0.66        14.56        13.97        12.99        14.33         0.92 
TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A97P TCGA-E7-A97Q 
        1.22        13.68        14.07        12.95        14.37         8.09 
TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 
       32.02        16.77         8.94        33.04         4.01        12.62 
TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SN 
       22.52        27.98        60.66        24.30        23.41        29.16 
TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N 
        5.52        25.74        46.78        19.79        12.85        22.98 
TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS 
       27.35        14.96        20.91         3.62        26.73        53.88 
TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 
       11.01        19.33         5.36         8.25        27.45        18.08 
TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB 
       58.92         2.70         7.10        13.35        62.86        18.81 
TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH 
        6.15        12.69        12.36         2.27         3.06         4.31 
TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A871 
        9.67        10.85        31.07         7.13        10.65         8.94 
TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EC TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK 
        3.25         6.48        22.88        61.94        30.61        15.95 
TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY 
       26.93        35.24        33.01         7.23        20.12        17.62 
TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 
       66.02         6.94        64.44        19.46        21.40         2.24 
TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS 
       15.81         4.50        15.91        14.07        17.75        24.92 
TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS 
        8.94        13.91         7.73         2.10         3.12        20.98 
TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 
        2.20         7.36        10.92        11.31        11.31         7.63 
TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATO TCGA-GU-AATP 
       27.09        20.05         5.62         4.73        10.65        32.98 
TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF 
        7.00        14.27        21.34        19.10        19.82        20.28 
TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A6ZA TCGA-H4-A2HO 
        8.48        10.59        27.35         8.58        22.72         1.51 
TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS 
       19.40        38.60         3.06         9.01         8.22        25.02 
TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RH 
        3.45        21.24         2.76         9.14        27.68         9.07 
TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO 
       11.70         1.74         1.81        15.42         6.38        11.80 
TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X 
       15.32        15.58        13.48        12.23        16.67        14.24 
TCGA-S5-A6DX TCGA-S5-AA26 TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L 
        1.84         3.75        12.43        31.56        17.62        37.05 
TCGA-UY-A78M TCGA-UY-A78N TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A9PA TCGA-UY-A9PB 
       22.68        86.83        76.01        65.75        35.24        29.56 
TCGA-UY-A9PD TCGA-UY-A9PE TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH 
       17.82         4.54         1.87        17.88        48.62        64.80 
TCGA-XF-A9SJ TCGA-XF-A9SL TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY 
        3.22        66.41        12.76        11.90        23.64        21.04 
TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T5 
       28.24        26.27        18.90         2.24        16.27        66.64 
TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMG TCGA-XF-AAMH 
        2.10        13.74        92.98        10.82       110.60        11.31 
TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMW 
       54.90         7.63        71.57        91.73         2.96         8.32 
TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN2 
        6.77        98.99        44.32        56.48        30.94        61.45 
TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 
       86.30        27.06        75.39        18.81         3.88         9.63 
TCGA-YC-A9TC TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R2 
        0.66        11.97        13.64        18.64         7.36        21.11 
TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RC 
       24.13        30.28        27.19        21.86        28.41        74.56 
TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-A9RM 
       13.41         3.48        52.73        52.60        82.49        47.84 
TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4U TCGA-ZF-AA4V 
       20.22         2.89        34.06        19.69         8.61        59.38 
TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA56 
       63.02        38.73        35.41        57.90        19.40         8.52 
TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-ZF-AA5P 
       19.17         5.52        10.13 

  DENND5B MUTATED DENND5B WILD-TYPE 
             1.64              0.10 
  DENND5B MUTATED DENND5B WILD-TYPE 
           166.03            140.81 
  DENND5B MUTATED DENND5B WILD-TYPE 
            17.98             15.35 
[1] "1.6 - 166.0 (18.0)" "0.1 - 140.8 (15.3)"
[1] "hr=" "1.3"
D104V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  DENND5B MUTATED         0        6         7        6
  DENND5B WILD-TYPE       4      111       115      122
D104V3, multiclass
           clus
vv          DENND5B MUTATED DENND5B WILD-TYPE
  STAGE I                 0                 4
  STAGE II                6               111
  STAGE III               7               115
  STAGE IV                6               122
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1+T2  T3  T4
  DENND5B MUTATED          6  10   2
  DENND5B WILD-TYPE      108 169  50
D104V4, multiclass
          clus
vv         DENND5B MUTATED DENND5B WILD-TYPE
  T0+T1+T2               6               108
  T3                    10               169
  T4                     2                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"
                   vv
clus                 N0  N1  N2  N3
  DENND5B MUTATED    12   1   5   1
  DENND5B WILD-TYPE 201  40  70   7
D104V5, multiclass
    clus
vv   DENND5B MUTATED DENND5B WILD-TYPE
  N0              12               201
  N1               1                40
  N2               5                70
  N3               1                 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"
D104V6, binary
                   cls
clus                  0   1
  DENND5B MUTATED    11   1
  DENND5B WILD-TYPE 171   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  DENND5B MUTATED     11    1
  DENND5B WILD-TYPE  171    9
   clus
vv  DENND5B MUTATED DENND5B WILD-TYPE
  0              11               171
  1               1                 9
[1] 2 2
[1] FALSE
D104V7, binary
                   cls
clus                  0   1
  DENND5B MUTATED     5  14
  DENND5B WILD-TYPE  91 266
[1] "tbl2"
                   cls
clus                [,1] [,2]
  DENND5B MUTATED      5   14
  DENND5B WILD-TYPE   91  266
        clus
vv       DENND5B MUTATED DENND5B WILD-TYPE
  FEMALE               5                91
  MALE                14               266
[1] 2 2
[1] FALSE
D104V8, continuous
D104V9, continuous
D104V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DENND5B MUTATED       2                         1    16
  DENND5B WILD-TYPE    36                        20   285
D104V11, multiclass
                           clus
vv                          DENND5B MUTATED DENND5B WILD-TYPE
  ASIAN                                   2                36
  BLACK OR AFRICAN AMERICAN               1                20
  WHITE                                  16               285
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D104V12, binary
                   cls
clus                  0   1
  DENND5B MUTATED     0  18
  DENND5B WILD-TYPE   8 320
[1] "tbl2"
                   cls
clus                [,1] [,2]
  DENND5B MUTATED      0   18
  DENND5B WILD-TYPE    8  320
                        clus
vv                       DENND5B MUTATED DENND5B WILD-TYPE
  HISPANIC OR LATINO                   0                 8
  NOT HISPANIC OR LATINO              18               320
[1] 2 2
[1] FALSE

Clustering(105) Variable = SF3B3 MUTATION ANALYSIS
D105V1, survival
                 sevent
clus2               0   1
  SF3B3 MUTATED    14   5
  SF3B3 WILD-TYPE 205 146
  SF3B3 MUTATED SF3B3 WILD-TYPE 
             19             351 
  SF3B3 MUTATED SF3B3 WILD-TYPE 
              5             146 
$`SF3B3 MUTATED`
TCGA-BT-A20N TCGA-BT-A3PJ TCGA-CF-A47Y TCGA-CU-A0YO TCGA-DK-A1AA TCGA-DK-A3IQ 
       32.84        12.82        12.26         4.90        19.00        17.72 
TCGA-DK-A6AW TCGA-DK-A6B2 TCGA-DK-AA6X TCGA-DK-AA71 TCGA-E7-A519 TCGA-FD-A62P 
       41.56        15.68         7.53        13.64        16.70         6.28 
TCGA-FD-A6TC TCGA-G2-A2EO TCGA-G2-A3VY TCGA-G2-AA3B TCGA-GU-AATO TCGA-UY-A9PB 
        6.15        35.24        17.62        66.02        10.65        29.56 
TCGA-ZF-A9RG 
       52.60 

$`SF3B3 WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        91.63       103.50       105.70         8.35 
TCGA-4Z-AA7M TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7S 
       16.27        44.94        16.83        16.77        17.16        34.98 
TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 
       27.62        49.12         0.62        41.75        51.16        66.54 
TCGA-4Z-AA84 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BL-A13I 
       15.12        10.22        47.80        33.83        40.08         7.33 
TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J 
        2.66         6.74        12.39         6.58        13.15        19.04 
TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U 
       12.16        17.88        19.50         5.06        14.89        14.96 
TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A2LD 
        5.06         8.35         8.25        17.16        16.18        20.48 
TCGA-BT-A3PH TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E TCGA-BT-A42F 
        4.67         9.96        17.56        28.70        24.26        28.41 
TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-C4-A0F6 TCGA-C4-A0F7 TCGA-CF-A1HR 
        8.98         1.94         2.93        23.01         2.04         0.46 
TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W 
        0.43         0.69        10.95        12.66        12.46        12.10 
TCGA-CF-A47X TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A9FF TCGA-CF-A9FM 
       12.62        13.12        12.00        12.10        11.87        13.08 
TCGA-CU-A0YN TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 
       12.92         7.20         5.46         5.19        16.31         1.84 
TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AB 
       13.58        21.86         2.14        66.41        18.41        16.70 
TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX 
      130.88       112.44        16.14        17.62        15.62         1.81 
TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL 
       10.59         7.79       123.85        87.32         2.20        13.58 
TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV 
        7.82         8.22        50.27        21.30        23.21         9.67 
TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV 
       20.81        10.55       140.81        48.00        17.98        64.18 
TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6P 
       76.60        67.36        41.06        30.67        38.24        15.02 
TCGA-DK-AA6Q TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA74 
       13.58       166.03        12.36        10.49         8.65        43.50 
TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 
       12.03        10.62        43.59        15.35        38.83        24.66 
TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF 
        0.10         0.49         2.24        17.39         0.56         0.66 
TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7DV 
       14.56        13.97        12.99        14.33         0.92         1.22 
TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B3 
       13.68        14.07        12.95        14.37         8.09        32.02 
TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 
       16.77         8.94        33.04         4.01        12.62        22.52 
TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN 
       27.98        60.66        24.30        23.41        17.98        29.16 
TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N 
        5.52        25.74        46.78        19.79        12.85        22.98 
TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS 
       27.35        14.96        20.91         3.62        26.73        53.88 
TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ 
       11.01        19.33         5.36         5.69         8.25        27.45 
TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TA 
       18.08        58.92         2.70         7.10        13.35        62.86 
TCGA-FD-A6TB TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH 
       18.81        12.69        12.36         2.27         3.06         4.31 
TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF 
        9.67        10.85        31.07         7.13        10.65        17.23 
TCGA-FJ-A871 TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EC TCGA-G2-A2EF TCGA-G2-A2EJ 
        8.94         3.25         6.48        22.88        61.94        30.61 
TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3C 
       15.95        26.93        33.01         7.23        20.12         6.94 
TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB 
       64.44        19.46        21.40         2.24        15.81         4.50 
TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GC-A6I3 
       15.91        14.07        17.75        24.92         8.94        13.91 
TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GD-A76B 
        7.73         2.10         3.12        20.98         2.20         7.36 
TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A764 
       10.92        11.31        11.31         7.63        27.09        20.05 
TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATP TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW 
        5.62         4.73        32.98         7.00        14.27        21.34 
TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK 
       19.10        19.82        20.28         8.48        10.59        27.35 
TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE 
        8.58        19.07        22.72         1.51        19.40        38.60 
TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV 
        3.06         9.01         8.22        25.02         3.45        21.24 
TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ 
        2.76         9.14        27.68         9.07        11.70         1.74 
TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO TCGA-LC-A66R TCGA-LT-A5Z6 
        1.81        15.42         6.38        11.80        15.32        15.58 
TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 
       13.48        12.23        16.67        14.24         1.84         3.75 
TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78N 
       12.43        31.56        17.62        37.05        22.68        86.83 
TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A9PA TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF 
       76.01        65.75        35.24        17.82         4.54         1.64 
TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SJ 
        1.87        17.88        48.62        64.80        79.66         3.22 
TCGA-XF-A9SL TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ 
       66.41        12.76        11.90        23.64        21.04        28.24 
TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 
       26.27        18.90         2.24        16.27        66.64         2.10 
TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMG TCGA-XF-AAMH TCGA-XF-AAMJ 
       13.74        92.98        10.82       110.60        11.31        54.90 
TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX 
        7.63        71.57        91.73         2.96         8.32         6.77 
TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 
       98.99        44.32        56.48        30.94        61.45        86.30 
TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YC-A9TC 
       27.06        75.39        18.81         3.88         9.63         0.66 
TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R3 
       11.97        13.64        18.64         7.36        21.11        24.13 
TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RD 
       30.28        27.19        21.86        28.41        74.56        13.41 
TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N 
        3.48        52.73        82.49        47.84        20.22         2.89 
TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA4X 
       34.06        19.69         8.61        59.38        60.16        63.02 
TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 
       38.73        35.41        57.90        19.40         8.52        47.15 
TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-ZF-AA5P 
       19.17         5.52        10.13 

  SF3B3 MUTATED SF3B3 WILD-TYPE 
            4.9             0.1 
  SF3B3 MUTATED SF3B3 WILD-TYPE 
          66.02          166.03 
  SF3B3 MUTATED SF3B3 WILD-TYPE 
          16.70           15.58 
[1] "4.9 - 66.0 (16.7)"  "0.1 - 166.0 (15.6)"
[1] "hr=" "1.6"
D105V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  SF3B3 MUTATED         0        8         8        3
  SF3B3 WILD-TYPE       4      109       114      125
D105V3, multiclass
           clus
vv          SF3B3 MUTATED SF3B3 WILD-TYPE
  STAGE I               0               4
  STAGE II              8             109
  STAGE III             8             114
  STAGE IV              3             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"
                 vv
clus              T0+T1+T2  T3  T4
  SF3B3 MUTATED          6   9   2
  SF3B3 WILD-TYPE      108 170  50
D105V4, multiclass
          clus
vv         SF3B3 MUTATED SF3B3 WILD-TYPE
  T0+T1+T2             6             108
  T3                   9             170
  T4                   2              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"
                 vv
clus               N0  N1  N2  N3
  SF3B3 MUTATED    13   1   2   1
  SF3B3 WILD-TYPE 200  40  73   7
D105V5, multiclass
    clus
vv   SF3B3 MUTATED SF3B3 WILD-TYPE
  N0            13             200
  N1             1              40
  N2             2              73
  N3             1               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"
D105V6, binary
                 cls
clus                0   1
  SF3B3 MUTATED    11   0
  SF3B3 WILD-TYPE 171  10
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SF3B3 MUTATED     11    0
  SF3B3 WILD-TYPE  171   10
   clus
vv  SF3B3 MUTATED SF3B3 WILD-TYPE
  0            11             171
  1             0              10
[1] 2 2
[1] FALSE
D105V7, binary
                 cls
clus                0   1
  SF3B3 MUTATED     3  16
  SF3B3 WILD-TYPE  93 264
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SF3B3 MUTATED      3   16
  SF3B3 WILD-TYPE   93  264
        clus
vv       SF3B3 MUTATED SF3B3 WILD-TYPE
  FEMALE             3              93
  MALE              16             264
[1] 2 2
[1] FALSE
D105V8, continuous
D105V9, continuous
D105V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SF3B3 MUTATED       2                         0    16
  SF3B3 WILD-TYPE    36                        21   285
D105V11, multiclass
                           clus
vv                          SF3B3 MUTATED SF3B3 WILD-TYPE
  ASIAN                                 2              36
  BLACK OR AFRICAN AMERICAN             0              21
  WHITE                                16             285
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D105V12, binary
                 cls
clus                0   1
  SF3B3 MUTATED     0  18
  SF3B3 WILD-TYPE   8 320
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SF3B3 MUTATED      0   18
  SF3B3 WILD-TYPE    8  320
                        clus
vv                       SF3B3 MUTATED SF3B3 WILD-TYPE
  HISPANIC OR LATINO                 0               8
  NOT HISPANIC OR LATINO            18             320
[1] 2 2
[1] FALSE

Clustering(106) Variable = KIAA1522 MUTATION ANALYSIS
D106V1, survival
                    sevent
clus2                  0   1
  KIAA1522 MUTATED     9   6
  KIAA1522 WILD-TYPE 210 145
  KIAA1522 MUTATED KIAA1522 WILD-TYPE 
                15                355 
  KIAA1522 MUTATED KIAA1522 WILD-TYPE 
                 6                145 
$`KIAA1522 MUTATED`
TCGA-CU-A72E TCGA-DK-A6B6 TCGA-E7-A85H TCGA-FD-A3NA TCGA-FD-A5BX TCGA-FD-A62O 
       13.58        30.67        12.95        60.66         5.69         7.10 
TCGA-FD-A6TE TCGA-FJ-A3ZF TCGA-G2-A3VY TCGA-GU-AATO TCGA-MV-A51V TCGA-S5-A6DX 
       12.36        17.23        17.62        10.65        13.48         1.84 
TCGA-SY-A9G5 TCGA-UY-A78M TCGA-UY-A9PB 
       31.56        22.68        29.56 

$`KIAA1522 WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        91.63       103.50       105.70         8.35 
TCGA-4Z-AA7M TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7S 
       16.27        44.94        16.83        16.77        17.16        34.98 
TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 
       27.62        49.12         0.62        41.75        51.16        66.54 
TCGA-4Z-AA84 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BL-A13I 
       15.12        10.22        47.80        33.83        40.08         7.33 
TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J 
        2.66         6.74        12.39         6.58        13.15        19.04 
TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T 
       32.84        12.16        17.88        19.50         5.06        14.89 
TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB 
       14.96         5.06         8.35         8.25        17.16        16.18 
TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C 
       20.48         4.67        12.82         9.96        17.56        28.70 
TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-C4-A0F6 
       24.26        28.41         8.98         1.94         2.93        23.01 
TCGA-C4-A0F7 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T 
        2.04         0.46         0.43         0.69        10.95        12.66 
TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA 
       12.46        12.10        12.62        12.26        13.12        12.00 
TCGA-CF-A7I0 TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR 
       12.10        11.87        13.08        12.92         4.90         7.20 
TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-DK-A1A3 TCGA-DK-A1A5 
        5.46         5.19        16.31         1.84        21.86         2.14 
TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD 
       66.41        18.41        19.00        16.70       130.88       112.44 
TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 
       16.14        17.62        15.62         1.81        10.59         7.79 
TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN 
      123.85        87.32         2.20        13.58         7.82         8.22 
TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW 
       17.72        50.27        21.30        23.21         9.67        20.81 
TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW 
       10.55       140.81        48.00        17.98        64.18        41.56 
TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-AA6L TCGA-DK-AA6P 
       76.60        67.36        15.68        41.06        38.24        15.02 
TCGA-DK-AA6Q TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA6X 
       13.58       166.03        12.36        10.49         8.65         7.53 
TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A2PC TCGA-E5-A4TZ 
       13.64        43.50        12.03        10.62        43.59        15.35 
TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 
       38.83        24.66         0.10         0.49         2.24        16.70 
TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME 
       17.39         0.56         0.66        14.56        13.97        12.99 
TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A97P 
       14.33         0.92         1.22        13.68        14.07        14.37 
TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 
        8.09        32.02        16.77         8.94        33.04         4.01 
TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM 
       12.62        22.52        27.98        24.30        23.41        17.98 
TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS 
       29.16         5.52        25.74        46.78        19.79        12.85 
TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BR 
       22.98        27.35        14.96        20.91         3.62        26.73 
TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BY TCGA-FD-A5BZ 
       53.88        11.01        19.33         5.36         8.25        27.45 
TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA 
       18.08        58.92         2.70         6.28        13.35        62.86 
TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH 
       18.81         6.15        12.69         2.27         3.06         4.31 
TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A871 
        9.67        10.85        31.07         7.13        10.65         8.94 
TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EC TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK 
        3.25         6.48        22.88        61.94        30.61        15.95 
TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3B 
       26.93        35.24        33.01         7.23        20.12        66.02 
TCGA-G2-AA3C TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO 
        6.94        64.44        19.46        21.40         2.24        15.81 
TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A6I1 
        4.50        15.91        14.07        17.75        24.92         8.94 
TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 
       13.91         7.73         2.10         3.12        20.98         2.20 
TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 
        7.36        10.92        11.31        11.31         7.63        27.09 
TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATP TCGA-GU-AATQ TCGA-GV-A3JV 
       20.05         5.62         4.73        32.98         7.00        14.27 
TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI 
       21.34        19.10        19.82        20.28         8.48        10.59 
TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-H4-A2HQ 
       27.35         8.58        19.07        22.72         1.51        19.40 
TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU 
       38.60         3.06         9.01         8.22        25.02         3.45 
TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RH TCGA-K4-A5RI 
       21.24         2.76         9.14        27.68         9.07        11.70 
TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO TCGA-LC-A66R 
        1.74         1.81        15.42         6.38        11.80        15.32 
TCGA-LT-A5Z6 TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-AA26 TCGA-SY-A9G0 
       15.58        12.23        16.67        14.24         3.75        12.43 
TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78N TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A9PA 
       17.62        37.05        86.83        76.01        65.75        35.24 
TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG 
       17.82         4.54         1.64         1.87        17.88        48.62 
TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SL TCGA-XF-A9SV TCGA-XF-A9SW 
       64.80        79.66         3.22        66.41        12.76        11.90 
TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 
       23.64        21.04        28.24        26.27        18.90         2.24 
TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMF 
       16.27        66.64         2.10        13.74        92.98        10.82 
TCGA-XF-AAMG TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR 
      110.60        11.31        54.90         7.63        71.57        91.73 
TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN0 
        2.96         8.32         6.77        98.99        44.32        56.48 
TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN7 
       30.94        61.45        86.30        27.06        75.39        18.81 
TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R0 
        3.88         9.63         0.66        11.97        13.64        18.64 
TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R7 
        7.36        21.11        24.13        30.28        27.19        21.86 
TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RG 
       28.41        74.56        13.41         3.48        52.73        52.60 
TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4R TCGA-ZF-AA4T 
       82.49        47.84        20.22         2.89        34.06        19.69 
TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 
        8.61        59.38        60.16        63.02        38.73        35.41 
TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N 
       57.90        19.40         8.52        47.15        19.17         5.52 
TCGA-ZF-AA5P 
       10.13 

  KIAA1522 MUTATED KIAA1522 WILD-TYPE 
              1.84               0.10 
  KIAA1522 MUTATED KIAA1522 WILD-TYPE 
             60.66             166.03 
  KIAA1522 MUTATED KIAA1522 WILD-TYPE 
             13.58              15.68 
[1] "1.8 - 60.7 (13.6)"  "0.1 - 166.0 (15.7)"
[1] "hr=" "1.1"
D106V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  KIAA1522 MUTATED         0        3         5        7
  KIAA1522 WILD-TYPE       4      114       117      121
D106V3, multiclass
           clus
vv          KIAA1522 MUTATED KIAA1522 WILD-TYPE
  STAGE I                  0                  4
  STAGE II                 3                114
  STAGE III                5                117
  STAGE IV                 7                121
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1+T2  T3  T4
  KIAA1522 MUTATED          2   7   3
  KIAA1522 WILD-TYPE      112 172  49
D106V4, multiclass
          clus
vv         KIAA1522 MUTATED KIAA1522 WILD-TYPE
  T0+T1+T2                2                112
  T3                      7                172
  T4                      3                 49
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  KIAA1522 MUTATED     6   1   6   0
  KIAA1522 WILD-TYPE 207  40  69   8
D106V5, multiclass
    clus
vv   KIAA1522 MUTATED KIAA1522 WILD-TYPE
  N0                6                207
  N1                1                 40
  N2                6                 69
  N3                0                  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"
D106V6, binary
                    cls
clus                   0   1
  KIAA1522 MUTATED     5   0
  KIAA1522 WILD-TYPE 177  10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1522 MUTATED      5    0
  KIAA1522 WILD-TYPE  177   10
   clus
vv  KIAA1522 MUTATED KIAA1522 WILD-TYPE
  0                5                177
  1                0                 10
[1] 2 2
[1] FALSE
D106V7, binary
                    cls
clus                   0   1
  KIAA1522 MUTATED     1  14
  KIAA1522 WILD-TYPE  95 266
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1522 MUTATED      1   14
  KIAA1522 WILD-TYPE   95  266
        clus
vv       KIAA1522 MUTATED KIAA1522 WILD-TYPE
  FEMALE                1                 95
  MALE                 14                266
[1] 2 2
[1] FALSE
D106V8, continuous
D106V9, continuous
D106V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  KIAA1522 MUTATED       3                         0    12
  KIAA1522 WILD-TYPE    35                        21   289
D106V11, multiclass
                           clus
vv                          KIAA1522 MUTATED KIAA1522 WILD-TYPE
  ASIAN                                    3                 35
  BLACK OR AFRICAN AMERICAN                0                 21
  WHITE                                   12                289
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D106V12, binary
                    cls
clus                   0   1
  KIAA1522 MUTATED     0  15
  KIAA1522 WILD-TYPE   8 323
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1522 MUTATED      0   15
  KIAA1522 WILD-TYPE    8  323
                        clus
vv                       KIAA1522 MUTATED KIAA1522 WILD-TYPE
  HISPANIC OR LATINO                    0                  8
  NOT HISPANIC OR LATINO               15                323
[1] 2 2
[1] FALSE

Clustering(107) Variable = GTF2I MUTATION ANALYSIS
D107V1, survival
                 sevent
clus2               0   1
  GTF2I MUTATED     8   7
  GTF2I WILD-TYPE 211 144
  GTF2I MUTATED GTF2I WILD-TYPE 
             15             355 
  GTF2I MUTATED GTF2I WILD-TYPE 
              7             144 
$`GTF2I MUTATED`
TCGA-4Z-AA7Q TCGA-BT-A42C TCGA-DK-AA6S TCGA-E5-A4TZ TCGA-FD-A3SO TCGA-G2-A2EK 
       16.77        28.70       166.03        15.35         5.52        15.95 
TCGA-GC-A6I3 TCGA-GU-AATP TCGA-K4-A54R TCGA-MV-A51V TCGA-XF-AAN0 TCGA-ZF-A9RC 
       13.91        32.98        27.68        13.48        56.48        74.56 
TCGA-ZF-A9RD TCGA-ZF-AA4N TCGA-ZF-AA4R 
       13.41         2.89        34.06 

$`GTF2I WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        91.63       103.50       105.70         8.35 
TCGA-4Z-AA7M TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7W 
       16.27        44.94        16.83        17.16        34.98        27.62 
TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA84 
       49.12         0.62        41.75        51.16        66.54        15.12 
TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J 
       10.22        47.80        33.83        40.08         7.33         2.66 
TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N 
        6.74        12.39         6.58        13.15        19.04        32.84 
TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U 
       12.16        17.88        19.50         5.06        14.89        14.96 
TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A2LD 
        5.06         8.35         8.25        17.16        16.18        20.48 
TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42E TCGA-BT-A42F 
        4.67        12.82         9.96        17.56        24.26        28.41 
TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-C4-A0F6 TCGA-C4-A0F7 TCGA-CF-A1HR 
        8.98         1.94         2.93        23.01         2.04         0.46 
TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W 
        0.43         0.69        10.95        12.66        12.46        12.10 
TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A9FF 
       12.62        12.26        13.12        12.00        12.10        11.87 
TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3QU 
       13.08        12.92         4.90         7.20         5.46         5.19 
TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 
       16.31         1.84        13.58        21.86         2.14        66.41 
TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE 
       18.41        19.00        16.70       130.88       112.44        16.14 
TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 
       17.62        15.62         1.81        10.59         7.79       123.85 
TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ 
       87.32         2.20        13.58         7.82         8.22        17.72 
TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX 
       50.27        21.30        23.21         9.67        20.81        10.55 
TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 
      140.81        48.00        17.98        64.18        41.56        76.60 
TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6P 
       67.36        15.68        41.06        30.67        38.24        15.02 
TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA71 
       13.58        12.36        10.49         8.65         7.53        13.64 
TCGA-DK-AA74 TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A2PC TCGA-E5-A4U1 TCGA-E7-A3X6 
       43.50        12.03        10.62        43.59        38.83        24.66 
TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KE 
        0.10         0.49         2.24        16.70        17.39         0.56 
TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DU 
        0.66        14.56        13.97        12.99        14.33         0.92 
TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A97P TCGA-E7-A97Q 
        1.22        13.68        14.07        12.95        14.37         8.09 
TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 
       32.02        16.77         8.94        33.04         4.01        12.62 
TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM 
       22.52        27.98        60.66        24.30        23.41        17.98 
TCGA-FD-A3SN TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N 
       29.16        25.74        46.78        19.79        12.85        22.98 
TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS 
       27.35        14.96        20.91         3.62        26.73        53.88 
TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ 
       11.01        19.33         5.36         5.69         8.25        27.45 
TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S 
       18.08        58.92         2.70         7.10         6.28        13.35 
TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF 
       62.86        18.81         6.15        12.69        12.36         2.27 
TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 
        3.06         4.31         9.67        10.85        31.07         7.13 
TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FJ-A871 TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EC 
       10.65        17.23         8.94         3.25         6.48        22.88 
TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB 
       61.94        30.61        26.93        35.24        33.01         7.23 
TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3D TCGA-G2-AA3F 
       20.12        17.62        66.02         6.94        64.44        19.46 
TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD 
       21.40         2.24        15.81         4.50        15.91        14.07 
TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ 
       17.75        24.92         8.94         7.73         2.10         3.12 
TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R 
       20.98         2.20         7.36        10.92        11.31        11.31 
TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATO 
        7.63        27.09        20.05         5.62         4.73        10.65 
TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF 
        7.00        14.27        21.34        19.10        19.82        20.28 
TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA 
        8.48        10.59        27.35         8.58        19.07        22.72 
TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE 
        1.51        19.40        38.60         3.06         9.01         8.22 
TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A5RH 
       25.02         3.45        21.24         2.76         9.14         9.07 
TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO 
       11.70         1.74         1.81        15.42         6.38        11.80 
TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX 
       15.32        15.58        12.23        16.67        14.24         1.84 
TCGA-S5-AA26 TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M 
        3.75        12.43        31.56        17.62        37.05        22.68 
TCGA-UY-A78N TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD 
       86.83        76.01        65.75        35.24        29.56        17.82 
TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH 
        4.54         1.64         1.87        17.88        48.62        64.80 
TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SL TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SX 
       79.66         3.22        66.41        12.76        11.90        23.64 
TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 
       21.04        28.24        26.27        18.90         2.24        16.27 
TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMG 
       66.64         2.10        13.74        92.98        10.82       110.60 
TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMT 
       11.31        54.90         7.63        71.57        91.73         2.96 
TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN1 TCGA-XF-AAN2 
        8.32         6.77        98.99        44.32        30.94        61.45 
TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 
       86.30        27.06        75.39        18.81         3.88         9.63 
TCGA-YC-A9TC TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R2 
        0.66        11.97        13.64        18.64         7.36        21.11 
TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RE 
       24.13        30.28        27.19        21.86        28.41         3.48 
TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4T 
       52.73        52.60        82.49        47.84        20.22        19.69 
TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 
        8.61        59.38        60.16        63.02        38.73        35.41 
TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N 
       57.90        19.40         8.52        47.15        19.17         5.52 
TCGA-ZF-AA5P 
       10.13 

  GTF2I MUTATED GTF2I WILD-TYPE 
           2.89            0.10 
  GTF2I MUTATED GTF2I WILD-TYPE 
         166.03          140.81 
  GTF2I MUTATED GTF2I WILD-TYPE 
          16.77           15.58 
[1] "2.9 - 166.0 (16.8)" "0.1 - 140.8 (15.6)"
[1] "hr=" "1.1"
D107V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  GTF2I MUTATED         0        4         4        7
  GTF2I WILD-TYPE       4      113       118      121
D107V3, multiclass
           clus
vv          GTF2I MUTATED GTF2I WILD-TYPE
  STAGE I               0               4
  STAGE II              4             113
  STAGE III             4             118
  STAGE IV              7             121
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1+T2  T3  T4
  GTF2I MUTATED          2   8   2
  GTF2I WILD-TYPE      112 171  50
D107V4, multiclass
          clus
vv         GTF2I MUTATED GTF2I WILD-TYPE
  T0+T1+T2             2             112
  T3                   8             171
  T4                   2              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"
                 vv
clus               N0  N1  N2  N3
  GTF2I MUTATED     6   3   4   0
  GTF2I WILD-TYPE 207  38  71   8
D107V5, multiclass
    clus
vv   GTF2I MUTATED GTF2I WILD-TYPE
  N0             6             207
  N1             3              38
  N2             4              71
  N3             0               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"
D107V6, binary
                 cls
clus                0   1
  GTF2I MUTATED     6   0
  GTF2I WILD-TYPE 176  10
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GTF2I MUTATED      6    0
  GTF2I WILD-TYPE  176   10
   clus
vv  GTF2I MUTATED GTF2I WILD-TYPE
  0             6             176
  1             0              10
[1] 2 2
[1] FALSE
D107V7, binary
                 cls
clus                0   1
  GTF2I MUTATED     2  13
  GTF2I WILD-TYPE  94 267
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GTF2I MUTATED      2   13
  GTF2I WILD-TYPE   94  267
        clus
vv       GTF2I MUTATED GTF2I WILD-TYPE
  FEMALE             2              94
  MALE              13             267
[1] 2 2
[1] FALSE
D107V8, continuous
D107V9, continuous
D107V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  GTF2I MUTATED       0                         1    14
  GTF2I WILD-TYPE    38                        20   287
D107V11, multiclass
                           clus
vv                          GTF2I MUTATED GTF2I WILD-TYPE
  ASIAN                                 0              38
  BLACK OR AFRICAN AMERICAN             1              20
  WHITE                                14             287
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D107V12, binary
                 cls
clus                0   1
  GTF2I MUTATED     0  14
  GTF2I WILD-TYPE   8 324
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GTF2I MUTATED      0   14
  GTF2I WILD-TYPE    8  324
                        clus
vv                       GTF2I MUTATED GTF2I WILD-TYPE
  HISPANIC OR LATINO                 0               8
  NOT HISPANIC OR LATINO            14             324
[1] 2 2
[1] FALSE

Clustering(108) Variable = MOAP1 MUTATION ANALYSIS
D108V1, survival
                 sevent
clus2               0   1
  MOAP1 MUTATED     7   0
  MOAP1 WILD-TYPE 212 151
  MOAP1 MUTATED MOAP1 WILD-TYPE 
              7             363 
  MOAP1 MUTATED MOAP1 WILD-TYPE 
              0             151 
$`MOAP1 MUTATED`
TCGA-CF-A27C TCGA-DK-A6AW TCGA-DK-AA6X TCGA-GC-A3YS TCGA-GD-A2C5 TCGA-XF-A9T0 
        0.69        41.56         7.53        24.92         7.73        26.27 
TCGA-ZF-AA51 
       38.73 

$`MOAP1 WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        91.63       103.50       105.70         8.35 
TCGA-4Z-AA7M TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7S 
       16.27        44.94        16.83        16.77        17.16        34.98 
TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 
       27.62        49.12         0.62        41.75        51.16        66.54 
TCGA-4Z-AA84 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BL-A13I 
       15.12        10.22        47.80        33.83        40.08         7.33 
TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J 
        2.66         6.74        12.39         6.58        13.15        19.04 
TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T 
       32.84        12.16        17.88        19.50         5.06        14.89 
TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB 
       14.96         5.06         8.35         8.25        17.16        16.18 
TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C 
       20.48         4.67        12.82         9.96        17.56        28.70 
TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-C4-A0F6 
       24.26        28.41         8.98         1.94         2.93        23.01 
TCGA-C4-A0F7 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V 
        2.04         0.46         0.43        10.95        12.66        12.46 
TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 
       12.10        12.62        12.26        13.12        12.00        12.10 
TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ 
       11.87        13.08        12.92         4.90         7.20         5.46 
TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 
        5.19        16.31         1.84        13.58        21.86         2.14 
TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD 
       66.41        18.41        19.00        16.70       130.88       112.44 
TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 
       16.14        17.62        15.62         1.81        10.59         7.79 
TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN 
      123.85        87.32         2.20        13.58         7.82         8.22 
TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW 
       17.72        50.27        21.30        23.21         9.67        20.81 
TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6B0 
       10.55       140.81        48.00        17.98        64.18        76.60 
TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6P 
       67.36        15.68        41.06        30.67        38.24        15.02 
TCGA-DK-AA6Q TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA71 
       13.58       166.03        12.36        10.49         8.65        13.64 
TCGA-DK-AA74 TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E5-A4U1 
       43.50        12.03        10.62        43.59        15.35        38.83 
TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 
       24.66         0.10         0.49         2.24        16.70        17.39 
TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF 
        0.56         0.66        14.56        13.97        12.99        14.33 
TCGA-E7-A7DU TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A97P 
        0.92         1.22        13.68        14.07        12.95        14.37 
TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 
        8.09        32.02        16.77         8.94        33.04         4.01 
TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL 
       12.62        22.52        27.98        60.66        24.30        23.41 
TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR 
       17.98        29.16         5.52        25.74        46.78        19.79 
TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X 
       12.85        22.98        27.35        14.96        20.91         3.62 
TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX 
       26.73        53.88        11.01        19.33         5.36         5.69 
TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O 
        8.25        27.45        18.08        58.92         2.70         7.10 
TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD 
        6.28        13.35        62.86        18.81         6.15        12.69 
TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FD-A6TK 
       12.36         2.27         3.06         4.31         9.67        10.85 
TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FJ-A871 TCGA-FT-A3EE 
       31.07         7.13        10.65        17.23         8.94         3.25 
TCGA-FT-A61P TCGA-G2-A2EC TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL 
        6.48        22.88        61.94        30.61        15.95        26.93 
TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B 
       35.24        33.01         7.23        20.12        17.62        66.02 
TCGA-G2-AA3C TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO 
        6.94        64.44        19.46        21.40         2.24        15.81 
TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A6I1 TCGA-GC-A6I3 
        4.50        15.91        14.07        17.75         8.94        13.91 
TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42P 
        2.10         3.12        20.98         2.20         7.36        10.92 
TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 
       11.31        11.31         7.63        27.09        20.05         5.62 
TCGA-GU-A767 TCGA-GU-AATO TCGA-GU-AATP TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW 
        4.73        10.65        32.98         7.00        14.27        21.34 
TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK 
       19.10        19.82        20.28         8.48        10.59        27.35 
TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE 
        8.58        19.07        22.72         1.51        19.40        38.60 
TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV 
        3.06         9.01         8.22        25.02         3.45        21.24 
TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ 
        2.76         9.14        27.68         9.07        11.70         1.74 
TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO TCGA-LC-A66R TCGA-LT-A5Z6 
        1.81        15.42         6.38        11.80        15.32        15.58 
TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 
       13.48        12.23        16.67        14.24         1.84         3.75 
TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78N 
       12.43        31.56        17.62        37.05        22.68        86.83 
TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE 
       76.01        65.75        35.24        29.56        17.82         4.54 
TCGA-UY-A9PF TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI 
        1.64         1.87        17.88        48.62        64.80        79.66 
TCGA-XF-A9SJ TCGA-XF-A9SL TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY 
        3.22        66.41        12.76        11.90        23.64        21.04 
TCGA-XF-A9SZ TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 
       28.24        18.90         2.24        16.27        66.64         2.10 
TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMG TCGA-XF-AAMH TCGA-XF-AAMJ 
       13.74        92.98        10.82       110.60        11.31        54.90 
TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX 
        7.63        71.57        91.73         2.96         8.32         6.77 
TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 
       98.99        44.32        56.48        30.94        61.45        86.30 
TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YC-A9TC 
       27.06        75.39        18.81         3.88         9.63         0.66 
TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R3 
       11.97        13.64        18.64         7.36        21.11        24.13 
TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RD 
       30.28        27.19        21.86        28.41        74.56        13.41 
TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-A9RN 
        3.48        52.73        52.60        82.49        47.84        20.22 
TCGA-ZF-AA4N TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W 
        2.89        34.06        19.69         8.61        59.38        60.16 
TCGA-ZF-AA4X TCGA-ZF-AA52 TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 
       63.02        35.41        57.90        19.40         8.52        47.15 
TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-ZF-AA5P 
       19.17         5.52        10.13 

  MOAP1 MUTATED MOAP1 WILD-TYPE 
           0.69            0.10 
  MOAP1 MUTATED MOAP1 WILD-TYPE 
          41.56          166.03 
  MOAP1 MUTATED MOAP1 WILD-TYPE 
          24.92           15.62 
[1] "0.7 - 41.6 (24.9)"  "0.1 - 166.0 (15.6)"
[1] "hr="     "9200000"
D108V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  MOAP1 MUTATED         0        3         1        2
  MOAP1 WILD-TYPE       4      114       121      126
D108V3, multiclass
           clus
vv          MOAP1 MUTATED MOAP1 WILD-TYPE
  STAGE I               0               4
  STAGE II              3             114
  STAGE III             1             121
  STAGE IV              2             126
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1+T2  T3  T4
  MOAP1 MUTATED          2   4   0
  MOAP1 WILD-TYPE      112 175  52
D108V4, multiclass
          clus
vv         MOAP1 MUTATED MOAP1 WILD-TYPE
  T0+T1+T2             2             112
  T3                   4             175
  T4                   0              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"
                 vv
clus               N0  N1  N2  N3
  MOAP1 MUTATED     4   1   1   0
  MOAP1 WILD-TYPE 209  40  74   8
D108V5, multiclass
    clus
vv   MOAP1 MUTATED MOAP1 WILD-TYPE
  N0             4             209
  N1             1              40
  N2             1              74
  N3             0               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"
D108V6, binary
                 cls
clus                0   1
  MOAP1 MUTATED     4   0
  MOAP1 WILD-TYPE 178  10
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MOAP1 MUTATED      4    0
  MOAP1 WILD-TYPE  178   10
   clus
vv  MOAP1 MUTATED MOAP1 WILD-TYPE
  0             4             178
  1             0              10
[1] 2 2
[1] FALSE
D108V7, binary
                 cls
clus                0   1
  MOAP1 MUTATED     2   5
  MOAP1 WILD-TYPE  94 275
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MOAP1 MUTATED      2    5
  MOAP1 WILD-TYPE   94  275
        clus
vv       MOAP1 MUTATED MOAP1 WILD-TYPE
  FEMALE             2              94
  MALE               5             275
[1] 2 2
[1] FALSE
D108V8, continuous
D108V9, continuous
D108V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MOAP1 MUTATED       1                         0     6
  MOAP1 WILD-TYPE    37                        21   295
D108V11, multiclass
                           clus
vv                          MOAP1 MUTATED MOAP1 WILD-TYPE
  ASIAN                                 1              37
  BLACK OR AFRICAN AMERICAN             0              21
  WHITE                                 6             295
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D108V12, binary
                 cls
clus                0   1
  MOAP1 MUTATED     0   7
  MOAP1 WILD-TYPE   8 331
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MOAP1 MUTATED      0    7
  MOAP1 WILD-TYPE    8  331
                        clus
vv                       MOAP1 MUTATED MOAP1 WILD-TYPE
  HISPANIC OR LATINO                 0               8
  NOT HISPANIC OR LATINO             7             331
[1] 2 2
[1] FALSE

Clustering(109) Variable = GAR1 MUTATION ANALYSIS
D109V1, survival
                sevent
clus2              0   1
  GAR1 MUTATED     3   1
  GAR1 WILD-TYPE 216 150
  GAR1 MUTATED GAR1 WILD-TYPE 
             4            366 
  GAR1 MUTATED GAR1 WILD-TYPE 
             1            150 
$`GAR1 MUTATED`
TCGA-BT-A2LB TCGA-E5-A2PC TCGA-G2-AA3B TCGA-GU-A763 
       16.18        43.59        66.02        27.09 

$`GAR1 WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        91.63       103.50       105.70         8.35 
TCGA-4Z-AA7M TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7S 
       16.27        44.94        16.83        16.77        17.16        34.98 
TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 
       27.62        49.12         0.62        41.75        51.16        66.54 
TCGA-4Z-AA84 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BL-A13I 
       15.12        10.22        47.80        33.83        40.08         7.33 
TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J 
        2.66         6.74        12.39         6.58        13.15        19.04 
TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T 
       32.84        12.16        17.88        19.50         5.06        14.89 
TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LD 
       14.96         5.06         8.35         8.25        17.16        20.48 
TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E 
        4.67        12.82         9.96        17.56        28.70        24.26 
TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-C4-A0F6 TCGA-C4-A0F7 
       28.41         8.98         1.94         2.93        23.01         2.04 
TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V 
        0.46         0.43         0.69        10.95        12.66        12.46 
TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 
       12.10        12.62        12.26        13.12        12.00        12.10 
TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ 
       11.87        13.08        12.92         4.90         7.20         5.46 
TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 
        5.19        16.31         1.84        13.58        21.86         2.14 
TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD 
       66.41        18.41        19.00        16.70       130.88       112.44 
TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 
       16.14        17.62        15.62         1.81        10.59         7.79 
TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN 
      123.85        87.32         2.20        13.58         7.82         8.22 
TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW 
       17.72        50.27        21.30        23.21         9.67        20.81 
TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW 
       10.55       140.81        48.00        17.98        64.18        41.56 
TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L 
       76.60        67.36        15.68        41.06        30.67        38.24 
TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6W 
       15.02        13.58       166.03        12.36        10.49         8.65 
TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A4TZ 
        7.53        13.64        43.50        12.03        10.62        15.35 
TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 
       38.83        24.66         0.10         0.49         2.24        16.70 
TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME 
       17.39         0.56         0.66        14.56        13.97        12.99 
TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H 
       14.33         0.92         1.22        13.68        14.07        12.95 
TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 
       14.37         8.09        32.02        16.77         8.94        33.04 
TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ 
        4.01        12.62        22.52        27.98        60.66        24.30 
TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ 
       23.41        17.98        29.16         5.52        25.74        46.78 
TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U 
       19.79        12.85        22.98        27.35        14.96        20.91 
TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV 
        3.62        26.73        53.88        11.01        19.33         5.36 
TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N 
        5.69         8.25        27.45        18.08        58.92         2.70 
TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC 
        7.10         6.28        13.35        62.86        18.81         6.15 
TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI 
       12.69        12.36         2.27         3.06         4.31         9.67 
TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FJ-A871 
       10.85        31.07         7.13        10.65        17.23         8.94 
TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EC TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK 
        3.25         6.48        22.88        61.94        30.61        15.95 
TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY 
       26.93        35.24        33.01         7.23        20.12        17.62 
TCGA-G2-AA3C TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO 
        6.94        64.44        19.46        21.40         2.24        15.81 
TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A6I1 
        4.50        15.91        14.07        17.75        24.92         8.94 
TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 
       13.91         7.73         2.10         3.12        20.98         2.20 
TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A764 
        7.36        10.92        11.31        11.31         7.63        20.05 
TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATO TCGA-GU-AATP TCGA-GU-AATQ TCGA-GV-A3JV 
        5.62         4.73        10.65        32.98         7.00        14.27 
TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI 
       21.34        19.10        19.82        20.28         8.48        10.59 
TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-H4-A2HQ 
       27.35         8.58        19.07        22.72         1.51        19.40 
TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU 
       38.60         3.06         9.01         8.22        25.02         3.45 
TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RH TCGA-K4-A5RI 
       21.24         2.76         9.14        27.68         9.07        11.70 
TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO TCGA-LC-A66R 
        1.74         1.81        15.42         6.38        11.80        15.32 
TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX 
       15.58        13.48        12.23        16.67        14.24         1.84 
TCGA-S5-AA26 TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M 
        3.75        12.43        31.56        17.62        37.05        22.68 
TCGA-UY-A78N TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD 
       86.83        76.01        65.75        35.24        29.56        17.82 
TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH 
        4.54         1.64         1.87        17.88        48.62        64.80 
TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SL TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SX 
       79.66         3.22        66.41        12.76        11.90        23.64 
TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 
       21.04        28.24        26.27        18.90         2.24        16.27 
TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMG 
       66.64         2.10        13.74        92.98        10.82       110.60 
TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMT 
       11.31        54.90         7.63        71.57        91.73         2.96 
TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN0 TCGA-XF-AAN1 
        8.32         6.77        98.99        44.32        56.48        30.94 
TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN7 TCGA-XF-AAN8 
       61.45        86.30        27.06        75.39        18.81         3.88 
TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R0 TCGA-ZF-A9R1 
        9.63         0.66        11.97        13.64        18.64         7.36 
TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 
       21.11        24.13        30.28        27.19        21.86        28.41 
TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RL 
       74.56        13.41         3.48        52.73        52.60        82.49 
TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4U 
       47.84        20.22         2.89        34.06        19.69         8.61 
TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA53 
       59.38        60.16        63.02        38.73        35.41        57.90 
TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-ZF-AA5P 
       19.40         8.52        47.15        19.17         5.52        10.13 

  GAR1 MUTATED GAR1 WILD-TYPE 
         16.18           0.10 
  GAR1 MUTATED GAR1 WILD-TYPE 
         66.02         166.03 
  GAR1 MUTATED GAR1 WILD-TYPE 
         35.34          15.50 
[1] "16.2 - 66.0 (35.3)" "0.1 - 166.0 (15.5)"
[1] "hr=" "2.7"
D109V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  GAR1 MUTATED         0        1         2        1
  GAR1 WILD-TYPE       4      116       120      127
D109V3, multiclass
           clus
vv          GAR1 MUTATED GAR1 WILD-TYPE
  STAGE I              0              4
  STAGE II             1            116
  STAGE III            2            120
  STAGE IV             1            127
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1+T2  T3  T4
  GAR1 MUTATED          2   1   1
  GAR1 WILD-TYPE      112 178  51
D109V4, multiclass
          clus
vv         GAR1 MUTATED GAR1 WILD-TYPE
  T0+T1+T2            2            112
  T3                  1            178
  T4                  1             51
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  GAR1 MUTATED     3   1   0   0
  GAR1 WILD-TYPE 210  40  75   8
D109V5, multiclass
    clus
vv   GAR1 MUTATED GAR1 WILD-TYPE
  N0            3            210
  N1            1             40
  N2            0             75
  N3            0              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"
D109V6, binary
                cls
clus               0   1
  GAR1 MUTATED     3   0
  GAR1 WILD-TYPE 179  10
[1] "tbl2"
                cls
clus             [,1] [,2]
  GAR1 MUTATED      3    0
  GAR1 WILD-TYPE  179   10
   clus
vv  GAR1 MUTATED GAR1 WILD-TYPE
  0            3            179
  1            0             10
[1] 2 2
[1] FALSE
D109V7, binary
                cls
clus               0   1
  GAR1 MUTATED     3   1
  GAR1 WILD-TYPE  93 279
[1] "tbl2"
                cls
clus             [,1] [,2]
  GAR1 MUTATED      3    1
  GAR1 WILD-TYPE   93  279
        clus
vv       GAR1 MUTATED GAR1 WILD-TYPE
  FEMALE            3             93
  MALE              1            279
[1] 2 2
[1] FALSE
D109V8, continuous
[1] "Remove cluster labels:" "GAR1 MUTATED"          
clus
  GAR1 MUTATED GAR1 WILD-TYPE 
             1            119 
    TCGA-2F-A9KO     TCGA-2F-A9KP     TCGA-2F-A9KQ     TCGA-2F-A9KR 
"GAR1 WILD-TYPE" "GAR1 WILD-TYPE" "GAR1 WILD-TYPE" "GAR1 WILD-TYPE" 
    TCGA-2F-A9KT     TCGA-2F-A9KW     TCGA-CF-A1HS     TCGA-CF-A27C 
"GAR1 WILD-TYPE" "GAR1 WILD-TYPE" "GAR1 WILD-TYPE" "GAR1 WILD-TYPE" 
    TCGA-CF-A3MF     TCGA-CF-A3MG     TCGA-CF-A3MH     TCGA-CF-A3MI 
"GAR1 WILD-TYPE" "GAR1 WILD-TYPE" "GAR1 WILD-TYPE" "GAR1 WILD-TYPE" 
    TCGA-CF-A47S     TCGA-CF-A47T     TCGA-CF-A47V     TCGA-CF-A47W 
"GAR1 WILD-TYPE" "GAR1 WILD-TYPE" "GAR1 WILD-TYPE" "GAR1 WILD-TYPE" 
    TCGA-CF-A47X     TCGA-CF-A47Y     TCGA-CF-A5U8     TCGA-CF-A5UA 
"GAR1 WILD-TYPE" "GAR1 WILD-TYPE" "GAR1 WILD-TYPE" "GAR1 WILD-TYPE" 
    TCGA-CF-A7I0     TCGA-DK-A2HX     TCGA-DK-A3IN     TCGA-DK-A3IV 
"GAR1 WILD-TYPE" "GAR1 WILD-TYPE" "GAR1 WILD-TYPE" "GAR1 WILD-TYPE" 
    TCGA-DK-A3WX     TCGA-DK-A3X2     TCGA-DK-A6B2     TCGA-DK-A6B5 
"GAR1 WILD-TYPE" "GAR1 WILD-TYPE" "GAR1 WILD-TYPE" "GAR1 WILD-TYPE" 
    TCGA-DK-A6B6     TCGA-DK-AA6P     TCGA-DK-AA6S     TCGA-DK-AA6U 
"GAR1 WILD-TYPE" "GAR1 WILD-TYPE" "GAR1 WILD-TYPE" "GAR1 WILD-TYPE" 
    TCGA-DK-AA6W     TCGA-DK-AA76     TCGA-E5-A4TZ     TCGA-E5-A4U1 
"GAR1 WILD-TYPE" "GAR1 WILD-TYPE" "GAR1 WILD-TYPE" "GAR1 WILD-TYPE" 
    TCGA-E7-A519     TCGA-E7-A541     TCGA-E7-A7DU     TCGA-E7-A7DV 
"GAR1 WILD-TYPE" "GAR1 WILD-TYPE" "GAR1 WILD-TYPE" "GAR1 WILD-TYPE" 
    TCGA-FT-A61P     TCGA-G2-A2EC     TCGA-G2-A2EF     TCGA-G2-A2EJ 
"GAR1 WILD-TYPE" "GAR1 WILD-TYPE" "GAR1 WILD-TYPE" "GAR1 WILD-TYPE" 
    TCGA-G2-A2EK     TCGA-G2-A2EL     TCGA-G2-A2EO     TCGA-G2-A2ES 
"GAR1 WILD-TYPE" "GAR1 WILD-TYPE" "GAR1 WILD-TYPE" "GAR1 WILD-TYPE" 
    TCGA-G2-A3IB     TCGA-G2-A3IE     TCGA-G2-A3VY     TCGA-GC-A3BM 
"GAR1 WILD-TYPE" "GAR1 WILD-TYPE" "GAR1 WILD-TYPE" "GAR1 WILD-TYPE" 
    TCGA-GC-A3I6     TCGA-GC-A3OO     TCGA-GC-A3RC     TCGA-GC-A3RD 
"GAR1 WILD-TYPE" "GAR1 WILD-TYPE" "GAR1 WILD-TYPE" "GAR1 WILD-TYPE" 
    TCGA-GC-A3YS     TCGA-GC-A6I1     TCGA-GC-A6I3     TCGA-GD-A3OS 
"GAR1 WILD-TYPE" "GAR1 WILD-TYPE" "GAR1 WILD-TYPE" "GAR1 WILD-TYPE" 
    TCGA-GD-A6C6     TCGA-GV-A3JV     TCGA-GV-A3JW     TCGA-GV-A3JX 
"GAR1 WILD-TYPE" "GAR1 WILD-TYPE" "GAR1 WILD-TYPE" "GAR1 WILD-TYPE" 
    TCGA-GV-A3JZ     TCGA-GV-A3QF     TCGA-GV-A3QH     TCGA-GV-A3QI 
"GAR1 WILD-TYPE" "GAR1 WILD-TYPE" "GAR1 WILD-TYPE" "GAR1 WILD-TYPE" 
    TCGA-GV-A3QK     TCGA-GV-A40E     TCGA-GV-A40G     TCGA-GV-A6ZA 
"GAR1 WILD-TYPE" "GAR1 WILD-TYPE" "GAR1 WILD-TYPE" "GAR1 WILD-TYPE" 
    TCGA-SY-A9G0     TCGA-SY-A9G5     TCGA-UY-A78L     TCGA-UY-A78M 
"GAR1 WILD-TYPE" "GAR1 WILD-TYPE" "GAR1 WILD-TYPE" "GAR1 WILD-TYPE" 
    TCGA-UY-A78N     TCGA-XF-A8HH     TCGA-XF-A8HI     TCGA-XF-A9SG 
"GAR1 WILD-TYPE" "GAR1 WILD-TYPE" "GAR1 WILD-TYPE" "GAR1 WILD-TYPE" 
    TCGA-XF-A9SH     TCGA-XF-A9SI     TCGA-XF-A9SJ     TCGA-XF-A9SL 
"GAR1 WILD-TYPE" "GAR1 WILD-TYPE" "GAR1 WILD-TYPE" "GAR1 WILD-TYPE" 
    TCGA-XF-A9SV     TCGA-XF-A9SW     TCGA-XF-A9SX     TCGA-XF-A9SY 
"GAR1 WILD-TYPE" "GAR1 WILD-TYPE" "GAR1 WILD-TYPE" "GAR1 WILD-TYPE" 
    TCGA-XF-A9SZ     TCGA-XF-A9T0     TCGA-XF-A9T2     TCGA-XF-A9T3 
"GAR1 WILD-TYPE" "GAR1 WILD-TYPE" "GAR1 WILD-TYPE" "GAR1 WILD-TYPE" 
    TCGA-XF-A9T4     TCGA-XF-A9T5     TCGA-XF-A9T6     TCGA-XF-A9T8 
"GAR1 WILD-TYPE" "GAR1 WILD-TYPE" "GAR1 WILD-TYPE" "GAR1 WILD-TYPE" 
    TCGA-XF-AAME     TCGA-XF-AAMF     TCGA-XF-AAMG     TCGA-XF-AAMH 
"GAR1 WILD-TYPE" "GAR1 WILD-TYPE" "GAR1 WILD-TYPE" "GAR1 WILD-TYPE" 
    TCGA-XF-AAMJ     TCGA-XF-AAML     TCGA-XF-AAMQ     TCGA-XF-AAMR 
"GAR1 WILD-TYPE" "GAR1 WILD-TYPE" "GAR1 WILD-TYPE" "GAR1 WILD-TYPE" 
    TCGA-XF-AAMT     TCGA-XF-AAMW     TCGA-XF-AAMX     TCGA-XF-AAMY 
"GAR1 WILD-TYPE" "GAR1 WILD-TYPE" "GAR1 WILD-TYPE" "GAR1 WILD-TYPE" 
    TCGA-XF-AAMZ     TCGA-XF-AAN0     TCGA-XF-AAN1     TCGA-XF-AAN2 
"GAR1 WILD-TYPE" "GAR1 WILD-TYPE" "GAR1 WILD-TYPE" "GAR1 WILD-TYPE" 
    TCGA-XF-AAN3     TCGA-XF-AAN4     TCGA-XF-AAN5     TCGA-XF-AAN7 
"GAR1 WILD-TYPE" "GAR1 WILD-TYPE" "GAR1 WILD-TYPE" "GAR1 WILD-TYPE" 
    TCGA-XF-AAN8     TCGA-YF-AA3L     TCGA-YF-AA3M 
"GAR1 WILD-TYPE" "GAR1 WILD-TYPE" "GAR1 WILD-TYPE" 
D109V9, continuous
[1] "Remove cluster labels:" "GAR1 MUTATED"          
clus
  GAR1 MUTATED GAR1 WILD-TYPE 
             2            203 
    TCGA-2F-A9KO     TCGA-2F-A9KP     TCGA-2F-A9KR     TCGA-4Z-AA7M 
"GAR1 WILD-TYPE" "GAR1 WILD-TYPE" "GAR1 WILD-TYPE" "GAR1 WILD-TYPE" 
    TCGA-4Z-AA89     TCGA-BL-A0C8     TCGA-BL-A13I     TCGA-BL-A13J 
"GAR1 WILD-TYPE" "GAR1 WILD-TYPE" "GAR1 WILD-TYPE" "GAR1 WILD-TYPE" 
    TCGA-BL-A3JM     TCGA-BL-A5ZZ     TCGA-BT-A20J     TCGA-BT-A20N 
"GAR1 WILD-TYPE" "GAR1 WILD-TYPE" "GAR1 WILD-TYPE" "GAR1 WILD-TYPE" 
    TCGA-BT-A2LA     TCGA-BT-A42B     TCGA-BT-A42C     TCGA-BT-A42E 
"GAR1 WILD-TYPE" "GAR1 WILD-TYPE" "GAR1 WILD-TYPE" "GAR1 WILD-TYPE" 
    TCGA-C4-A0EZ     TCGA-C4-A0F0     TCGA-C4-A0F1     TCGA-C4-A0F6 
"GAR1 WILD-TYPE" "GAR1 WILD-TYPE" "GAR1 WILD-TYPE" "GAR1 WILD-TYPE" 
    TCGA-CF-A3MH     TCGA-CF-A3MI     TCGA-CF-A47W     TCGA-CF-A47X 
"GAR1 WILD-TYPE" "GAR1 WILD-TYPE" "GAR1 WILD-TYPE" "GAR1 WILD-TYPE" 
    TCGA-CF-A5UA     TCGA-CF-A9FH     TCGA-CU-A0YN     TCGA-CU-A0YR 
"GAR1 WILD-TYPE" "GAR1 WILD-TYPE" "GAR1 WILD-TYPE" "GAR1 WILD-TYPE" 
    TCGA-CU-A3KJ     TCGA-CU-A3QU     TCGA-CU-A3YL     TCGA-CU-A5W6 
"GAR1 WILD-TYPE" "GAR1 WILD-TYPE" "GAR1 WILD-TYPE" "GAR1 WILD-TYPE" 
    TCGA-CU-A72E     TCGA-DK-A1A3     TCGA-DK-A1A5     TCGA-DK-A1A6 
"GAR1 WILD-TYPE" "GAR1 WILD-TYPE" "GAR1 WILD-TYPE" "GAR1 WILD-TYPE" 
    TCGA-DK-A1AA     TCGA-DK-A1AC     TCGA-DK-A1AE     TCGA-DK-A2HX 
"GAR1 WILD-TYPE" "GAR1 WILD-TYPE" "GAR1 WILD-TYPE" "GAR1 WILD-TYPE" 
    TCGA-DK-A2I6     TCGA-DK-A3IL     TCGA-DK-A3IM     TCGA-DK-A3IN 
"GAR1 WILD-TYPE" "GAR1 WILD-TYPE" "GAR1 WILD-TYPE" "GAR1 WILD-TYPE" 
    TCGA-DK-A3IQ     TCGA-DK-A3IU     TCGA-DK-A3IV     TCGA-DK-A3WX 
"GAR1 WILD-TYPE" "GAR1 WILD-TYPE" "GAR1 WILD-TYPE" "GAR1 WILD-TYPE" 
    TCGA-DK-A3X1     TCGA-DK-A3X2     TCGA-DK-A6AV     TCGA-DK-A6AW 
"GAR1 WILD-TYPE" "GAR1 WILD-TYPE" "GAR1 WILD-TYPE" "GAR1 WILD-TYPE" 
    TCGA-DK-A6B0     TCGA-DK-A6B2     TCGA-DK-A6B6     TCGA-DK-AA6L 
"GAR1 WILD-TYPE" "GAR1 WILD-TYPE" "GAR1 WILD-TYPE" "GAR1 WILD-TYPE" 
    TCGA-DK-AA6P     TCGA-DK-AA6T     TCGA-DK-AA6U     TCGA-DK-AA74 
"GAR1 WILD-TYPE" "GAR1 WILD-TYPE" "GAR1 WILD-TYPE" "GAR1 WILD-TYPE" 
    TCGA-DK-AA76     TCGA-E5-A4TZ     TCGA-E7-A4XJ     TCGA-E7-A519 
"GAR1 WILD-TYPE" "GAR1 WILD-TYPE" "GAR1 WILD-TYPE" "GAR1 WILD-TYPE" 
    TCGA-E7-A5KF     TCGA-E7-A678     TCGA-E7-A6ME     TCGA-E7-A6MF 
"GAR1 WILD-TYPE" "GAR1 WILD-TYPE" "GAR1 WILD-TYPE" "GAR1 WILD-TYPE" 
    TCGA-E7-A7PW     TCGA-E7-A7XN     TCGA-E7-A85H     TCGA-E7-A97Q 
"GAR1 WILD-TYPE" "GAR1 WILD-TYPE" "GAR1 WILD-TYPE" "GAR1 WILD-TYPE" 
    TCGA-FD-A3B3     TCGA-FD-A3B4     TCGA-FD-A3B5     TCGA-FD-A3B6 
"GAR1 WILD-TYPE" "GAR1 WILD-TYPE" "GAR1 WILD-TYPE" "GAR1 WILD-TYPE" 
    TCGA-FD-A3B7     TCGA-FD-A3B8     TCGA-FD-A3N5     TCGA-FD-A3N6 
"GAR1 WILD-TYPE" "GAR1 WILD-TYPE" "GAR1 WILD-TYPE" "GAR1 WILD-TYPE" 
    TCGA-FD-A3NA     TCGA-FD-A3SJ     TCGA-FD-A3SM     TCGA-FD-A3SN 
"GAR1 WILD-TYPE" "GAR1 WILD-TYPE" "GAR1 WILD-TYPE" "GAR1 WILD-TYPE" 
    TCGA-FD-A3SO     TCGA-FD-A3SP     TCGA-FD-A3SQ     TCGA-FD-A3SR 
"GAR1 WILD-TYPE" "GAR1 WILD-TYPE" "GAR1 WILD-TYPE" "GAR1 WILD-TYPE" 
    TCGA-FD-A3SS     TCGA-FD-A43N     TCGA-FD-A43P     TCGA-FD-A43S 
"GAR1 WILD-TYPE" "GAR1 WILD-TYPE" "GAR1 WILD-TYPE" "GAR1 WILD-TYPE" 
    TCGA-FD-A43U     TCGA-FD-A43X     TCGA-FD-A5BT     TCGA-FD-A5BU 
"GAR1 WILD-TYPE" "GAR1 WILD-TYPE" "GAR1 WILD-TYPE" "GAR1 WILD-TYPE" 
    TCGA-FD-A5BV     TCGA-FD-A5BX     TCGA-FD-A5C0     TCGA-FD-A62N 
"GAR1 WILD-TYPE" "GAR1 WILD-TYPE" "GAR1 WILD-TYPE" "GAR1 WILD-TYPE" 
    TCGA-FD-A6TB     TCGA-FD-A6TC     TCGA-FD-A6TE     TCGA-FD-A6TG 
"GAR1 WILD-TYPE" "GAR1 WILD-TYPE" "GAR1 WILD-TYPE" "GAR1 WILD-TYPE" 
    TCGA-FD-A6TH     TCGA-FD-A6TK     TCGA-FJ-A3Z9     TCGA-FJ-A3ZE 
"GAR1 WILD-TYPE" "GAR1 WILD-TYPE" "GAR1 WILD-TYPE" "GAR1 WILD-TYPE" 
    TCGA-FJ-A3ZF     TCGA-FJ-A871     TCGA-FT-A61P     TCGA-G2-A2EF 
"GAR1 WILD-TYPE" "GAR1 WILD-TYPE" "GAR1 WILD-TYPE" "GAR1 WILD-TYPE" 
    TCGA-G2-A2EJ     TCGA-G2-A2EL     TCGA-G2-A2ES     TCGA-G2-A3IE 
"GAR1 WILD-TYPE" "GAR1 WILD-TYPE" "GAR1 WILD-TYPE" "GAR1 WILD-TYPE" 
    TCGA-G2-AA3C     TCGA-G2-AA3D     TCGA-G2-AA3F     TCGA-GC-A3BM 
"GAR1 WILD-TYPE" "GAR1 WILD-TYPE" "GAR1 WILD-TYPE" "GAR1 WILD-TYPE" 
    TCGA-GC-A3RB     TCGA-GC-A3WC     TCGA-GC-A3YS     TCGA-GD-A2C5 
"GAR1 WILD-TYPE" "GAR1 WILD-TYPE" "GAR1 WILD-TYPE" "GAR1 WILD-TYPE" 
    TCGA-GD-A3OQ     TCGA-GD-A3OS     TCGA-GD-A6C6     TCGA-GU-A42P 
"GAR1 WILD-TYPE" "GAR1 WILD-TYPE" "GAR1 WILD-TYPE" "GAR1 WILD-TYPE" 
    TCGA-GU-A42Q     TCGA-GU-A42R     TCGA-GU-A764     TCGA-GU-AATO 
"GAR1 WILD-TYPE" "GAR1 WILD-TYPE" "GAR1 WILD-TYPE" "GAR1 WILD-TYPE" 
    TCGA-GU-AATP     TCGA-GU-AATQ     TCGA-GV-A3JV     TCGA-GV-A3JX 
"GAR1 WILD-TYPE" "GAR1 WILD-TYPE" "GAR1 WILD-TYPE" "GAR1 WILD-TYPE" 
    TCGA-GV-A3JZ     TCGA-GV-A3QF     TCGA-GV-A3QG     TCGA-GV-A3QH 
"GAR1 WILD-TYPE" "GAR1 WILD-TYPE" "GAR1 WILD-TYPE" "GAR1 WILD-TYPE" 
    TCGA-GV-A3QI     TCGA-GV-A3QK     TCGA-GV-A40E     TCGA-GV-A40G 
"GAR1 WILD-TYPE" "GAR1 WILD-TYPE" "GAR1 WILD-TYPE" "GAR1 WILD-TYPE" 
    TCGA-H4-A2HO     TCGA-H4-A2HQ     TCGA-HQ-A5ND     TCGA-HQ-A5NE 
"GAR1 WILD-TYPE" "GAR1 WILD-TYPE" "GAR1 WILD-TYPE" "GAR1 WILD-TYPE" 
    TCGA-K4-A3WS     TCGA-K4-A3WV     TCGA-K4-A5RH     TCGA-K4-A5RI 
"GAR1 WILD-TYPE" "GAR1 WILD-TYPE" "GAR1 WILD-TYPE" "GAR1 WILD-TYPE" 
    TCGA-K4-A83P     TCGA-K4-AAQO     TCGA-PQ-A6FI     TCGA-PQ-A6FN 
"GAR1 WILD-TYPE" "GAR1 WILD-TYPE" "GAR1 WILD-TYPE" "GAR1 WILD-TYPE" 
    TCGA-R3-A69X     TCGA-S5-A6DX     TCGA-SY-A9G0     TCGA-UY-A78N 
"GAR1 WILD-TYPE" "GAR1 WILD-TYPE" "GAR1 WILD-TYPE" "GAR1 WILD-TYPE" 
    TCGA-UY-A8OB     TCGA-UY-A9PB     TCGA-UY-A9PE     TCGA-UY-A9PF 
"GAR1 WILD-TYPE" "GAR1 WILD-TYPE" "GAR1 WILD-TYPE" "GAR1 WILD-TYPE" 
    TCGA-XF-A9SJ     TCGA-XF-A9SL     TCGA-XF-A9SV     TCGA-XF-A9SX 
"GAR1 WILD-TYPE" "GAR1 WILD-TYPE" "GAR1 WILD-TYPE" "GAR1 WILD-TYPE" 
    TCGA-XF-A9SY     TCGA-XF-A9SZ     TCGA-XF-A9T3     TCGA-XF-A9T8 
"GAR1 WILD-TYPE" "GAR1 WILD-TYPE" "GAR1 WILD-TYPE" "GAR1 WILD-TYPE" 
    TCGA-XF-AAMF     TCGA-XF-AAMH     TCGA-XF-AAMQ     TCGA-XF-AAMT 
"GAR1 WILD-TYPE" "GAR1 WILD-TYPE" "GAR1 WILD-TYPE" "GAR1 WILD-TYPE" 
    TCGA-XF-AAN0     TCGA-XF-AAN1     TCGA-XF-AAN2     TCGA-XF-AAN4 
"GAR1 WILD-TYPE" "GAR1 WILD-TYPE" "GAR1 WILD-TYPE" "GAR1 WILD-TYPE" 
    TCGA-XF-AAN5     TCGA-XF-AAN7     TCGA-XF-AAN8     TCGA-YF-AA3L 
"GAR1 WILD-TYPE" "GAR1 WILD-TYPE" "GAR1 WILD-TYPE" "GAR1 WILD-TYPE" 
    TCGA-YF-AA3M     TCGA-ZF-A9R0     TCGA-ZF-A9R2     TCGA-ZF-A9R3 
"GAR1 WILD-TYPE" "GAR1 WILD-TYPE" "GAR1 WILD-TYPE" "GAR1 WILD-TYPE" 
    TCGA-ZF-A9R5     TCGA-ZF-A9R7     TCGA-ZF-A9R9     TCGA-ZF-A9RD 
"GAR1 WILD-TYPE" "GAR1 WILD-TYPE" "GAR1 WILD-TYPE" "GAR1 WILD-TYPE" 
    TCGA-ZF-A9RF     TCGA-ZF-A9RL     TCGA-ZF-A9RM     TCGA-ZF-AA4U 
"GAR1 WILD-TYPE" "GAR1 WILD-TYPE" "GAR1 WILD-TYPE" "GAR1 WILD-TYPE" 
    TCGA-ZF-AA4V     TCGA-ZF-AA51     TCGA-ZF-AA52     TCGA-ZF-AA58 
"GAR1 WILD-TYPE" "GAR1 WILD-TYPE" "GAR1 WILD-TYPE" "GAR1 WILD-TYPE" 
    TCGA-ZF-AA5H     TCGA-ZF-AA5N     TCGA-ZF-AA5P 
"GAR1 WILD-TYPE" "GAR1 WILD-TYPE" "GAR1 WILD-TYPE" 
D109V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  GAR1 MUTATED       0                         0     4
  GAR1 WILD-TYPE    38                        21   297
D109V11, multiclass
                           clus
vv                          GAR1 MUTATED GAR1 WILD-TYPE
  ASIAN                                0             38
  BLACK OR AFRICAN AMERICAN            0             21
  WHITE                                4            297
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D109V12, binary
                cls
clus               0   1
  GAR1 MUTATED     0   4
  GAR1 WILD-TYPE   8 334
[1] "tbl2"
                cls
clus             [,1] [,2]
  GAR1 MUTATED      0    4
  GAR1 WILD-TYPE    8  334
                        clus
vv                       GAR1 MUTATED GAR1 WILD-TYPE
  HISPANIC OR LATINO                0              8
  NOT HISPANIC OR LATINO            4            334
[1] 2 2
[1] FALSE

Clustering(110) Variable = RFTN2 MUTATION ANALYSIS
D110V1, survival
                 sevent
clus2               0   1
  RFTN2 MUTATED     6   5
  RFTN2 WILD-TYPE 213 146
  RFTN2 MUTATED RFTN2 WILD-TYPE 
             11             359 
  RFTN2 MUTATED RFTN2 WILD-TYPE 
              5             146 
$`RFTN2 MUTATED`
TCGA-2F-A9KR TCGA-BT-A20J TCGA-BT-A20R TCGA-BT-A20T TCGA-CU-A0YO TCGA-DK-A6AW 
      103.50        19.04         5.06        14.89         4.90        41.56 
TCGA-FD-A6TA TCGA-GU-A766 TCGA-UY-A78M TCGA-XF-AAMG TCGA-ZF-A9R5 
       62.86         5.62        22.68       110.60        27.19 

$`RFTN2 WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KT TCGA-2F-A9KW TCGA-4Z-AA7M 
       22.29        11.97        91.63       105.70         8.35        16.27 
TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7W 
       44.94        16.83        16.77        17.16        34.98        27.62 
TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA84 
       49.12         0.62        41.75        51.16        66.54        15.12 
TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J 
       10.22        47.80        33.83        40.08         7.33         2.66 
TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20N TCGA-BT-A20O 
        6.74        12.39         6.58        13.15        32.84        12.16 
TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X 
       17.88        19.50        14.96         5.06         8.35         8.25 
TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK 
       17.16        16.18        20.48         4.67        12.82         9.96 
TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 
       17.56        28.70        24.26        28.41         8.98         1.94 
TCGA-C4-A0F1 TCGA-C4-A0F6 TCGA-C4-A0F7 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C 
        2.93        23.01         2.04         0.46         0.43         0.69 
TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y 
       10.95        12.66        12.46        12.10        12.62        12.26 
TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A0YN 
       13.12        12.00        12.10        11.87        13.08        12.92 
TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E 
        7.20         5.46         5.19        16.31         1.84        13.58 
TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB 
       21.86         2.14        66.41        18.41        19.00        16.70 
TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX 
      130.88       112.44        16.14        17.62        15.62         1.81 
TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL 
       10.59         7.79       123.85        87.32         2.20        13.58 
TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU 
        7.82         8.22        17.72        50.27        21.30        23.21 
TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A3X2 
        9.67        20.81        10.55       140.81        48.00        17.98 
TCGA-DK-A6AV TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 
       64.18        76.60        67.36        15.68        41.06        30.67 
TCGA-DK-AA6L TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6U 
       38.24        15.02        13.58       166.03        12.36        10.49 
TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA76 TCGA-DK-AA77 
        8.65         7.53        13.64        43.50        12.03        10.62 
TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ 
       43.59        15.35        38.83        24.66         0.10         0.49 
TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 
        2.24        16.70        17.39         0.56         0.66        14.56 
TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7DV TCGA-E7-A7PW 
       13.97        12.99        14.33         0.92         1.22        13.68 
TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 
       14.07        12.95        14.37         8.09        32.02        16.77 
TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 
        8.94        33.04         4.01        12.62        22.52        27.98 
TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO 
       60.66        24.30        23.41        17.98        29.16         5.52 
TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P 
       25.74        46.78        19.79        12.85        22.98        27.35 
TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT 
       14.96        20.91         3.62        26.73        53.88        11.01 
TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 
       19.33         5.36         5.69         8.25        27.45        18.08 
TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TB 
       58.92         2.70         7.10         6.28        13.35        18.81 
TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH 
        6.15        12.69        12.36         2.27         3.06         4.31 
TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF 
        9.67        10.85        31.07         7.13        10.65        17.23 
TCGA-FJ-A871 TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EC TCGA-G2-A2EF TCGA-G2-A2EJ 
        8.94         3.25         6.48        22.88        61.94        30.61 
TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE 
       15.95        26.93        35.24        33.01         7.23        20.12 
TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3BM 
       17.62        66.02         6.94        64.44        19.46        21.40 
TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC 
        2.24        15.81         4.50        15.91        14.07        17.75 
TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ 
       24.92         8.94        13.91         7.73         2.10         3.12 
TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R 
       20.98         2.20         7.36        10.92        11.31        11.31 
TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A767 TCGA-GU-AATO TCGA-GU-AATP 
        7.63        27.09        20.05         4.73        10.65        32.98 
TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF 
        7.00        14.27        21.34        19.10        19.82        20.28 
TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA 
        8.48        10.59        27.35         8.58        19.07        22.72 
TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE 
        1.51        19.40        38.60         3.06         9.01         8.22 
TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R 
       25.02         3.45        21.24         2.76         9.14        27.68 
TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P 
        9.07        11.70         1.74         1.81        15.42         6.38 
TCGA-K4-AAQO TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN 
       11.80        15.32        15.58        13.48        12.23        16.67 
TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78K 
       14.24         1.84         3.75        12.43        31.56        17.62 
TCGA-UY-A78L TCGA-UY-A78N TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A9PA TCGA-UY-A9PB 
       37.05        86.83        76.01        65.75        35.24        29.56 
TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG 
       17.82         4.54         1.64         1.87        17.88        48.62 
TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SL TCGA-XF-A9SV TCGA-XF-A9SW 
       64.80        79.66         3.22        66.41        12.76        11.90 
TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 
       23.64        21.04        28.24        26.27        18.90         2.24 
TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMF 
       16.27        66.64         2.10        13.74        92.98        10.82 
TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMT 
       11.31        54.90         7.63        71.57        91.73         2.96 
TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN0 TCGA-XF-AAN1 
        8.32         6.77        98.99        44.32        56.48        30.94 
TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN7 TCGA-XF-AAN8 
       61.45        86.30        27.06        75.39        18.81         3.88 
TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R0 TCGA-ZF-A9R1 
        9.63         0.66        11.97        13.64        18.64         7.36 
TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RC 
       21.11        24.13        30.28        21.86        28.41        74.56 
TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-A9RM 
       13.41         3.48        52.73        52.60        82.49        47.84 
TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4U TCGA-ZF-AA4V 
       20.22         2.89        34.06        19.69         8.61        59.38 
TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA53 TCGA-ZF-AA54 
       60.16        63.02        38.73        35.41        57.90        19.40 
TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-ZF-AA5P 
        8.52        47.15        19.17         5.52        10.13 

  RFTN2 MUTATED RFTN2 WILD-TYPE 
            4.9             0.1 
  RFTN2 MUTATED RFTN2 WILD-TYPE 
         110.60          166.03 
  RFTN2 MUTATED RFTN2 WILD-TYPE 
          22.68           15.58 
[1] "4.9 - 110.6 (22.7)" "0.1 - 166.0 (15.6)"
[1] "hr=" "1.2"
D110V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  RFTN2 MUTATED         0        3         3        5
  RFTN2 WILD-TYPE       4      114       119      123
D110V3, multiclass
           clus
vv          RFTN2 MUTATED RFTN2 WILD-TYPE
  STAGE I               0               4
  STAGE II              3             114
  STAGE III             3             119
  STAGE IV              5             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"
                 vv
clus              T0+T1+T2  T3  T4
  RFTN2 MUTATED          4   6   1
  RFTN2 WILD-TYPE      110 173  51
D110V4, multiclass
          clus
vv         RFTN2 MUTATED RFTN2 WILD-TYPE
  T0+T1+T2             4             110
  T3                   6             173
  T4                   1              51
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  RFTN2 MUTATED     6   2   3   0
  RFTN2 WILD-TYPE 207  39  72   8
D110V5, multiclass
    clus
vv   RFTN2 MUTATED RFTN2 WILD-TYPE
  N0             6             207
  N1             2              39
  N2             3              72
  N3             0               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"
D110V6, binary
                 cls
clus                0   1
  RFTN2 MUTATED     5   0
  RFTN2 WILD-TYPE 177  10
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RFTN2 MUTATED      5    0
  RFTN2 WILD-TYPE  177   10
   clus
vv  RFTN2 MUTATED RFTN2 WILD-TYPE
  0             5             177
  1             0              10
[1] 2 2
[1] FALSE
D110V7, binary
                 cls
clus                0   1
  RFTN2 MUTATED     3   8
  RFTN2 WILD-TYPE  93 272
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RFTN2 MUTATED      3    8
  RFTN2 WILD-TYPE   93  272
        clus
vv       RFTN2 MUTATED RFTN2 WILD-TYPE
  FEMALE             3              93
  MALE               8             272
[1] 2 2
[1] FALSE
D110V8, continuous
D110V9, continuous
D110V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RFTN2 MUTATED       1                         0     9
  RFTN2 WILD-TYPE    37                        21   292
D110V11, multiclass
                           clus
vv                          RFTN2 MUTATED RFTN2 WILD-TYPE
  ASIAN                                 1              37
  BLACK OR AFRICAN AMERICAN             0              21
  WHITE                                 9             292
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D110V12, binary
                 cls
clus                0   1
  RFTN2 MUTATED     1   9
  RFTN2 WILD-TYPE   7 329
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RFTN2 MUTATED      1    9
  RFTN2 WILD-TYPE    7  329
                        clus
vv                       RFTN2 MUTATED RFTN2 WILD-TYPE
  HISPANIC OR LATINO                 1               7
  NOT HISPANIC OR LATINO             9             329
[1] 2 2
[1] FALSE

Clustering(111) Variable = ZFP36L2 MUTATION ANALYSIS
D111V1, survival
                   sevent
clus2                 0   1
  ZFP36L2 MUTATED    12   3
  ZFP36L2 WILD-TYPE 207 148
  ZFP36L2 MUTATED ZFP36L2 WILD-TYPE 
               15               355 
  ZFP36L2 MUTATED ZFP36L2 WILD-TYPE 
                3               148 
$`ZFP36L2 MUTATED`
TCGA-BT-A3PJ TCGA-DK-A2I4 TCGA-DK-A6B0 TCGA-DK-AA77 TCGA-E7-A4XJ TCGA-E7-A85H 
       12.82       123.85        76.60        10.62         2.24        12.95 
TCGA-FD-A6TB TCGA-GC-A3YS TCGA-GV-A3QF TCGA-GV-A3QK TCGA-K4-A54R TCGA-K4-AAQO 
       18.81        24.92        20.28        27.35        27.68        11.80 
TCGA-MV-A51V TCGA-SY-A9G5 TCGA-UY-A78M 
       13.48        31.56        22.68 

$`ZFP36L2 WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        91.63       103.50       105.70         8.35 
TCGA-4Z-AA7M TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7S 
       16.27        44.94        16.83        16.77        17.16        34.98 
TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 
       27.62        49.12         0.62        41.75        51.16        66.54 
TCGA-4Z-AA84 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BL-A13I 
       15.12        10.22        47.80        33.83        40.08         7.33 
TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J 
        2.66         6.74        12.39         6.58        13.15        19.04 
TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T 
       32.84        12.16        17.88        19.50         5.06        14.89 
TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB 
       14.96         5.06         8.35         8.25        17.16        16.18 
TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E 
       20.48         4.67         9.96        17.56        28.70        24.26 
TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-C4-A0F6 TCGA-C4-A0F7 
       28.41         8.98         1.94         2.93        23.01         2.04 
TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V 
        0.46         0.43         0.69        10.95        12.66        12.46 
TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 
       12.10        12.62        12.26        13.12        12.00        12.10 
TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ 
       11.87        13.08        12.92         4.90         7.20         5.46 
TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 
        5.19        16.31         1.84        13.58        21.86         2.14 
TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD 
       66.41        18.41        19.00        16.70       130.88       112.44 
TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 
       16.14        17.62        15.62         1.81        10.59         7.79 
TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ 
       87.32         2.20        13.58         7.82         8.22        17.72 
TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX 
       50.27        21.30        23.21         9.67        20.81        10.55 
TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B1 
      140.81        48.00        17.98        64.18        41.56        67.36 
TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6P TCGA-DK-AA6Q 
       15.68        41.06        30.67        38.24        15.02        13.58 
TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA71 
      166.03        12.36        10.49         8.65         7.53        13.64 
TCGA-DK-AA74 TCGA-DK-AA76 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 
       43.50        12.03        43.59        15.35        38.83        24.66 
TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF 
        0.10         0.49        16.70        17.39         0.56         0.66 
TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7DV 
       14.56        13.97        12.99        14.33         0.92         1.22 
TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 
       13.68        14.07        14.37         8.09        32.02        16.77 
TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 
        8.94        33.04         4.01        12.62        22.52        27.98 
TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO 
       60.66        24.30        23.41        17.98        29.16         5.52 
TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P 
       25.74        46.78        19.79        12.85        22.98        27.35 
TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT 
       14.96        20.91         3.62        26.73        53.88        11.01 
TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 
       19.33         5.36         5.69         8.25        27.45        18.08 
TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA 
       58.92         2.70         7.10         6.28        13.35        62.86 
TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH 
        6.15        12.69        12.36         2.27         3.06         4.31 
TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF 
        9.67        10.85        31.07         7.13        10.65        17.23 
TCGA-FJ-A871 TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EC TCGA-G2-A2EF TCGA-G2-A2EJ 
        8.94         3.25         6.48        22.88        61.94        30.61 
TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE 
       15.95        26.93        35.24        33.01         7.23        20.12 
TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3BM 
       17.62        66.02         6.94        64.44        19.46        21.40 
TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC 
        2.24        15.81         4.50        15.91        14.07        17.75 
TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS 
        8.94        13.91         7.73         2.10         3.12        20.98 
TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 
        2.20         7.36        10.92        11.31        11.31         7.63 
TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATO TCGA-GU-AATP 
       27.09        20.05         5.62         4.73        10.65        32.98 
TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QH 
        7.00        14.27        21.34        19.10        19.82         8.48 
TCGA-GV-A3QI TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-H4-A2HQ 
       10.59         8.58        19.07        22.72         1.51        19.40 
TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU 
       38.60         3.06         9.01         8.22        25.02         3.45 
TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ 
       21.24         2.76         9.14         9.07        11.70         1.74 
TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-PQ-A6FI 
        1.81        15.42         6.38        15.32        15.58        12.23 
TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 TCGA-SY-A9G0 TCGA-UY-A78K 
       16.67        14.24         1.84         3.75        12.43        17.62 
TCGA-UY-A78L TCGA-UY-A78N TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A9PA TCGA-UY-A9PB 
       37.05        86.83        76.01        65.75        35.24        29.56 
TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG 
       17.82         4.54         1.64         1.87        17.88        48.62 
TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SL TCGA-XF-A9SV TCGA-XF-A9SW 
       64.80        79.66         3.22        66.41        12.76        11.90 
TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 
       23.64        21.04        28.24        26.27        18.90         2.24 
TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMF 
       16.27        66.64         2.10        13.74        92.98        10.82 
TCGA-XF-AAMG TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR 
      110.60        11.31        54.90         7.63        71.57        91.73 
TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN0 
        2.96         8.32         6.77        98.99        44.32        56.48 
TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN7 
       30.94        61.45        86.30        27.06        75.39        18.81 
TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R0 
        3.88         9.63         0.66        11.97        13.64        18.64 
TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R7 
        7.36        21.11        24.13        30.28        27.19        21.86 
TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RG 
       28.41        74.56        13.41         3.48        52.73        52.60 
TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4R TCGA-ZF-AA4T 
       82.49        47.84        20.22         2.89        34.06        19.69 
TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 
        8.61        59.38        60.16        63.02        38.73        35.41 
TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N 
       57.90        19.40         8.52        47.15        19.17         5.52 
TCGA-ZF-AA5P 
       10.13 

  ZFP36L2 MUTATED ZFP36L2 WILD-TYPE 
             2.24              0.10 
  ZFP36L2 MUTATED ZFP36L2 WILD-TYPE 
           123.85            166.03 
  ZFP36L2 MUTATED ZFP36L2 WILD-TYPE 
            20.28             15.58 
[1] "2.2 - 123.8 (20.3)" "0.1 - 166.0 (15.6)"
[1] "hr=" "2.5"
D111V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  ZFP36L2 MUTATED         0        4         7        4
  ZFP36L2 WILD-TYPE       4      113       115      124
D111V3, multiclass
           clus
vv          ZFP36L2 MUTATED ZFP36L2 WILD-TYPE
  STAGE I                 0                 4
  STAGE II                4               113
  STAGE III               7               115
  STAGE IV                4               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"
                   vv
clus                T0+T1+T2  T3  T4
  ZFP36L2 MUTATED          5   8   2
  ZFP36L2 WILD-TYPE      109 171  50
D111V4, multiclass
          clus
vv         ZFP36L2 MUTATED ZFP36L2 WILD-TYPE
  T0+T1+T2               5               109
  T3                     8               171
  T4                     2                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"
                   vv
clus                 N0  N1  N2  N3
  ZFP36L2 MUTATED    10   1   3   1
  ZFP36L2 WILD-TYPE 203  40  72   7
D111V5, multiclass
    clus
vv   ZFP36L2 MUTATED ZFP36L2 WILD-TYPE
  N0              10               203
  N1               1                40
  N2               3                72
  N3               1                 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"
D111V6, binary
                   cls
clus                  0   1
  ZFP36L2 MUTATED     9   0
  ZFP36L2 WILD-TYPE 173  10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZFP36L2 MUTATED      9    0
  ZFP36L2 WILD-TYPE  173   10
   clus
vv  ZFP36L2 MUTATED ZFP36L2 WILD-TYPE
  0               9               173
  1               0                10
[1] 2 2
[1] FALSE
D111V7, binary
                   cls
clus                  0   1
  ZFP36L2 MUTATED     2  13
  ZFP36L2 WILD-TYPE  94 267
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZFP36L2 MUTATED      2   13
  ZFP36L2 WILD-TYPE   94  267
        clus
vv       ZFP36L2 MUTATED ZFP36L2 WILD-TYPE
  FEMALE               2                94
  MALE                13               267
[1] 2 2
[1] FALSE
D111V8, continuous
D111V9, continuous
D111V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ZFP36L2 MUTATED       3                         0    12
  ZFP36L2 WILD-TYPE    35                        21   289
D111V11, multiclass
                           clus
vv                          ZFP36L2 MUTATED ZFP36L2 WILD-TYPE
  ASIAN                                   3                35
  BLACK OR AFRICAN AMERICAN               0                21
  WHITE                                  12               289
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D111V12, binary
                   cls
clus                  0   1
  ZFP36L2 MUTATED     0  15
  ZFP36L2 WILD-TYPE   8 323
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZFP36L2 MUTATED      0   15
  ZFP36L2 WILD-TYPE    8  323
                        clus
vv                       ZFP36L2 MUTATED ZFP36L2 WILD-TYPE
  HISPANIC OR LATINO                   0                 8
  NOT HISPANIC OR LATINO              15               323
[1] 2 2
[1] FALSE

Clustering(112) Variable = GUCY2C MUTATION ANALYSIS
D112V1, survival
                  sevent
clus2                0   1
  GUCY2C MUTATED     8   3
  GUCY2C WILD-TYPE 211 148
  GUCY2C MUTATED GUCY2C WILD-TYPE 
              11              359 
  GUCY2C MUTATED GUCY2C WILD-TYPE 
               3              148 
$`GUCY2C MUTATED`
TCGA-4Z-AA7O TCGA-4Z-AA89 TCGA-CF-A1HS TCGA-DK-A6B1 TCGA-FD-A3SQ TCGA-G2-A2EJ 
       16.83        33.83         0.43        67.36        46.78        30.61 
TCGA-GC-A6I3 TCGA-XF-A9T8 TCGA-XF-AAN0 TCGA-ZF-A9RC TCGA-ZF-AA58 
       13.91        13.74        56.48        74.56        47.15 

$`GUCY2C WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        91.63       103.50       105.70         8.35 
TCGA-4Z-AA7M TCGA-4Z-AA7N TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7W 
       16.27        44.94        16.77        17.16        34.98        27.62 
TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA84 
       49.12         0.62        41.75        51.16        66.54        15.12 
TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM 
       10.22        47.80        40.08         7.33         2.66         6.74 
TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O 
       12.39         6.58        13.15        19.04        32.84        12.16 
TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20V 
       17.88        19.50         5.06        14.89        14.96         5.06 
TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH 
        8.35         8.25        17.16        16.18        20.48         4.67 
TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E TCGA-BT-A42F 
       12.82         9.96        17.56        28.70        24.26        28.41 
TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-C4-A0F6 TCGA-C4-A0F7 TCGA-CF-A1HR 
        8.98         1.94         2.93        23.01         2.04         0.46 
TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X 
        0.69        10.95        12.66        12.46        12.10        12.62 
TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A9FF TCGA-CF-A9FM 
       12.26        13.12        12.00        12.10        11.87        13.08 
TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL 
       12.92         4.90         7.20         5.46         5.19        16.31 
TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 
        1.84        13.58        21.86         2.14        66.41        18.41 
TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF 
       19.00        16.70       130.88       112.44        16.14        17.62 
TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A2I6 
       15.62         1.81        10.59         7.79       123.85        87.32 
TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS 
        2.20        13.58         7.82         8.22        17.72        50.27 
TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY 
       21.30        23.21         9.67        20.81        10.55       140.81 
TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B2 
       48.00        17.98        64.18        41.56        76.60        15.68 
TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6S 
       41.06        30.67        38.24        15.02        13.58       166.03 
TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA74 
       12.36        10.49         8.65         7.53        13.64        43.50 
TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 
       12.03        10.62        43.59        15.35        38.83        24.66 
TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KE 
        0.10         0.49         2.24        16.70        17.39         0.56 
TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DU 
        0.66        14.56        13.97        12.99        14.33         0.92 
TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A97P TCGA-E7-A97Q 
        1.22        13.68        14.07        12.95        14.37         8.09 
TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 
       32.02        16.77         8.94        33.04         4.01        12.62 
TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM 
       22.52        27.98        60.66        24.30        23.41        17.98 
TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N 
       29.16         5.52        25.74        19.79        12.85        22.98 
TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS 
       27.35        14.96        20.91         3.62        26.73        53.88 
TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ 
       11.01        19.33         5.36         5.69         8.25        27.45 
TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S 
       18.08        58.92         2.70         7.10         6.28        13.35 
TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF 
       62.86        18.81         6.15        12.69        12.36         2.27 
TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 
        3.06         4.31         9.67        10.85        31.07         7.13 
TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FJ-A871 TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EC 
       10.65        17.23         8.94         3.25         6.48        22.88 
TCGA-G2-A2EF TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB 
       61.94        15.95        26.93        35.24        33.01         7.23 
TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3D TCGA-G2-AA3F 
       20.12        17.62        66.02         6.94        64.44        19.46 
TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD 
       21.40         2.24        15.81         4.50        15.91        14.07 
TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ 
       17.75        24.92         8.94         7.73         2.10         3.12 
TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R 
       20.98         2.20         7.36        10.92        11.31        11.31 
TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATO 
        7.63        27.09        20.05         5.62         4.73        10.65 
TCGA-GU-AATP TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ 
       32.98         7.00        14.27        21.34        19.10        19.82 
TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G 
       20.28         8.48        10.59        27.35         8.58        19.07 
TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND 
       22.72         1.51        19.40        38.60         3.06         9.01 
TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC 
        8.22        25.02         3.45        21.24         2.76         9.14 
TCGA-K4-A54R TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB 
       27.68         9.07        11.70         1.74         1.81        15.42 
TCGA-K4-A83P TCGA-K4-AAQO TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI 
        6.38        11.80        15.32        15.58        13.48        12.23 
TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 TCGA-SY-A9G0 TCGA-SY-A9G5 
       16.67        14.24         1.84         3.75        12.43        31.56 
TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78N TCGA-UY-A78O TCGA-UY-A8OB 
       17.62        37.05        22.68        86.83        76.01        65.75 
TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HH 
       35.24        29.56        17.82         4.54         1.64         1.87 
TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SL 
       17.88        48.62        64.80        79.66         3.22        66.41 
TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T0 
       12.76        11.90        23.64        21.04        28.24        26.27 
TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-AAME 
       18.90         2.24        16.27        66.64         2.10        92.98 
TCGA-XF-AAMF TCGA-XF-AAMG TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ 
       10.82       110.60        11.31        54.90         7.63        71.57 
TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAMZ 
       91.73         2.96         8.32         6.77        98.99        44.32 
TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN7 
       30.94        61.45        86.30        27.06        75.39        18.81 
TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R0 
        3.88         9.63         0.66        11.97        13.64        18.64 
TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R7 
        7.36        21.11        24.13        30.28        27.19        21.86 
TCGA-ZF-A9R9 TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RL 
       28.41        13.41         3.48        52.73        52.60        82.49 
TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4U 
       47.84        20.22         2.89        34.06        19.69         8.61 
TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA53 
       59.38        60.16        63.02        38.73        35.41        57.90 
TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-ZF-AA5P 
       19.40         8.52        19.17         5.52        10.13 

  GUCY2C MUTATED GUCY2C WILD-TYPE 
            0.43             0.10 
  GUCY2C MUTATED GUCY2C WILD-TYPE 
           74.56           166.03 
  GUCY2C MUTATED GUCY2C WILD-TYPE 
           33.83            15.42 
[1] "0.4 - 74.6 (33.8)"  "0.1 - 166.0 (15.4)"
[1] "hr=" "2.3"
D112V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  GUCY2C MUTATED         0        3         2        5
  GUCY2C WILD-TYPE       4      114       120      123
D112V3, multiclass
           clus
vv          GUCY2C MUTATED GUCY2C WILD-TYPE
  STAGE I                0                4
  STAGE II               3              114
  STAGE III              2              120
  STAGE IV               5              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"
                  vv
clus               T0+T1+T2  T3  T4
  GUCY2C MUTATED          2   6   2
  GUCY2C WILD-TYPE      112 173  50
D112V4, multiclass
          clus
vv         GUCY2C MUTATED GUCY2C WILD-TYPE
  T0+T1+T2              2              112
  T3                    6              173
  T4                    2               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"
                  vv
clus                N0  N1  N2  N3
  GUCY2C MUTATED     7   1   3   0
  GUCY2C WILD-TYPE 206  40  72   8
D112V5, multiclass
    clus
vv   GUCY2C MUTATED GUCY2C WILD-TYPE
  N0              7              206
  N1              1               40
  N2              3               72
  N3              0                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"
D112V6, binary
                  cls
clus                 0   1
  GUCY2C MUTATED     6   0
  GUCY2C WILD-TYPE 176  10
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GUCY2C MUTATED      6    0
  GUCY2C WILD-TYPE  176   10
   clus
vv  GUCY2C MUTATED GUCY2C WILD-TYPE
  0              6              176
  1              0               10
[1] 2 2
[1] FALSE
D112V7, binary
                  cls
clus                 0   1
  GUCY2C MUTATED     4   7
  GUCY2C WILD-TYPE  92 273
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GUCY2C MUTATED      4    7
  GUCY2C WILD-TYPE   92  273
        clus
vv       GUCY2C MUTATED GUCY2C WILD-TYPE
  FEMALE              4               92
  MALE                7              273
[1] 2 2
[1] FALSE
D112V8, continuous
D112V9, continuous
D112V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  GUCY2C MUTATED       1                         2     8
  GUCY2C WILD-TYPE    37                        19   293
D112V11, multiclass
                           clus
vv                          GUCY2C MUTATED GUCY2C WILD-TYPE
  ASIAN                                  1               37
  BLACK OR AFRICAN AMERICAN              2               19
  WHITE                                  8              293
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D112V12, binary
                  cls
clus                 0   1
  GUCY2C MUTATED     0   9
  GUCY2C WILD-TYPE   8 329
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GUCY2C MUTATED      0    9
  GUCY2C WILD-TYPE    8  329
                        clus
vv                       GUCY2C MUTATED GUCY2C WILD-TYPE
  HISPANIC OR LATINO                  0                8
  NOT HISPANIC OR LATINO              9              329
[1] 2 2
[1] FALSE

Clustering(113) Variable = COPZ2 MUTATION ANALYSIS
D113V1, survival
                 sevent
clus2               0   1
  COPZ2 MUTATED     3   0
  COPZ2 WILD-TYPE 216 151
  COPZ2 MUTATED COPZ2 WILD-TYPE 
              3             367 
  COPZ2 MUTATED COPZ2 WILD-TYPE 
              0             151 
$`COPZ2 MUTATED`
TCGA-DK-A1AD TCGA-DK-A6B6 TCGA-G2-A3VY 
      112.44        30.67        17.62 

$`COPZ2 WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        91.63       103.50       105.70         8.35 
TCGA-4Z-AA7M TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7S 
       16.27        44.94        16.83        16.77        17.16        34.98 
TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 
       27.62        49.12         0.62        41.75        51.16        66.54 
TCGA-4Z-AA84 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BL-A13I 
       15.12        10.22        47.80        33.83        40.08         7.33 
TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J 
        2.66         6.74        12.39         6.58        13.15        19.04 
TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T 
       32.84        12.16        17.88        19.50         5.06        14.89 
TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB 
       14.96         5.06         8.35         8.25        17.16        16.18 
TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C 
       20.48         4.67        12.82         9.96        17.56        28.70 
TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-C4-A0F6 
       24.26        28.41         8.98         1.94         2.93        23.01 
TCGA-C4-A0F7 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T 
        2.04         0.46         0.43         0.69        10.95        12.66 
TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA 
       12.46        12.10        12.62        12.26        13.12        12.00 
TCGA-CF-A7I0 TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR 
       12.10        11.87        13.08        12.92         4.90         7.20 
TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 
        5.46         5.19        16.31         1.84        13.58        21.86 
TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC 
        2.14        66.41        18.41        19.00        16.70       130.88 
TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 
       16.14        17.62        15.62         1.81        10.59         7.79 
TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN 
      123.85        87.32         2.20        13.58         7.82         8.22 
TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW 
       17.72        50.27        21.30        23.21         9.67        20.81 
TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW 
       10.55       140.81        48.00        17.98        64.18        41.56 
TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-AA6L TCGA-DK-AA6P 
       76.60        67.36        15.68        41.06        38.24        15.02 
TCGA-DK-AA6Q TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA6X 
       13.58       166.03        12.36        10.49         8.65         7.53 
TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A2PC TCGA-E5-A4TZ 
       13.64        43.50        12.03        10.62        43.59        15.35 
TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 
       38.83        24.66         0.10         0.49         2.24        16.70 
TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME 
       17.39         0.56         0.66        14.56        13.97        12.99 
TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H 
       14.33         0.92         1.22        13.68        14.07        12.95 
TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 
       14.37         8.09        32.02        16.77         8.94        33.04 
TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ 
        4.01        12.62        22.52        27.98        60.66        24.30 
TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ 
       23.41        17.98        29.16         5.52        25.74        46.78 
TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U 
       19.79        12.85        22.98        27.35        14.96        20.91 
TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV 
        3.62        26.73        53.88        11.01        19.33         5.36 
TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N 
        5.69         8.25        27.45        18.08        58.92         2.70 
TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC 
        7.10         6.28        13.35        62.86        18.81         6.15 
TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI 
       12.69        12.36         2.27         3.06         4.31         9.67 
TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FJ-A871 
       10.85        31.07         7.13        10.65        17.23         8.94 
TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EC TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK 
        3.25         6.48        22.88        61.94        30.61        15.95 
TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3B 
       26.93        35.24        33.01         7.23        20.12        66.02 
TCGA-G2-AA3C TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO 
        6.94        64.44        19.46        21.40         2.24        15.81 
TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A6I1 
        4.50        15.91        14.07        17.75        24.92         8.94 
TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 
       13.91         7.73         2.10         3.12        20.98         2.20 
TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 
        7.36        10.92        11.31        11.31         7.63        27.09 
TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATO TCGA-GU-AATP TCGA-GU-AATQ 
       20.05         5.62         4.73        10.65        32.98         7.00 
TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH 
       14.27        21.34        19.10        19.82        20.28         8.48 
TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO 
       10.59        27.35         8.58        19.07        22.72         1.51 
TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS 
       19.40        38.60         3.06         9.01         8.22        25.02 
TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RH 
        3.45        21.24         2.76         9.14        27.68         9.07 
TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO 
       11.70         1.74         1.81        15.42         6.38        11.80 
TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X 
       15.32        15.58        13.48        12.23        16.67        14.24 
TCGA-S5-A6DX TCGA-S5-AA26 TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L 
        1.84         3.75        12.43        31.56        17.62        37.05 
TCGA-UY-A78M TCGA-UY-A78N TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A9PA TCGA-UY-A9PB 
       22.68        86.83        76.01        65.75        35.24        29.56 
TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG 
       17.82         4.54         1.64         1.87        17.88        48.62 
TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SL TCGA-XF-A9SV TCGA-XF-A9SW 
       64.80        79.66         3.22        66.41        12.76        11.90 
TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 
       23.64        21.04        28.24        26.27        18.90         2.24 
TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMF 
       16.27        66.64         2.10        13.74        92.98        10.82 
TCGA-XF-AAMG TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR 
      110.60        11.31        54.90         7.63        71.57        91.73 
TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN0 
        2.96         8.32         6.77        98.99        44.32        56.48 
TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN7 
       30.94        61.45        86.30        27.06        75.39        18.81 
TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R0 
        3.88         9.63         0.66        11.97        13.64        18.64 
TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R7 
        7.36        21.11        24.13        30.28        27.19        21.86 
TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RG 
       28.41        74.56        13.41         3.48        52.73        52.60 
TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4R TCGA-ZF-AA4T 
       82.49        47.84        20.22         2.89        34.06        19.69 
TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 
        8.61        59.38        60.16        63.02        38.73        35.41 
TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N 
       57.90        19.40         8.52        47.15        19.17         5.52 
TCGA-ZF-AA5P 
       10.13 

  COPZ2 MUTATED COPZ2 WILD-TYPE 
          17.62            0.10 
  COPZ2 MUTATED COPZ2 WILD-TYPE 
         112.44          166.03 
  COPZ2 MUTATED COPZ2 WILD-TYPE 
          30.67           15.58 
[1] "17.6 - 112.4 (30.7)" "0.1 - 166.0 (15.6)" 
[1] "hr="     "9200000"
D113V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  COPZ2 MUTATED         0        2         0        1
  COPZ2 WILD-TYPE       4      115       122      127
D113V3, multiclass
           clus
vv          COPZ2 MUTATED COPZ2 WILD-TYPE
  STAGE I               0               4
  STAGE II              2             115
  STAGE III             0             122
  STAGE IV              1             127
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1+T2  T3  T4
  COPZ2 MUTATED          0   1   0
  COPZ2 WILD-TYPE      114 178  52
D113V4, multiclass
[1] "Remove cluster labels:" "COPZ2 MUTATED"         
clus
  COPZ2 MUTATED COPZ2 WILD-TYPE 
              1             344 
     TCGA-2F-A9KO      TCGA-2F-A9KP      TCGA-2F-A9KQ      TCGA-2F-A9KR 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-2F-A9KT      TCGA-2F-A9KW      TCGA-4Z-AA7M      TCGA-4Z-AA7N 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-4Z-AA7O      TCGA-4Z-AA7Q      TCGA-4Z-AA7R      TCGA-4Z-AA7S 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-4Z-AA7W      TCGA-4Z-AA7Y      TCGA-4Z-AA80      TCGA-4Z-AA81 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-4Z-AA82      TCGA-4Z-AA83      TCGA-4Z-AA84      TCGA-4Z-AA86 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-4Z-AA87      TCGA-4Z-AA89      TCGA-BL-A0C8      TCGA-BL-A13I 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-BL-A13J      TCGA-BL-A3JM      TCGA-BL-A5ZZ      TCGA-BT-A0S7 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-BT-A0YX      TCGA-BT-A20J      TCGA-BT-A20N      TCGA-BT-A20O 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-BT-A20P      TCGA-BT-A20Q      TCGA-BT-A20R      TCGA-BT-A20T 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-BT-A20U      TCGA-BT-A20V      TCGA-BT-A20W      TCGA-BT-A20X 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-BT-A2LA      TCGA-BT-A2LB      TCGA-BT-A2LD      TCGA-BT-A3PH 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-BT-A3PJ      TCGA-BT-A3PK      TCGA-BT-A42B      TCGA-BT-A42E 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-BT-A42F      TCGA-C4-A0EZ      TCGA-C4-A0F0      TCGA-C4-A0F1 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-C4-A0F6      TCGA-C4-A0F7      TCGA-CF-A1HR      TCGA-CF-A1HS 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-CF-A27C      TCGA-CF-A3MF      TCGA-CF-A3MG      TCGA-CF-A3MH 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-CF-A3MI      TCGA-CF-A47S      TCGA-CF-A47T      TCGA-CF-A47V 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-CF-A47W      TCGA-CF-A47X      TCGA-CF-A47Y      TCGA-CF-A5U8 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-CF-A5UA      TCGA-CF-A7I0      TCGA-CF-A9FF      TCGA-CF-A9FH 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-CF-A9FM      TCGA-CU-A0YN      TCGA-CU-A0YO      TCGA-CU-A0YR 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-CU-A3KJ      TCGA-CU-A3QU      TCGA-CU-A3YL      TCGA-CU-A5W6 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-CU-A72E      TCGA-DK-A1A3      TCGA-DK-A1A5      TCGA-DK-A1A6 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-DK-A1A7      TCGA-DK-A1AA      TCGA-DK-A1AB      TCGA-DK-A1AC 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-DK-A1AE      TCGA-DK-A1AF      TCGA-DK-A1AG      TCGA-DK-A2HX 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-DK-A2I1      TCGA-DK-A2I2      TCGA-DK-A2I4      TCGA-DK-A2I6 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-DK-A3IK      TCGA-DK-A3IL      TCGA-DK-A3IM      TCGA-DK-A3IN 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-DK-A3IQ      TCGA-DK-A3IS      TCGA-DK-A3IT      TCGA-DK-A3IU 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-DK-A3WW      TCGA-DK-A3WX      TCGA-DK-A3WY      TCGA-DK-A3X1 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-DK-A3X2      TCGA-DK-A6AV      TCGA-DK-A6AW      TCGA-DK-A6B0 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-DK-A6B1      TCGA-DK-A6B2      TCGA-DK-A6B5      TCGA-DK-AA6L 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-DK-AA6Q      TCGA-DK-AA6S      TCGA-DK-AA6W      TCGA-DK-AA71 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-DK-AA74      TCGA-DK-AA77      TCGA-E5-A2PC      TCGA-E5-A4TZ 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-E5-A4U1      TCGA-E7-A3X6      TCGA-E7-A4IJ      TCGA-E7-A4XJ 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-E7-A519      TCGA-E7-A541      TCGA-E7-A5KE      TCGA-E7-A5KF 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-E7-A677      TCGA-E7-A678      TCGA-E7-A6ME      TCGA-E7-A6MF 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-E7-A7DU      TCGA-E7-A7DV      TCGA-E7-A7PW      TCGA-E7-A7XN 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-E7-A85H      TCGA-E7-A97P      TCGA-E7-A97Q      TCGA-FD-A3B3 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-FD-A3B4      TCGA-FD-A3B5      TCGA-FD-A3B6      TCGA-FD-A3B7 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-FD-A3B8      TCGA-FD-A3N5      TCGA-FD-A3N6      TCGA-FD-A3NA 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-FD-A3SJ      TCGA-FD-A3SL      TCGA-FD-A3SM      TCGA-FD-A3SN 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-FD-A3SO      TCGA-FD-A3SP      TCGA-FD-A3SQ      TCGA-FD-A3SR 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-FD-A3SS      TCGA-FD-A43N      TCGA-FD-A43P      TCGA-FD-A43S 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-FD-A43U      TCGA-FD-A43X      TCGA-FD-A5BR      TCGA-FD-A5BS 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-FD-A5BT      TCGA-FD-A5BU      TCGA-FD-A5BV      TCGA-FD-A5BX 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-FD-A5BY      TCGA-FD-A5BZ      TCGA-FD-A5C0      TCGA-FD-A5C1 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-FD-A62N      TCGA-FD-A62O      TCGA-FD-A62P      TCGA-FD-A62S 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-FD-A6TA      TCGA-FD-A6TB      TCGA-FD-A6TC      TCGA-FD-A6TD 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-FD-A6TE      TCGA-FD-A6TF      TCGA-FD-A6TG      TCGA-FD-A6TH 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-FD-A6TI      TCGA-FD-A6TK      TCGA-FJ-A3Z7      TCGA-FJ-A3Z9 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-FJ-A871      TCGA-FT-A3EE      TCGA-FT-A61P      TCGA-G2-A2EO 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-G2-A2ES      TCGA-G2-AA3B      TCGA-G2-AA3C      TCGA-G2-AA3D 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-G2-AA3F      TCGA-GC-A3BM      TCGA-GC-A3I6      TCGA-GC-A3OO 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-GC-A3RB      TCGA-GC-A3RC      TCGA-GC-A3RD      TCGA-GC-A3WC 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-GC-A3YS      TCGA-GC-A6I1      TCGA-GC-A6I3      TCGA-GD-A2C5 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-GD-A3OP      TCGA-GD-A3OQ      TCGA-GD-A6C6      TCGA-GD-A76B 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-GU-A42P      TCGA-GU-A42Q      TCGA-GU-A42R      TCGA-GU-A762 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-GU-A763      TCGA-GU-A764      TCGA-GU-A766      TCGA-GU-A767 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-GU-AATO      TCGA-GU-AATP      TCGA-GU-AATQ      TCGA-GV-A3JV 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-GV-A3JW      TCGA-GV-A3JX      TCGA-GV-A3JZ      TCGA-GV-A3QF 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-GV-A3QG      TCGA-GV-A3QI      TCGA-GV-A3QK      TCGA-GV-A40G 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-GV-A6ZA      TCGA-H4-A2HO      TCGA-HQ-A2OE      TCGA-HQ-A2OF 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-HQ-A5ND      TCGA-HQ-A5NE      TCGA-K4-A3WS      TCGA-K4-A3WU 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-K4-A3WV      TCGA-K4-A4AB      TCGA-K4-A4AC      TCGA-K4-A54R 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-K4-A5RH      TCGA-K4-A5RI      TCGA-K4-A5RJ      TCGA-K4-A6FZ 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-K4-A6MB      TCGA-K4-A83P      TCGA-K4-AAQO      TCGA-LC-A66R 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-MV-A51V      TCGA-PQ-A6FI      TCGA-PQ-A6FN      TCGA-R3-A69X 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-S5-A6DX      TCGA-S5-AA26      TCGA-SY-A9G0      TCGA-SY-A9G5 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-UY-A78M      TCGA-UY-A78N      TCGA-UY-A78O      TCGA-UY-A8OB 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-UY-A9PA      TCGA-UY-A9PB      TCGA-UY-A9PD      TCGA-UY-A9PE 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-UY-A9PF      TCGA-XF-A8HH      TCGA-XF-A8HI      TCGA-XF-A9SG 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-XF-A9SH      TCGA-XF-A9SI      TCGA-XF-A9SJ      TCGA-XF-A9SL 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-XF-A9SV      TCGA-XF-A9SW      TCGA-XF-A9SX      TCGA-XF-A9SY 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-XF-A9SZ      TCGA-XF-A9T0      TCGA-XF-A9T2      TCGA-XF-A9T3 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-XF-A9T4      TCGA-XF-A9T5      TCGA-XF-A9T6      TCGA-XF-A9T8 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-XF-AAME      TCGA-XF-AAMF      TCGA-XF-AAMG      TCGA-XF-AAMH 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-XF-AAMJ      TCGA-XF-AAML      TCGA-XF-AAMQ      TCGA-XF-AAMR 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-XF-AAMT      TCGA-XF-AAMW      TCGA-XF-AAMX      TCGA-XF-AAMY 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-XF-AAMZ      TCGA-XF-AAN0      TCGA-XF-AAN1      TCGA-XF-AAN2 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-XF-AAN3      TCGA-XF-AAN4      TCGA-XF-AAN5      TCGA-XF-AAN7 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-XF-AAN8      TCGA-YC-A8S6      TCGA-YF-AA3L      TCGA-YF-AA3M 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-ZF-A9R0      TCGA-ZF-A9R1      TCGA-ZF-A9R2      TCGA-ZF-A9R3 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-ZF-A9R4      TCGA-ZF-A9R5      TCGA-ZF-A9R9      TCGA-ZF-A9RC 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-ZF-A9RD      TCGA-ZF-A9RF      TCGA-ZF-A9RG      TCGA-ZF-A9RM 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-ZF-A9RN      TCGA-ZF-AA4R      TCGA-ZF-AA4T      TCGA-ZF-AA4U 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-ZF-AA4V      TCGA-ZF-AA4W      TCGA-ZF-AA4X      TCGA-ZF-AA51 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-ZF-AA52      TCGA-ZF-AA53      TCGA-ZF-AA54      TCGA-ZF-AA56 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-ZF-AA58      TCGA-ZF-AA5H      TCGA-ZF-AA5N      TCGA-ZF-AA5P 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
                 vv
clus               N0  N1  N2  N3
  COPZ2 MUTATED     0   0   1   0
  COPZ2 WILD-TYPE 213  41  74   8
D113V5, multiclass
[1] "Remove cluster labels:" "COPZ2 MUTATED"         
clus
  COPZ2 MUTATED COPZ2 WILD-TYPE 
              1             336 
     TCGA-2F-A9KO      TCGA-2F-A9KP      TCGA-2F-A9KQ      TCGA-2F-A9KR 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-2F-A9KT      TCGA-2F-A9KW      TCGA-4Z-AA7M      TCGA-4Z-AA7N 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-4Z-AA7O      TCGA-4Z-AA7R      TCGA-4Z-AA7S      TCGA-4Z-AA7W 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-4Z-AA7Y      TCGA-4Z-AA80      TCGA-4Z-AA81      TCGA-4Z-AA82 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-4Z-AA83      TCGA-4Z-AA84      TCGA-4Z-AA86      TCGA-4Z-AA87 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-4Z-AA89      TCGA-BL-A13I      TCGA-BL-A13J      TCGA-BL-A3JM 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-BL-A5ZZ      TCGA-BT-A0S7      TCGA-BT-A0YX      TCGA-BT-A20J 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-BT-A20N      TCGA-BT-A20O      TCGA-BT-A20P      TCGA-BT-A20Q 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-BT-A20R      TCGA-BT-A20T      TCGA-BT-A20U      TCGA-BT-A20V 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-BT-A20W      TCGA-BT-A20X      TCGA-BT-A2LA      TCGA-BT-A2LB 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-BT-A2LD      TCGA-BT-A3PH      TCGA-BT-A3PJ      TCGA-BT-A3PK 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-BT-A42B      TCGA-BT-A42C      TCGA-BT-A42E      TCGA-BT-A42F 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-C4-A0EZ      TCGA-C4-A0F0      TCGA-C4-A0F1      TCGA-C4-A0F6 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-C4-A0F7      TCGA-CF-A1HR      TCGA-CF-A1HS      TCGA-CF-A27C 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-CF-A3MF      TCGA-CF-A3MG      TCGA-CF-A3MH      TCGA-CF-A3MI 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-CF-A47S      TCGA-CF-A47T      TCGA-CF-A47V      TCGA-CF-A47W 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-CF-A47X      TCGA-CF-A47Y      TCGA-CF-A5U8      TCGA-CF-A5UA 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-CF-A7I0      TCGA-CF-A9FF      TCGA-CF-A9FH      TCGA-CF-A9FM 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-CU-A0YN      TCGA-CU-A0YO      TCGA-CU-A0YR      TCGA-CU-A3KJ 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-CU-A3QU      TCGA-CU-A3YL      TCGA-CU-A5W6      TCGA-CU-A72E 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-DK-A1A3      TCGA-DK-A1A5      TCGA-DK-A1A6      TCGA-DK-A1A7 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-DK-A1AA      TCGA-DK-A1AB      TCGA-DK-A1AC      TCGA-DK-A1AE 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-DK-A1AF      TCGA-DK-A1AG      TCGA-DK-A2HX      TCGA-DK-A2I1 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-DK-A2I2      TCGA-DK-A2I4      TCGA-DK-A2I6      TCGA-DK-A3IK 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-DK-A3IL      TCGA-DK-A3IM      TCGA-DK-A3IN      TCGA-DK-A3IQ 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-DK-A3IS      TCGA-DK-A3IT      TCGA-DK-A3IU      TCGA-DK-A3WW 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-DK-A3WX      TCGA-DK-A3WY      TCGA-DK-A3X1      TCGA-DK-A3X2 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-DK-A6AV      TCGA-DK-A6AW      TCGA-DK-A6B0      TCGA-DK-A6B1 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-DK-A6B2      TCGA-DK-A6B5      TCGA-DK-AA6L      TCGA-DK-AA6P 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-DK-AA6Q      TCGA-DK-AA6S      TCGA-DK-AA6T      TCGA-DK-AA6U 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-DK-AA6W      TCGA-DK-AA6X      TCGA-DK-AA71      TCGA-DK-AA74 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-DK-AA76      TCGA-DK-AA77      TCGA-E5-A2PC      TCGA-E5-A4TZ 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-E5-A4U1      TCGA-E7-A3Y1      TCGA-E7-A4XJ      TCGA-E7-A541 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-E7-A5KE      TCGA-E7-A5KF      TCGA-E7-A677      TCGA-E7-A678 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-E7-A7DU      TCGA-E7-A7DV      TCGA-E7-A7XN      TCGA-E7-A85H 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-E7-A97Q      TCGA-FD-A3B3      TCGA-FD-A3B4      TCGA-FD-A3B5 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-FD-A3B6      TCGA-FD-A3B7      TCGA-FD-A3B8      TCGA-FD-A3N5 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-FD-A3N6      TCGA-FD-A3NA      TCGA-FD-A3SJ      TCGA-FD-A3SL 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-FD-A3SM      TCGA-FD-A3SN      TCGA-FD-A3SO      TCGA-FD-A3SP 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-FD-A3SQ      TCGA-FD-A3SR      TCGA-FD-A3SS      TCGA-FD-A43N 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-FD-A43P      TCGA-FD-A43S      TCGA-FD-A43U      TCGA-FD-A43X 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-FD-A5BR      TCGA-FD-A5BS      TCGA-FD-A5BT      TCGA-FD-A5BU 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-FD-A5BV      TCGA-FD-A5BX      TCGA-FD-A5BY      TCGA-FD-A5BZ 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-FD-A5C0      TCGA-FD-A5C1      TCGA-FD-A62N      TCGA-FD-A62O 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-FD-A62P      TCGA-FD-A62S      TCGA-FD-A6TA      TCGA-FD-A6TB 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-FD-A6TC      TCGA-FD-A6TD      TCGA-FD-A6TE      TCGA-FD-A6TF 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-FD-A6TG      TCGA-FD-A6TH      TCGA-FD-A6TI      TCGA-FD-A6TK 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-FJ-A3Z7      TCGA-FJ-A3Z9      TCGA-FJ-A3ZE      TCGA-FJ-A3ZF 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-FT-A3EE      TCGA-FT-A61P      TCGA-G2-A2EC      TCGA-G2-A2EF 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-G2-A2EJ      TCGA-G2-A2EK      TCGA-G2-A2EL      TCGA-G2-A2EO 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-G2-A2ES      TCGA-G2-AA3B      TCGA-G2-AA3C      TCGA-G2-AA3D 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-G2-AA3F      TCGA-GC-A3BM      TCGA-GC-A3I6      TCGA-GC-A3OO 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-GC-A3RB      TCGA-GC-A3RC      TCGA-GC-A3RD      TCGA-GC-A3WC 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-GC-A3YS      TCGA-GC-A6I1      TCGA-GC-A6I3      TCGA-GD-A2C5 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-GD-A3OP      TCGA-GD-A3OQ      TCGA-GD-A6C6      TCGA-GD-A76B 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-GU-A42P      TCGA-GU-A42Q      TCGA-GU-A42R      TCGA-GU-A762 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-GU-A763      TCGA-GU-A764      TCGA-GU-A766      TCGA-GU-A767 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-GU-AATO      TCGA-GU-AATP      TCGA-GU-AATQ      TCGA-GV-A3JV 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-GV-A3JX      TCGA-GV-A3JZ      TCGA-GV-A3QF      TCGA-GV-A3QG 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-GV-A3QI      TCGA-GV-A3QK      TCGA-GV-A40G      TCGA-GV-A6ZA 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-H4-A2HO      TCGA-HQ-A2OE      TCGA-HQ-A2OF      TCGA-HQ-A5ND 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-HQ-A5NE      TCGA-K4-A3WS      TCGA-K4-A3WU      TCGA-K4-A3WV 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-K4-A4AB      TCGA-K4-A4AC      TCGA-K4-A54R      TCGA-K4-A5RH 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-K4-A5RI      TCGA-K4-A5RJ      TCGA-K4-A6FZ      TCGA-K4-A6MB 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-K4-A83P      TCGA-K4-AAQO      TCGA-LC-A66R      TCGA-MV-A51V 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-PQ-A6FI      TCGA-PQ-A6FN      TCGA-R3-A69X      TCGA-S5-A6DX 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-S5-AA26      TCGA-SY-A9G0      TCGA-SY-A9G5      TCGA-UY-A78K 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-UY-A78L      TCGA-UY-A78M      TCGA-UY-A78N      TCGA-UY-A78O 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-UY-A8OB      TCGA-UY-A9PA      TCGA-UY-A9PB      TCGA-UY-A9PD 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-UY-A9PE      TCGA-UY-A9PF      TCGA-XF-A8HH      TCGA-XF-A8HI 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-XF-A9SG      TCGA-XF-A9SH      TCGA-XF-A9SI      TCGA-XF-A9SJ 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-XF-A9SL      TCGA-XF-A9SV      TCGA-XF-A9SW      TCGA-XF-A9SX 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-XF-A9SY      TCGA-XF-A9SZ      TCGA-XF-A9T0      TCGA-XF-A9T2 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-XF-A9T3      TCGA-XF-A9T4      TCGA-XF-A9T5      TCGA-XF-A9T6 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-XF-A9T8      TCGA-XF-AAME      TCGA-XF-AAMF      TCGA-XF-AAMG 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-XF-AAMH      TCGA-XF-AAMJ      TCGA-XF-AAML      TCGA-XF-AAMQ 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-XF-AAMR      TCGA-XF-AAMT      TCGA-XF-AAMW      TCGA-XF-AAMX 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-XF-AAMY      TCGA-XF-AAMZ      TCGA-XF-AAN0      TCGA-XF-AAN1 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-XF-AAN2      TCGA-XF-AAN3      TCGA-XF-AAN4      TCGA-XF-AAN5 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-XF-AAN7      TCGA-XF-AAN8      TCGA-YC-A8S6      TCGA-YF-AA3L 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-ZF-A9R1      TCGA-ZF-A9R2      TCGA-ZF-A9R5      TCGA-ZF-A9R9 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-ZF-A9RC      TCGA-ZF-A9RD      TCGA-ZF-A9RG      TCGA-ZF-A9RM 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-ZF-AA4R      TCGA-ZF-AA4T      TCGA-ZF-AA4V      TCGA-ZF-AA4W 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-ZF-AA56      TCGA-ZF-AA58      TCGA-ZF-AA5H      TCGA-ZF-AA5P 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
D113V6, binary
                 cls
clus                0   1
  COPZ2 MUTATED     1   0
  COPZ2 WILD-TYPE 181  10
[1] "tbl2"
                 cls
clus              [,1] [,2]
  COPZ2 MUTATED      1    0
  COPZ2 WILD-TYPE  181   10
   clus
vv  COPZ2 MUTATED COPZ2 WILD-TYPE
  0             1             181
  1             0              10
[1] 2 2
[1] FALSE
D113V7, binary
                 cls
clus                0   1
  COPZ2 MUTATED     0   3
  COPZ2 WILD-TYPE  96 277
[1] "tbl2"
                 cls
clus              [,1] [,2]
  COPZ2 MUTATED      0    3
  COPZ2 WILD-TYPE   96  277
        clus
vv       COPZ2 MUTATED COPZ2 WILD-TYPE
  FEMALE             0              96
  MALE               3             277
[1] 2 2
[1] FALSE
D113V8, continuous
[1] "Remove cluster labels:" "COPZ2 MUTATED"         
clus
  COPZ2 MUTATED COPZ2 WILD-TYPE 
              2             118 
     TCGA-2F-A9KO      TCGA-2F-A9KP      TCGA-2F-A9KQ      TCGA-2F-A9KR 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-2F-A9KT      TCGA-2F-A9KW      TCGA-CF-A1HS      TCGA-CF-A27C 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-CF-A3MF      TCGA-CF-A3MG      TCGA-CF-A3MH      TCGA-CF-A3MI 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-CF-A47S      TCGA-CF-A47T      TCGA-CF-A47V      TCGA-CF-A47W 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-CF-A47X      TCGA-CF-A47Y      TCGA-CF-A5U8      TCGA-CF-A5UA 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-CF-A7I0      TCGA-DK-A2HX      TCGA-DK-A3IN      TCGA-DK-A3IV 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-DK-A3WX      TCGA-DK-A3X2      TCGA-DK-A6B2      TCGA-DK-A6B5 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-DK-AA6P      TCGA-DK-AA6S      TCGA-DK-AA6U      TCGA-DK-AA6W 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-DK-AA76      TCGA-E5-A2PC      TCGA-E5-A4TZ      TCGA-E5-A4U1 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-E7-A519      TCGA-E7-A541      TCGA-E7-A7DU      TCGA-E7-A7DV 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-FT-A61P      TCGA-G2-A2EC      TCGA-G2-A2EF      TCGA-G2-A2EJ 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-G2-A2EK      TCGA-G2-A2EL      TCGA-G2-A2EO      TCGA-G2-A2ES 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-G2-A3IB      TCGA-G2-A3IE      TCGA-GC-A3BM      TCGA-GC-A3I6 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-GC-A3OO      TCGA-GC-A3RC      TCGA-GC-A3RD      TCGA-GC-A3YS 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-GC-A6I1      TCGA-GC-A6I3      TCGA-GD-A3OS      TCGA-GD-A6C6 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-GV-A3JV      TCGA-GV-A3JW      TCGA-GV-A3JX      TCGA-GV-A3JZ 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-GV-A3QF      TCGA-GV-A3QH      TCGA-GV-A3QI      TCGA-GV-A3QK 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-GV-A40E      TCGA-GV-A40G      TCGA-GV-A6ZA      TCGA-SY-A9G0 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-SY-A9G5      TCGA-UY-A78L      TCGA-UY-A78M      TCGA-UY-A78N 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-XF-A8HH      TCGA-XF-A8HI      TCGA-XF-A9SG      TCGA-XF-A9SH 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-XF-A9SI      TCGA-XF-A9SJ      TCGA-XF-A9SL      TCGA-XF-A9SV 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-XF-A9SW      TCGA-XF-A9SX      TCGA-XF-A9SY      TCGA-XF-A9SZ 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-XF-A9T0      TCGA-XF-A9T2      TCGA-XF-A9T3      TCGA-XF-A9T4 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-XF-A9T5      TCGA-XF-A9T6      TCGA-XF-A9T8      TCGA-XF-AAME 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-XF-AAMF      TCGA-XF-AAMG      TCGA-XF-AAMH      TCGA-XF-AAMJ 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-XF-AAML      TCGA-XF-AAMQ      TCGA-XF-AAMR      TCGA-XF-AAMT 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-XF-AAMW      TCGA-XF-AAMX      TCGA-XF-AAMY      TCGA-XF-AAMZ 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-XF-AAN0      TCGA-XF-AAN1      TCGA-XF-AAN2      TCGA-XF-AAN3 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-XF-AAN4      TCGA-XF-AAN5      TCGA-XF-AAN7      TCGA-XF-AAN8 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-YF-AA3L      TCGA-YF-AA3M 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
D113V9, continuous
[1] "Remove cluster labels:" "COPZ2 MUTATED"         
clus
  COPZ2 MUTATED COPZ2 WILD-TYPE 
              1             204 
     TCGA-2F-A9KO      TCGA-2F-A9KP      TCGA-2F-A9KR      TCGA-4Z-AA7M 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-4Z-AA89      TCGA-BL-A0C8      TCGA-BL-A13I      TCGA-BL-A13J 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-BL-A3JM      TCGA-BL-A5ZZ      TCGA-BT-A20J      TCGA-BT-A20N 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-BT-A2LA      TCGA-BT-A42B      TCGA-BT-A42C      TCGA-BT-A42E 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-C4-A0EZ      TCGA-C4-A0F0      TCGA-C4-A0F1      TCGA-C4-A0F6 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-CF-A3MH      TCGA-CF-A3MI      TCGA-CF-A47W      TCGA-CF-A47X 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-CF-A5UA      TCGA-CF-A9FH      TCGA-CU-A0YN      TCGA-CU-A0YR 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-CU-A3KJ      TCGA-CU-A3QU      TCGA-CU-A3YL      TCGA-CU-A5W6 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-CU-A72E      TCGA-DK-A1A3      TCGA-DK-A1A5      TCGA-DK-A1A6 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-DK-A1AA      TCGA-DK-A1AC      TCGA-DK-A1AE      TCGA-DK-A2HX 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-DK-A2I6      TCGA-DK-A3IL      TCGA-DK-A3IM      TCGA-DK-A3IN 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-DK-A3IQ      TCGA-DK-A3IU      TCGA-DK-A3IV      TCGA-DK-A3WX 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-DK-A3X1      TCGA-DK-A3X2      TCGA-DK-A6AV      TCGA-DK-A6AW 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-DK-A6B0      TCGA-DK-A6B2      TCGA-DK-AA6L      TCGA-DK-AA6P 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-DK-AA6T      TCGA-DK-AA6U      TCGA-DK-AA74      TCGA-DK-AA76 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-E5-A4TZ      TCGA-E7-A4XJ      TCGA-E7-A519      TCGA-E7-A5KF 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-E7-A678      TCGA-E7-A6ME      TCGA-E7-A6MF      TCGA-E7-A7PW 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-E7-A7XN      TCGA-E7-A85H      TCGA-E7-A97Q      TCGA-FD-A3B3 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-FD-A3B4      TCGA-FD-A3B5      TCGA-FD-A3B6      TCGA-FD-A3B7 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-FD-A3B8      TCGA-FD-A3N5      TCGA-FD-A3N6      TCGA-FD-A3NA 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-FD-A3SJ      TCGA-FD-A3SM      TCGA-FD-A3SN      TCGA-FD-A3SO 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-FD-A3SP      TCGA-FD-A3SQ      TCGA-FD-A3SR      TCGA-FD-A3SS 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-FD-A43N      TCGA-FD-A43P      TCGA-FD-A43S      TCGA-FD-A43U 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-FD-A43X      TCGA-FD-A5BT      TCGA-FD-A5BU      TCGA-FD-A5BV 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-FD-A5BX      TCGA-FD-A5C0      TCGA-FD-A62N      TCGA-FD-A6TB 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-FD-A6TC      TCGA-FD-A6TE      TCGA-FD-A6TG      TCGA-FD-A6TH 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-FD-A6TK      TCGA-FJ-A3Z9      TCGA-FJ-A3ZE      TCGA-FJ-A3ZF 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-FJ-A871      TCGA-FT-A61P      TCGA-G2-A2EF      TCGA-G2-A2EJ 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-G2-A2EL      TCGA-G2-A2ES      TCGA-G2-A3IE      TCGA-G2-AA3B 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-G2-AA3C      TCGA-G2-AA3D      TCGA-G2-AA3F      TCGA-GC-A3BM 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-GC-A3RB      TCGA-GC-A3WC      TCGA-GC-A3YS      TCGA-GD-A2C5 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-GD-A3OQ      TCGA-GD-A3OS      TCGA-GD-A6C6      TCGA-GU-A42P 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-GU-A42Q      TCGA-GU-A42R      TCGA-GU-A763      TCGA-GU-A764 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-GU-AATO      TCGA-GU-AATP      TCGA-GU-AATQ      TCGA-GV-A3JV 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-GV-A3JX      TCGA-GV-A3JZ      TCGA-GV-A3QF      TCGA-GV-A3QG 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-GV-A3QH      TCGA-GV-A3QI      TCGA-GV-A3QK      TCGA-GV-A40E 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-GV-A40G      TCGA-H4-A2HO      TCGA-H4-A2HQ      TCGA-HQ-A5ND 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-HQ-A5NE      TCGA-K4-A3WS      TCGA-K4-A3WV      TCGA-K4-A5RH 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-K4-A5RI      TCGA-K4-A83P      TCGA-K4-AAQO      TCGA-PQ-A6FI 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-PQ-A6FN      TCGA-R3-A69X      TCGA-S5-A6DX      TCGA-SY-A9G0 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-UY-A78N      TCGA-UY-A8OB      TCGA-UY-A9PB      TCGA-UY-A9PE 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-UY-A9PF      TCGA-XF-A9SJ      TCGA-XF-A9SL      TCGA-XF-A9SV 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-XF-A9SX      TCGA-XF-A9SY      TCGA-XF-A9SZ      TCGA-XF-A9T3 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-XF-A9T8      TCGA-XF-AAMF      TCGA-XF-AAMH      TCGA-XF-AAMQ 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-XF-AAMT      TCGA-XF-AAN0      TCGA-XF-AAN1      TCGA-XF-AAN2 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-XF-AAN4      TCGA-XF-AAN5      TCGA-XF-AAN7      TCGA-XF-AAN8 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-YF-AA3L      TCGA-YF-AA3M      TCGA-ZF-A9R0      TCGA-ZF-A9R2 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-ZF-A9R3      TCGA-ZF-A9R5      TCGA-ZF-A9R7      TCGA-ZF-A9R9 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-ZF-A9RD      TCGA-ZF-A9RF      TCGA-ZF-A9RL      TCGA-ZF-A9RM 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-ZF-AA4U      TCGA-ZF-AA4V      TCGA-ZF-AA51      TCGA-ZF-AA52 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-ZF-AA58      TCGA-ZF-AA5H      TCGA-ZF-AA5N      TCGA-ZF-AA5P 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
D113V10, continuous
[1] "Remove cluster labels:" "COPZ2 MUTATED"         
clus
  COPZ2 MUTATED COPZ2 WILD-TYPE 
              1             274 
     TCGA-2F-A9KO      TCGA-2F-A9KP      TCGA-2F-A9KQ      TCGA-2F-A9KR 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-2F-A9KT      TCGA-2F-A9KW      TCGA-4Z-AA7N      TCGA-4Z-AA7O 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-4Z-AA7R      TCGA-4Z-AA7S      TCGA-4Z-AA7W      TCGA-4Z-AA7Y 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-4Z-AA80      TCGA-4Z-AA81      TCGA-4Z-AA82      TCGA-4Z-AA84 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-4Z-AA86      TCGA-4Z-AA87      TCGA-4Z-AA89      TCGA-BL-A0C8 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-BL-A13I      TCGA-BL-A13J      TCGA-BL-A3JM      TCGA-BT-A0S7 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-BT-A0YX      TCGA-BT-A20J      TCGA-BT-A20N      TCGA-BT-A20O 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-BT-A20P      TCGA-BT-A20Q      TCGA-BT-A20T      TCGA-BT-A20V 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-BT-A20W      TCGA-BT-A20X      TCGA-BT-A2LA      TCGA-BT-A2LB 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-BT-A2LD      TCGA-BT-A3PH      TCGA-BT-A3PJ      TCGA-BT-A3PK 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-BT-A42B      TCGA-BT-A42C      TCGA-BT-A42E      TCGA-BT-A42F 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-CU-A0YN      TCGA-CU-A0YO      TCGA-CU-A0YR      TCGA-CU-A3KJ 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-CU-A3QU      TCGA-CU-A3YL      TCGA-CU-A5W6      TCGA-CU-A72E 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-DK-A1A3      TCGA-DK-A1A5      TCGA-DK-A1A6      TCGA-DK-A1A7 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-DK-A1AA      TCGA-DK-A1AB      TCGA-DK-A1AC      TCGA-DK-A1AE 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-DK-A1AF      TCGA-DK-A1AG      TCGA-DK-A2HX      TCGA-DK-A2I1 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-DK-A2I2      TCGA-DK-A2I4      TCGA-DK-A2I6      TCGA-DK-A3IK 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-DK-A3IL      TCGA-DK-A3IM      TCGA-DK-A3IN      TCGA-DK-A3IQ 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-DK-A3IS      TCGA-DK-A3IT      TCGA-DK-A3IU      TCGA-DK-A3WW 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-DK-A3WX      TCGA-DK-A3WY      TCGA-DK-A3X1      TCGA-DK-A3X2 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-DK-A6AV      TCGA-DK-A6AW      TCGA-DK-A6B0      TCGA-DK-A6B1 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-DK-A6B2      TCGA-DK-A6B5      TCGA-DK-AA6L      TCGA-DK-AA6Q 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-DK-AA6S      TCGA-DK-AA71      TCGA-DK-AA77      TCGA-E5-A2PC 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-E5-A4TZ      TCGA-E5-A4U1      TCGA-E7-A541      TCGA-E7-A7DU 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-E7-A7DV      TCGA-E7-A85H      TCGA-E7-A97Q      TCGA-FD-A3B3 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-FD-A3B4      TCGA-FD-A3B5      TCGA-FD-A3B6      TCGA-FD-A3B7 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-FD-A3B8      TCGA-FD-A3N5      TCGA-FD-A3N6      TCGA-FD-A3NA 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-FD-A3SJ      TCGA-FD-A3SL      TCGA-FD-A3SM      TCGA-FD-A3SN 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-FD-A3SO      TCGA-FD-A3SP      TCGA-FD-A3SQ      TCGA-FD-A3SR 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-FD-A3SS      TCGA-FD-A43N      TCGA-FD-A43P      TCGA-FD-A43S 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-FD-A43U      TCGA-FD-A43X      TCGA-FD-A5BR      TCGA-FD-A5BS 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-FD-A5BT      TCGA-FD-A5BU      TCGA-FD-A5BV      TCGA-FD-A5BX 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-FD-A5BY      TCGA-FD-A5BZ      TCGA-FD-A5C0      TCGA-FD-A5C1 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-FD-A62N      TCGA-FD-A62O      TCGA-FD-A62P      TCGA-FD-A62S 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-FD-A6TA      TCGA-FD-A6TB      TCGA-FD-A6TC      TCGA-FD-A6TD 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-FD-A6TE      TCGA-FD-A6TF      TCGA-FD-A6TG      TCGA-FD-A6TH 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-FD-A6TI      TCGA-FD-A6TK      TCGA-FJ-A3Z7      TCGA-FJ-A3Z9 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-FT-A3EE      TCGA-FT-A61P      TCGA-G2-AA3B      TCGA-G2-AA3C 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-G2-AA3D      TCGA-G2-AA3F      TCGA-GC-A3BM      TCGA-GC-A3I6 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-GC-A3OO      TCGA-GC-A3RB      TCGA-GC-A3RC      TCGA-GC-A3RD 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-GC-A3WC      TCGA-GC-A3YS      TCGA-GC-A6I1      TCGA-GC-A6I3 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-GD-A2C5      TCGA-GD-A3OP      TCGA-GD-A3OQ      TCGA-GD-A6C6 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-GD-A76B      TCGA-GU-A42P      TCGA-GU-A42Q      TCGA-GU-A42R 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-GU-A762      TCGA-GU-A763      TCGA-GU-A764      TCGA-GU-A766 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-GU-A767      TCGA-GU-AATO      TCGA-GU-AATP      TCGA-GU-AATQ 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-GV-A3JV      TCGA-GV-A3JX      TCGA-GV-A3JZ      TCGA-GV-A3QF 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-GV-A3QG      TCGA-GV-A3QI      TCGA-GV-A3QK      TCGA-GV-A40G 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-H4-A2HO      TCGA-HQ-A2OF      TCGA-HQ-A5ND      TCGA-HQ-A5NE 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-K4-A3WS      TCGA-K4-A3WV      TCGA-K4-A4AB      TCGA-K4-A4AC 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-K4-A54R      TCGA-K4-A5RH      TCGA-K4-A5RI      TCGA-K4-A5RJ 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-K4-A6FZ      TCGA-K4-A6MB      TCGA-K4-A83P      TCGA-LC-A66R 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-MV-A51V      TCGA-PQ-A6FI      TCGA-PQ-A6FN      TCGA-R3-A69X 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-S5-A6DX      TCGA-S5-AA26      TCGA-SY-A9G0      TCGA-SY-A9G5 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-UY-A78K      TCGA-UY-A78L      TCGA-UY-A78N      TCGA-UY-A78O 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-XF-A8HH      TCGA-XF-A8HI      TCGA-XF-A9SG      TCGA-XF-A9SH 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-XF-A9SI      TCGA-XF-A9SJ      TCGA-XF-A9SL      TCGA-XF-A9SV 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-XF-A9SW      TCGA-XF-A9SX      TCGA-XF-A9SY      TCGA-XF-A9SZ 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-XF-A9T0      TCGA-XF-A9T2      TCGA-XF-A9T3      TCGA-XF-A9T4 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-XF-A9T5      TCGA-XF-A9T6      TCGA-XF-A9T8      TCGA-XF-AAME 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-XF-AAMF      TCGA-XF-AAMG      TCGA-XF-AAMH      TCGA-XF-AAMJ 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-XF-AAML      TCGA-XF-AAMQ      TCGA-XF-AAMR      TCGA-XF-AAMT 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-XF-AAMW      TCGA-XF-AAMX      TCGA-XF-AAMY      TCGA-XF-AAMZ 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-XF-AAN0      TCGA-XF-AAN1      TCGA-XF-AAN2      TCGA-XF-AAN3 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-XF-AAN4      TCGA-XF-AAN5      TCGA-XF-AAN7      TCGA-XF-AAN8 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-YC-A8S6      TCGA-YF-AA3L      TCGA-ZF-A9R1      TCGA-ZF-A9R2 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-ZF-A9R5      TCGA-ZF-A9R9      TCGA-ZF-A9RC      TCGA-ZF-A9RD 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-ZF-A9RG      TCGA-ZF-A9RM      TCGA-ZF-AA4R      TCGA-ZF-AA4T 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-ZF-AA4V      TCGA-ZF-AA4W      TCGA-ZF-AA56      TCGA-ZF-AA58 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
     TCGA-ZF-AA5H      TCGA-ZF-AA5P 
"COPZ2 WILD-TYPE" "COPZ2 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  COPZ2 MUTATED       1                         0     2
  COPZ2 WILD-TYPE    37                        21   299
D113V11, multiclass
                           clus
vv                          COPZ2 MUTATED COPZ2 WILD-TYPE
  ASIAN                                 1              37
  BLACK OR AFRICAN AMERICAN             0              21
  WHITE                                 2             299
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D113V12, binary
                 cls
clus                0   1
  COPZ2 MUTATED     0   2
  COPZ2 WILD-TYPE   8 336
[1] "tbl2"
                 cls
clus              [,1] [,2]
  COPZ2 MUTATED      0    2
  COPZ2 WILD-TYPE    8  336
                        clus
vv                       COPZ2 MUTATED COPZ2 WILD-TYPE
  HISPANIC OR LATINO                 0               8
  NOT HISPANIC OR LATINO             2             336
[1] 2 2
[1] FALSE

Clustering(114) Variable = ZNF791 MUTATION ANALYSIS
D114V1, survival
                  sevent
clus2                0   1
  ZNF791 MUTATED     7   2
  ZNF791 WILD-TYPE 212 149
  ZNF791 MUTATED ZNF791 WILD-TYPE 
               9              361 
  ZNF791 MUTATED ZNF791 WILD-TYPE 
               2              149 
$`ZNF791 MUTATED`
TCGA-DK-A2I4 TCGA-DK-A6AW TCGA-DK-AA6S TCGA-FD-A6TC TCGA-FD-A6TG TCGA-FT-A61P 
      123.85        41.56       166.03         6.15         3.06         6.48 
TCGA-G2-A2EO TCGA-GC-A6I1 TCGA-ZF-AA4V 
       35.24         8.94        59.38 

$`ZNF791 WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        91.63       103.50       105.70         8.35 
TCGA-4Z-AA7M TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7S 
       16.27        44.94        16.83        16.77        17.16        34.98 
TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 
       27.62        49.12         0.62        41.75        51.16        66.54 
TCGA-4Z-AA84 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BL-A13I 
       15.12        10.22        47.80        33.83        40.08         7.33 
TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J 
        2.66         6.74        12.39         6.58        13.15        19.04 
TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T 
       32.84        12.16        17.88        19.50         5.06        14.89 
TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB 
       14.96         5.06         8.35         8.25        17.16        16.18 
TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C 
       20.48         4.67        12.82         9.96        17.56        28.70 
TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-C4-A0F6 
       24.26        28.41         8.98         1.94         2.93        23.01 
TCGA-C4-A0F7 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T 
        2.04         0.46         0.43         0.69        10.95        12.66 
TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA 
       12.46        12.10        12.62        12.26        13.12        12.00 
TCGA-CF-A7I0 TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR 
       12.10        11.87        13.08        12.92         4.90         7.20 
TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 
        5.46         5.19        16.31         1.84        13.58        21.86 
TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC 
        2.14        66.41        18.41        19.00        16.70       130.88 
TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 
      112.44        16.14        17.62        15.62         1.81        10.59 
TCGA-DK-A2I2 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN 
        7.79        87.32         2.20        13.58         7.82         8.22 
TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW 
       17.72        50.27        21.30        23.21         9.67        20.81 
TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6B0 
       10.55       140.81        48.00        17.98        64.18        76.60 
TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6P 
       67.36        15.68        41.06        30.67        38.24        15.02 
TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA71 
       13.58        12.36        10.49         8.65         7.53        13.64 
TCGA-DK-AA74 TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E5-A4U1 
       43.50        12.03        10.62        43.59        15.35        38.83 
TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 
       24.66         0.10         0.49         2.24        16.70        17.39 
TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF 
        0.56         0.66        14.56        13.97        12.99        14.33 
TCGA-E7-A7DU TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A97P 
        0.92         1.22        13.68        14.07        12.95        14.37 
TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 
        8.09        32.02        16.77         8.94        33.04         4.01 
TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL 
       12.62        22.52        27.98        60.66        24.30        23.41 
TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR 
       17.98        29.16         5.52        25.74        46.78        19.79 
TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X 
       12.85        22.98        27.35        14.96        20.91         3.62 
TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX 
       26.73        53.88        11.01        19.33         5.36         5.69 
TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O 
        8.25        27.45        18.08        58.92         2.70         7.10 
TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TD TCGA-FD-A6TE 
        6.28        13.35        62.86        18.81        12.69        12.36 
TCGA-FD-A6TF TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 
        2.27         4.31         9.67        10.85        31.07         7.13 
TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FJ-A871 TCGA-FT-A3EE TCGA-G2-A2EC TCGA-G2-A2EF 
       10.65        17.23         8.94         3.25        22.88        61.94 
TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE 
       30.61        15.95        26.93        33.01         7.23        20.12 
TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3BM 
       17.62        66.02         6.94        64.44        19.46        21.40 
TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC 
        2.24        15.81         4.50        15.91        14.07        17.75 
TCGA-GC-A3YS TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS 
       24.92        13.91         7.73         2.10         3.12        20.98 
TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 
        2.20         7.36        10.92        11.31        11.31         7.63 
TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATO TCGA-GU-AATP 
       27.09        20.05         5.62         4.73        10.65        32.98 
TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF 
        7.00        14.27        21.34        19.10        19.82        20.28 
TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA 
        8.48        10.59        27.35         8.58        19.07        22.72 
TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE 
        1.51        19.40        38.60         3.06         9.01         8.22 
TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R 
       25.02         3.45        21.24         2.76         9.14        27.68 
TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P 
        9.07        11.70         1.74         1.81        15.42         6.38 
TCGA-K4-AAQO TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN 
       11.80        15.32        15.58        13.48        12.23        16.67 
TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78K 
       14.24         1.84         3.75        12.43        31.56        17.62 
TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78N TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A9PA 
       37.05        22.68        86.83        76.01        65.75        35.24 
TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HH TCGA-XF-A8HI 
       29.56        17.82         4.54         1.64         1.87        17.88 
TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SL TCGA-XF-A9SV 
       48.62        64.80        79.66         3.22        66.41        12.76 
TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 
       11.90        23.64        21.04        28.24        26.27        18.90 
TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAME 
        2.24        16.27        66.64         2.10        13.74        92.98 
TCGA-XF-AAMF TCGA-XF-AAMG TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ 
       10.82       110.60        11.31        54.90         7.63        71.57 
TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAMZ 
       91.73         2.96         8.32         6.77        98.99        44.32 
TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN5 
       56.48        30.94        61.45        86.30        27.06        75.39 
TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-YF-AA3M 
       18.81         3.88         9.63         0.66        11.97        13.64 
TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R5 
       18.64         7.36        21.11        24.13        30.28        27.19 
TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RF 
       21.86        28.41        74.56        13.41         3.48        52.73 
TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4R 
       52.60        82.49        47.84        20.22         2.89        34.06 
TCGA-ZF-AA4T TCGA-ZF-AA4U TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 
       19.69         8.61        60.16        63.02        38.73        35.41 
TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N 
       57.90        19.40         8.52        47.15        19.17         5.52 
TCGA-ZF-AA5P 
       10.13 

  ZNF791 MUTATED ZNF791 WILD-TYPE 
            3.06             0.10 
  ZNF791 MUTATED ZNF791 WILD-TYPE 
          166.03           140.81 
  ZNF791 MUTATED ZNF791 WILD-TYPE 
           35.24            15.62 
[1] "3.1 - 166.0 (35.2)" "0.1 - 140.8 (15.6)"
[1] "hr=" "2.6"
D114V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  ZNF791 MUTATED         0        2         5        2
  ZNF791 WILD-TYPE       4      115       117      126
D114V3, multiclass
           clus
vv          ZNF791 MUTATED ZNF791 WILD-TYPE
  STAGE I                0                4
  STAGE II               2              115
  STAGE III              5              117
  STAGE IV               2              126
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1+T2  T3  T4
  ZNF791 MUTATED          2   6   1
  ZNF791 WILD-TYPE      112 173  51
D114V4, multiclass
          clus
vv         ZNF791 MUTATED ZNF791 WILD-TYPE
  T0+T1+T2              2              112
  T3                    6              173
  T4                    1               51
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  ZNF791 MUTATED     7   0   2   0
  ZNF791 WILD-TYPE 206  41  73   8
D114V5, multiclass
    clus
vv   ZNF791 MUTATED ZNF791 WILD-TYPE
  N0              7              206
  N1              0               41
  N2              2               73
  N3              0                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"
D114V6, binary
                  cls
clus                 0   1
  ZNF791 MUTATED     5   0
  ZNF791 WILD-TYPE 177  10
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF791 MUTATED      5    0
  ZNF791 WILD-TYPE  177   10
   clus
vv  ZNF791 MUTATED ZNF791 WILD-TYPE
  0              5              177
  1              0               10
[1] 2 2
[1] FALSE
D114V7, binary
                  cls
clus                 0   1
  ZNF791 MUTATED     2   7
  ZNF791 WILD-TYPE  94 273
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF791 MUTATED      2    7
  ZNF791 WILD-TYPE   94  273
        clus
vv       ZNF791 MUTATED ZNF791 WILD-TYPE
  FEMALE              2               94
  MALE                7              273
[1] 2 2
[1] FALSE
D114V8, continuous
D114V9, continuous
D114V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ZNF791 MUTATED       0                         0     9
  ZNF791 WILD-TYPE    38                        21   292
D114V11, multiclass
                           clus
vv                          ZNF791 MUTATED ZNF791 WILD-TYPE
  ASIAN                                  0               38
  BLACK OR AFRICAN AMERICAN              0               21
  WHITE                                  9              292
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D114V12, binary
                  cls
clus                 0   1
  ZNF791 MUTATED     0   9
  ZNF791 WILD-TYPE   8 329
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF791 MUTATED      0    9
  ZNF791 WILD-TYPE    8  329
                        clus
vv                       ZNF791 MUTATED ZNF791 WILD-TYPE
  HISPANIC OR LATINO                  0                8
  NOT HISPANIC OR LATINO              9              329
[1] 2 2
[1] FALSE

Clustering(115) Variable = BUD13 MUTATION ANALYSIS
D115V1, survival
                 sevent
clus2               0   1
  BUD13 MUTATED     9   2
  BUD13 WILD-TYPE 210 149
  BUD13 MUTATED BUD13 WILD-TYPE 
             11             359 
  BUD13 MUTATED BUD13 WILD-TYPE 
              2             149 
$`BUD13 MUTATED`
TCGA-CF-A47X TCGA-DK-A1A3 TCGA-E7-A4IJ TCGA-FD-A6TC TCGA-GV-A3QF TCGA-GV-A3QI 
       12.62        21.86         0.49         6.15        20.28        10.59 
TCGA-H4-A2HQ TCGA-K4-A3WU TCGA-K4-A3WV TCGA-ZF-AA4X TCGA-ZF-AA58 
       19.40         3.45        21.24        63.02        47.15 

$`BUD13 WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        91.63       103.50       105.70         8.35 
TCGA-4Z-AA7M TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7S 
       16.27        44.94        16.83        16.77        17.16        34.98 
TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 
       27.62        49.12         0.62        41.75        51.16        66.54 
TCGA-4Z-AA84 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BL-A13I 
       15.12        10.22        47.80        33.83        40.08         7.33 
TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J 
        2.66         6.74        12.39         6.58        13.15        19.04 
TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T 
       32.84        12.16        17.88        19.50         5.06        14.89 
TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB 
       14.96         5.06         8.35         8.25        17.16        16.18 
TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C 
       20.48         4.67        12.82         9.96        17.56        28.70 
TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-C4-A0F6 
       24.26        28.41         8.98         1.94         2.93        23.01 
TCGA-C4-A0F7 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T 
        2.04         0.46         0.43         0.69        10.95        12.66 
TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 
       12.46        12.10        12.26        13.12        12.00        12.10 
TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ 
       11.87        13.08        12.92         4.90         7.20         5.46 
TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1A6 
        5.19        16.31         1.84        13.58         2.14        66.41 
TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE 
       18.41        19.00        16.70       130.88       112.44        16.14 
TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 
       17.62        15.62         1.81        10.59         7.79       123.85 
TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ 
       87.32         2.20        13.58         7.82         8.22        17.72 
TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX 
       50.27        21.30        23.21         9.67        20.81        10.55 
TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 
      140.81        48.00        17.98        64.18        41.56        76.60 
TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6P 
       67.36        15.68        41.06        30.67        38.24        15.02 
TCGA-DK-AA6Q TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA6X 
       13.58       166.03        12.36        10.49         8.65         7.53 
TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A2PC TCGA-E5-A4TZ 
       13.64        43.50        12.03        10.62        43.59        15.35 
TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 
       38.83        24.66         0.10         2.24        16.70        17.39 
TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF 
        0.56         0.66        14.56        13.97        12.99        14.33 
TCGA-E7-A7DU TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A97P 
        0.92         1.22        13.68        14.07        12.95        14.37 
TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 
        8.09        32.02        16.77         8.94        33.04         4.01 
TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL 
       12.62        22.52        27.98        60.66        24.30        23.41 
TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR 
       17.98        29.16         5.52        25.74        46.78        19.79 
TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X 
       12.85        22.98        27.35        14.96        20.91         3.62 
TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX 
       26.73        53.88        11.01        19.33         5.36         5.69 
TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O 
        8.25        27.45        18.08        58.92         2.70         7.10 
TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TD TCGA-FD-A6TE 
        6.28        13.35        62.86        18.81        12.69        12.36 
TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z7 
        2.27         3.06         4.31         9.67        10.85        31.07 
TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FJ-A871 TCGA-FT-A3EE TCGA-FT-A61P 
        7.13        10.65        17.23         8.94         3.25         6.48 
TCGA-G2-A2EC TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO 
       22.88        61.94        30.61        15.95        26.93        35.24 
TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3C 
       33.01         7.23        20.12        17.62        66.02         6.94 
TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB 
       64.44        19.46        21.40         2.24        15.81         4.50 
TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GC-A6I3 
       15.91        14.07        17.75        24.92         8.94        13.91 
TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GD-A76B 
        7.73         2.10         3.12        20.98         2.20         7.36 
TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A764 
       10.92        11.31        11.31         7.63        27.09        20.05 
TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATO TCGA-GU-AATP TCGA-GU-AATQ TCGA-GV-A3JV 
        5.62         4.73        10.65        32.98         7.00        14.27 
TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QH TCGA-GV-A3QK TCGA-GV-A40E 
       21.34        19.10        19.82         8.48        27.35         8.58 
TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND 
       19.07        22.72         1.51        38.60         3.06         9.01 
TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RH 
        8.22        25.02         2.76         9.14        27.68         9.07 
TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO 
       11.70         1.74         1.81        15.42         6.38        11.80 
TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X 
       15.32        15.58        13.48        12.23        16.67        14.24 
TCGA-S5-A6DX TCGA-S5-AA26 TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L 
        1.84         3.75        12.43        31.56        17.62        37.05 
TCGA-UY-A78M TCGA-UY-A78N TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A9PA TCGA-UY-A9PB 
       22.68        86.83        76.01        65.75        35.24        29.56 
TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG 
       17.82         4.54         1.64         1.87        17.88        48.62 
TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SL TCGA-XF-A9SV TCGA-XF-A9SW 
       64.80        79.66         3.22        66.41        12.76        11.90 
TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 
       23.64        21.04        28.24        26.27        18.90         2.24 
TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMF 
       16.27        66.64         2.10        13.74        92.98        10.82 
TCGA-XF-AAMG TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR 
      110.60        11.31        54.90         7.63        71.57        91.73 
TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN0 
        2.96         8.32         6.77        98.99        44.32        56.48 
TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN7 
       30.94        61.45        86.30        27.06        75.39        18.81 
TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R0 
        3.88         9.63         0.66        11.97        13.64        18.64 
TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R7 
        7.36        21.11        24.13        30.28        27.19        21.86 
TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RG 
       28.41        74.56        13.41         3.48        52.73        52.60 
TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4R TCGA-ZF-AA4T 
       82.49        47.84        20.22         2.89        34.06        19.69 
TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA53 
        8.61        59.38        60.16        38.73        35.41        57.90 
TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-ZF-AA5P 
       19.40         8.52        19.17         5.52        10.13 

  BUD13 MUTATED BUD13 WILD-TYPE 
           0.49            0.10 
  BUD13 MUTATED BUD13 WILD-TYPE 
          63.02          166.03 
  BUD13 MUTATED BUD13 WILD-TYPE 
          19.40           15.62 
[1] "0.5 - 63.0 (19.4)"  "0.1 - 166.0 (15.6)"
[1] "hr=" "2.2"
D115V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  BUD13 MUTATED         0        4         3        4
  BUD13 WILD-TYPE       4      113       119      124
D115V3, multiclass
           clus
vv          BUD13 MUTATED BUD13 WILD-TYPE
  STAGE I               0               4
  STAGE II              4             113
  STAGE III             3             119
  STAGE IV              4             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"
                 vv
clus              T0+T1+T2  T3  T4
  BUD13 MUTATED          4   4   2
  BUD13 WILD-TYPE      110 175  50
D115V4, multiclass
          clus
vv         BUD13 MUTATED BUD13 WILD-TYPE
  T0+T1+T2             4             110
  T3                   4             175
  T4                   2              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"
                 vv
clus               N0  N1  N2  N3
  BUD13 MUTATED     5   0   3   0
  BUD13 WILD-TYPE 208  41  72   8
D115V5, multiclass
    clus
vv   BUD13 MUTATED BUD13 WILD-TYPE
  N0             5             208
  N1             0              41
  N2             3              72
  N3             0               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"
D115V6, binary
                 cls
clus                0   1
  BUD13 MUTATED     4   1
  BUD13 WILD-TYPE 178   9
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BUD13 MUTATED      4    1
  BUD13 WILD-TYPE  178    9
   clus
vv  BUD13 MUTATED BUD13 WILD-TYPE
  0             4             178
  1             1               9
[1] 2 2
[1] FALSE
D115V7, binary
                 cls
clus                0   1
  BUD13 MUTATED     4   7
  BUD13 WILD-TYPE  92 273
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BUD13 MUTATED      4    7
  BUD13 WILD-TYPE   92  273
        clus
vv       BUD13 MUTATED BUD13 WILD-TYPE
  FEMALE             4              92
  MALE               7             273
[1] 2 2
[1] FALSE
D115V8, continuous
D115V9, continuous
D115V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  BUD13 MUTATED       2                         1     8
  BUD13 WILD-TYPE    36                        20   293
D115V11, multiclass
                           clus
vv                          BUD13 MUTATED BUD13 WILD-TYPE
  ASIAN                                 2              36
  BLACK OR AFRICAN AMERICAN             1              20
  WHITE                                 8             293
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D115V12, binary
                 cls
clus                0   1
  BUD13 MUTATED     1  10
  BUD13 WILD-TYPE   7 328
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BUD13 MUTATED      1   10
  BUD13 WILD-TYPE    7  328
                        clus
vv                       BUD13 MUTATED BUD13 WILD-TYPE
  HISPANIC OR LATINO                 1               7
  NOT HISPANIC OR LATINO            10             328
[1] 2 2
[1] FALSE

Clustering(116) Variable = HES1 MUTATION ANALYSIS
D116V1, survival
                sevent
clus2              0   1
  HES1 MUTATED     6   4
  HES1 WILD-TYPE 213 147
  HES1 MUTATED HES1 WILD-TYPE 
            10            360 
  HES1 MUTATED HES1 WILD-TYPE 
             4            147 
$`HES1 MUTATED`
TCGA-4Z-AA80 TCGA-CU-A72E TCGA-DK-A1AC TCGA-DK-A2I4 TCGA-DK-A3WW TCGA-DK-AA71 
        0.62        13.58       130.88       123.85        20.81        13.64 
TCGA-FD-A5BU TCGA-GV-A3QF TCGA-S5-A6DX TCGA-ZF-AA4V 
       19.33        20.28         1.84        59.38 

$`HES1 WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        91.63       103.50       105.70         8.35 
TCGA-4Z-AA7M TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7S 
       16.27        44.94        16.83        16.77        17.16        34.98 
TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA84 
       27.62        49.12        41.75        51.16        66.54        15.12 
TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J 
       10.22        47.80        33.83        40.08         7.33         2.66 
TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N 
        6.74        12.39         6.58        13.15        19.04        32.84 
TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U 
       12.16        17.88        19.50         5.06        14.89        14.96 
TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A2LD 
        5.06         8.35         8.25        17.16        16.18        20.48 
TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E 
        4.67        12.82         9.96        17.56        28.70        24.26 
TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-C4-A0F6 TCGA-C4-A0F7 
       28.41         8.98         1.94         2.93        23.01         2.04 
TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V 
        0.46         0.43         0.69        10.95        12.66        12.46 
TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 
       12.10        12.62        12.26        13.12        12.00        12.10 
TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ 
       11.87        13.08        12.92         4.90         7.20         5.46 
TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 
        5.19        16.31         1.84        21.86         2.14        66.41 
TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF 
       18.41        19.00        16.70       112.44        16.14        17.62 
TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I6 TCGA-DK-A3IK 
       15.62         1.81        10.59         7.79        87.32         2.20 
TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT 
       13.58         7.82         8.22        17.72        50.27        21.30 
TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A3X2 
       23.21         9.67        10.55       140.81        48.00        17.98 
TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 
       64.18        41.56        76.60        67.36        15.68        41.06 
TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6S TCGA-DK-AA6T 
       30.67        38.24        15.02        13.58       166.03        12.36 
TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA74 TCGA-DK-AA76 TCGA-DK-AA77 
       10.49         8.65         7.53        43.50        12.03        10.62 
TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ 
       43.59        15.35        38.83        24.66         0.10         0.49 
TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 
        2.24        16.70        17.39         0.56         0.66        14.56 
TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7DV TCGA-E7-A7PW 
       13.97        12.99        14.33         0.92         1.22        13.68 
TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 
       14.07        12.95        14.37         8.09        32.02        16.77 
TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 
        8.94        33.04         4.01        12.62        22.52        27.98 
TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO 
       60.66        24.30        23.41        17.98        29.16         5.52 
TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P 
       25.74        46.78        19.79        12.85        22.98        27.35 
TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT 
       14.96        20.91         3.62        26.73        53.88        11.01 
TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 
        5.36         5.69         8.25        27.45        18.08        58.92 
TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB 
        2.70         7.10         6.28        13.35        62.86        18.81 
TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH 
        6.15        12.69        12.36         2.27         3.06         4.31 
TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF 
        9.67        10.85        31.07         7.13        10.65        17.23 
TCGA-FJ-A871 TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EC TCGA-G2-A2EF TCGA-G2-A2EJ 
        8.94         3.25         6.48        22.88        61.94        30.61 
TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE 
       15.95        26.93        35.24        33.01         7.23        20.12 
TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3BM 
       17.62        66.02         6.94        64.44        19.46        21.40 
TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC 
        2.24        15.81         4.50        15.91        14.07        17.75 
TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ 
       24.92         8.94        13.91         7.73         2.10         3.12 
TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R 
       20.98         2.20         7.36        10.92        11.31        11.31 
TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATO 
        7.63        27.09        20.05         5.62         4.73        10.65 
TCGA-GU-AATP TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ 
       32.98         7.00        14.27        21.34        19.10        19.82 
TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA 
        8.48        10.59        27.35         8.58        19.07        22.72 
TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE 
        1.51        19.40        38.60         3.06         9.01         8.22 
TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R 
       25.02         3.45        21.24         2.76         9.14        27.68 
TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P 
        9.07        11.70         1.74         1.81        15.42         6.38 
TCGA-K4-AAQO TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN 
       11.80        15.32        15.58        13.48        12.23        16.67 
TCGA-R3-A69X TCGA-S5-AA26 TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L 
       14.24         3.75        12.43        31.56        17.62        37.05 
TCGA-UY-A78M TCGA-UY-A78N TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A9PA TCGA-UY-A9PB 
       22.68        86.83        76.01        65.75        35.24        29.56 
TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG 
       17.82         4.54         1.64         1.87        17.88        48.62 
TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SL TCGA-XF-A9SV TCGA-XF-A9SW 
       64.80        79.66         3.22        66.41        12.76        11.90 
TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 
       23.64        21.04        28.24        26.27        18.90         2.24 
TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMF 
       16.27        66.64         2.10        13.74        92.98        10.82 
TCGA-XF-AAMG TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR 
      110.60        11.31        54.90         7.63        71.57        91.73 
TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN0 
        2.96         8.32         6.77        98.99        44.32        56.48 
TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN7 
       30.94        61.45        86.30        27.06        75.39        18.81 
TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R0 
        3.88         9.63         0.66        11.97        13.64        18.64 
TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R7 
        7.36        21.11        24.13        30.28        27.19        21.86 
TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RG 
       28.41        74.56        13.41         3.48        52.73        52.60 
TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4R TCGA-ZF-AA4T 
       82.49        47.84        20.22         2.89        34.06        19.69 
TCGA-ZF-AA4U TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA53 
        8.61        60.16        63.02        38.73        35.41        57.90 
TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-ZF-AA5P 
       19.40         8.52        47.15        19.17         5.52        10.13 

  HES1 MUTATED HES1 WILD-TYPE 
          0.62           0.10 
  HES1 MUTATED HES1 WILD-TYPE 
        130.88         166.03 
  HES1 MUTATED HES1 WILD-TYPE 
        19.805         15.600 
[1] "0.6 - 130.9 (19.8)" "0.1 - 166.0 (15.6)"
[1] "hr=" "1.3"
D116V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  HES1 MUTATED         0        3         4        3
  HES1 WILD-TYPE       4      114       118      125
D116V3, multiclass
           clus
vv          HES1 MUTATED HES1 WILD-TYPE
  STAGE I              0              4
  STAGE II             3            114
  STAGE III            4            118
  STAGE IV             3            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"
                vv
clus             T0+T1+T2  T3  T4
  HES1 MUTATED          3   6   1
  HES1 WILD-TYPE      111 173  51
D116V4, multiclass
          clus
vv         HES1 MUTATED HES1 WILD-TYPE
  T0+T1+T2            3            111
  T3                  6            173
  T4                  1             51
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  HES1 MUTATED     7   0   3   0
  HES1 WILD-TYPE 206  41  72   8
D116V5, multiclass
    clus
vv   HES1 MUTATED HES1 WILD-TYPE
  N0            7            206
  N1            0             41
  N2            3             72
  N3            0              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"
D116V6, binary
                cls
clus               0   1
  HES1 MUTATED     7   0
  HES1 WILD-TYPE 175  10
[1] "tbl2"
                cls
clus             [,1] [,2]
  HES1 MUTATED      7    0
  HES1 WILD-TYPE  175   10
   clus
vv  HES1 MUTATED HES1 WILD-TYPE
  0            7            175
  1            0             10
[1] 2 2
[1] FALSE
D116V7, binary
                cls
clus               0   1
  HES1 MUTATED     1   9
  HES1 WILD-TYPE  95 271
[1] "tbl2"
                cls
clus             [,1] [,2]
  HES1 MUTATED      1    9
  HES1 WILD-TYPE   95  271
        clus
vv       HES1 MUTATED HES1 WILD-TYPE
  FEMALE            1             95
  MALE              9            271
[1] 2 2
[1] FALSE
D116V8, continuous
[1] "Remove cluster labels:" "HES1 MUTATED"          
clus
  HES1 MUTATED HES1 WILD-TYPE 
             1            119 
    TCGA-2F-A9KO     TCGA-2F-A9KP     TCGA-2F-A9KQ     TCGA-2F-A9KR 
"HES1 WILD-TYPE" "HES1 WILD-TYPE" "HES1 WILD-TYPE" "HES1 WILD-TYPE" 
    TCGA-2F-A9KT     TCGA-2F-A9KW     TCGA-CF-A1HS     TCGA-CF-A27C 
"HES1 WILD-TYPE" "HES1 WILD-TYPE" "HES1 WILD-TYPE" "HES1 WILD-TYPE" 
    TCGA-CF-A3MF     TCGA-CF-A3MG     TCGA-CF-A3MH     TCGA-CF-A3MI 
"HES1 WILD-TYPE" "HES1 WILD-TYPE" "HES1 WILD-TYPE" "HES1 WILD-TYPE" 
    TCGA-CF-A47S     TCGA-CF-A47T     TCGA-CF-A47V     TCGA-CF-A47W 
"HES1 WILD-TYPE" "HES1 WILD-TYPE" "HES1 WILD-TYPE" "HES1 WILD-TYPE" 
    TCGA-CF-A47X     TCGA-CF-A47Y     TCGA-CF-A5U8     TCGA-CF-A5UA 
"HES1 WILD-TYPE" "HES1 WILD-TYPE" "HES1 WILD-TYPE" "HES1 WILD-TYPE" 
    TCGA-CF-A7I0     TCGA-DK-A2HX     TCGA-DK-A3IN     TCGA-DK-A3IV 
"HES1 WILD-TYPE" "HES1 WILD-TYPE" "HES1 WILD-TYPE" "HES1 WILD-TYPE" 
    TCGA-DK-A3WX     TCGA-DK-A3X2     TCGA-DK-A6B2     TCGA-DK-A6B5 
"HES1 WILD-TYPE" "HES1 WILD-TYPE" "HES1 WILD-TYPE" "HES1 WILD-TYPE" 
    TCGA-DK-A6B6     TCGA-DK-AA6P     TCGA-DK-AA6S     TCGA-DK-AA6U 
"HES1 WILD-TYPE" "HES1 WILD-TYPE" "HES1 WILD-TYPE" "HES1 WILD-TYPE" 
    TCGA-DK-AA6W     TCGA-DK-AA76     TCGA-E5-A2PC     TCGA-E5-A4TZ 
"HES1 WILD-TYPE" "HES1 WILD-TYPE" "HES1 WILD-TYPE" "HES1 WILD-TYPE" 
    TCGA-E5-A4U1     TCGA-E7-A519     TCGA-E7-A541     TCGA-E7-A7DU 
"HES1 WILD-TYPE" "HES1 WILD-TYPE" "HES1 WILD-TYPE" "HES1 WILD-TYPE" 
    TCGA-E7-A7DV     TCGA-FT-A61P     TCGA-G2-A2EC     TCGA-G2-A2EF 
"HES1 WILD-TYPE" "HES1 WILD-TYPE" "HES1 WILD-TYPE" "HES1 WILD-TYPE" 
    TCGA-G2-A2EJ     TCGA-G2-A2EK     TCGA-G2-A2EL     TCGA-G2-A2EO 
"HES1 WILD-TYPE" "HES1 WILD-TYPE" "HES1 WILD-TYPE" "HES1 WILD-TYPE" 
    TCGA-G2-A2ES     TCGA-G2-A3IB     TCGA-G2-A3IE     TCGA-G2-A3VY 
"HES1 WILD-TYPE" "HES1 WILD-TYPE" "HES1 WILD-TYPE" "HES1 WILD-TYPE" 
    TCGA-GC-A3BM     TCGA-GC-A3I6     TCGA-GC-A3OO     TCGA-GC-A3RC 
"HES1 WILD-TYPE" "HES1 WILD-TYPE" "HES1 WILD-TYPE" "HES1 WILD-TYPE" 
    TCGA-GC-A3RD     TCGA-GC-A3YS     TCGA-GC-A6I1     TCGA-GC-A6I3 
"HES1 WILD-TYPE" "HES1 WILD-TYPE" "HES1 WILD-TYPE" "HES1 WILD-TYPE" 
    TCGA-GD-A3OS     TCGA-GD-A6C6     TCGA-GV-A3JV     TCGA-GV-A3JW 
"HES1 WILD-TYPE" "HES1 WILD-TYPE" "HES1 WILD-TYPE" "HES1 WILD-TYPE" 
    TCGA-GV-A3JX     TCGA-GV-A3JZ     TCGA-GV-A3QH     TCGA-GV-A3QI 
"HES1 WILD-TYPE" "HES1 WILD-TYPE" "HES1 WILD-TYPE" "HES1 WILD-TYPE" 
    TCGA-GV-A3QK     TCGA-GV-A40E     TCGA-GV-A40G     TCGA-GV-A6ZA 
"HES1 WILD-TYPE" "HES1 WILD-TYPE" "HES1 WILD-TYPE" "HES1 WILD-TYPE" 
    TCGA-SY-A9G0     TCGA-SY-A9G5     TCGA-UY-A78L     TCGA-UY-A78M 
"HES1 WILD-TYPE" "HES1 WILD-TYPE" "HES1 WILD-TYPE" "HES1 WILD-TYPE" 
    TCGA-UY-A78N     TCGA-XF-A8HH     TCGA-XF-A8HI     TCGA-XF-A9SG 
"HES1 WILD-TYPE" "HES1 WILD-TYPE" "HES1 WILD-TYPE" "HES1 WILD-TYPE" 
    TCGA-XF-A9SH     TCGA-XF-A9SI     TCGA-XF-A9SJ     TCGA-XF-A9SL 
"HES1 WILD-TYPE" "HES1 WILD-TYPE" "HES1 WILD-TYPE" "HES1 WILD-TYPE" 
    TCGA-XF-A9SV     TCGA-XF-A9SW     TCGA-XF-A9SX     TCGA-XF-A9SY 
"HES1 WILD-TYPE" "HES1 WILD-TYPE" "HES1 WILD-TYPE" "HES1 WILD-TYPE" 
    TCGA-XF-A9SZ     TCGA-XF-A9T0     TCGA-XF-A9T2     TCGA-XF-A9T3 
"HES1 WILD-TYPE" "HES1 WILD-TYPE" "HES1 WILD-TYPE" "HES1 WILD-TYPE" 
    TCGA-XF-A9T4     TCGA-XF-A9T5     TCGA-XF-A9T6     TCGA-XF-A9T8 
"HES1 WILD-TYPE" "HES1 WILD-TYPE" "HES1 WILD-TYPE" "HES1 WILD-TYPE" 
    TCGA-XF-AAME     TCGA-XF-AAMF     TCGA-XF-AAMG     TCGA-XF-AAMH 
"HES1 WILD-TYPE" "HES1 WILD-TYPE" "HES1 WILD-TYPE" "HES1 WILD-TYPE" 
    TCGA-XF-AAMJ     TCGA-XF-AAML     TCGA-XF-AAMQ     TCGA-XF-AAMR 
"HES1 WILD-TYPE" "HES1 WILD-TYPE" "HES1 WILD-TYPE" "HES1 WILD-TYPE" 
    TCGA-XF-AAMT     TCGA-XF-AAMW     TCGA-XF-AAMX     TCGA-XF-AAMY 
"HES1 WILD-TYPE" "HES1 WILD-TYPE" "HES1 WILD-TYPE" "HES1 WILD-TYPE" 
    TCGA-XF-AAMZ     TCGA-XF-AAN0     TCGA-XF-AAN1     TCGA-XF-AAN2 
"HES1 WILD-TYPE" "HES1 WILD-TYPE" "HES1 WILD-TYPE" "HES1 WILD-TYPE" 
    TCGA-XF-AAN3     TCGA-XF-AAN4     TCGA-XF-AAN5     TCGA-XF-AAN7 
"HES1 WILD-TYPE" "HES1 WILD-TYPE" "HES1 WILD-TYPE" "HES1 WILD-TYPE" 
    TCGA-XF-AAN8     TCGA-YF-AA3L     TCGA-YF-AA3M 
"HES1 WILD-TYPE" "HES1 WILD-TYPE" "HES1 WILD-TYPE" 
D116V9, continuous
D116V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  HES1 MUTATED       0                         1     9
  HES1 WILD-TYPE    38                        20   292
D116V11, multiclass
                           clus
vv                          HES1 MUTATED HES1 WILD-TYPE
  ASIAN                                0             38
  BLACK OR AFRICAN AMERICAN            1             20
  WHITE                                9            292
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D116V12, binary
                cls
clus               0   1
  HES1 MUTATED     0   8
  HES1 WILD-TYPE   8 330
[1] "tbl2"
                cls
clus             [,1] [,2]
  HES1 MUTATED      0    8
  HES1 WILD-TYPE    8  330
                        clus
vv                       HES1 MUTATED HES1 WILD-TYPE
  HISPANIC OR LATINO                0              8
  NOT HISPANIC OR LATINO            8            330
[1] 2 2
[1] FALSE

Clustering(117) Variable = HORMAD1 MUTATION ANALYSIS
D117V1, survival
                   sevent
clus2                 0   1
  HORMAD1 MUTATED     9   2
  HORMAD1 WILD-TYPE 210 149
  HORMAD1 MUTATED HORMAD1 WILD-TYPE 
               11               359 
  HORMAD1 MUTATED HORMAD1 WILD-TYPE 
                2               149 
$`HORMAD1 MUTATED`
TCGA-DK-A1AD TCGA-DK-A3IT TCGA-DK-A3X1 TCGA-E7-A5KF TCGA-FJ-A3Z7 TCGA-G2-A2ES 
      112.44        21.30        48.00         0.66        31.07        33.01 
TCGA-G2-A3VY TCGA-GC-A3I6 TCGA-MV-A51V TCGA-ZF-A9R9 TCGA-ZF-AA4V 
       17.62         2.24        13.48        28.41        59.38 

$`HORMAD1 WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        91.63       103.50       105.70         8.35 
TCGA-4Z-AA7M TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7S 
       16.27        44.94        16.83        16.77        17.16        34.98 
TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 
       27.62        49.12         0.62        41.75        51.16        66.54 
TCGA-4Z-AA84 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BL-A13I 
       15.12        10.22        47.80        33.83        40.08         7.33 
TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J 
        2.66         6.74        12.39         6.58        13.15        19.04 
TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T 
       32.84        12.16        17.88        19.50         5.06        14.89 
TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB 
       14.96         5.06         8.35         8.25        17.16        16.18 
TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C 
       20.48         4.67        12.82         9.96        17.56        28.70 
TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-C4-A0F6 
       24.26        28.41         8.98         1.94         2.93        23.01 
TCGA-C4-A0F7 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T 
        2.04         0.46         0.43         0.69        10.95        12.66 
TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA 
       12.46        12.10        12.62        12.26        13.12        12.00 
TCGA-CF-A7I0 TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR 
       12.10        11.87        13.08        12.92         4.90         7.20 
TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 
        5.46         5.19        16.31         1.84        13.58        21.86 
TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC 
        2.14        66.41        18.41        19.00        16.70       130.88 
TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 
       16.14        17.62        15.62         1.81        10.59         7.79 
TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN 
      123.85        87.32         2.20        13.58         7.82         8.22 
TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX 
       17.72        50.27        23.21         9.67        20.81        10.55 
TCGA-DK-A3WY TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 
      140.81        17.98        64.18        41.56        76.60        67.36 
TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6P TCGA-DK-AA6Q 
       15.68        41.06        30.67        38.24        15.02        13.58 
TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA71 
      166.03        12.36        10.49         8.65         7.53        13.64 
TCGA-DK-AA74 TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E5-A4U1 
       43.50        12.03        10.62        43.59        15.35        38.83 
TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 
       24.66         0.10         0.49         2.24        16.70        17.39 
TCGA-E7-A5KE TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DU 
        0.56        14.56        13.97        12.99        14.33         0.92 
TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A97P TCGA-E7-A97Q 
        1.22        13.68        14.07        12.95        14.37         8.09 
TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 
       32.02        16.77         8.94        33.04         4.01        12.62 
TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM 
       22.52        27.98        60.66        24.30        23.41        17.98 
TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS 
       29.16         5.52        25.74        46.78        19.79        12.85 
TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BR 
       22.98        27.35        14.96        20.91         3.62        26.73 
TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY 
       53.88        11.01        19.33         5.36         5.69         8.25 
TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P 
       27.45        18.08        58.92         2.70         7.10         6.28 
TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE 
       13.35        62.86        18.81         6.15        12.69        12.36 
TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z9 
        2.27         3.06         4.31         9.67        10.85         7.13 
TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FJ-A871 TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EC 
       10.65        17.23         8.94         3.25         6.48        22.88 
TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A3IB 
       61.94        30.61        15.95        26.93        35.24         7.23 
TCGA-G2-A3IE TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3BM 
       20.12        66.02         6.94        64.44        19.46        21.40 
TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS 
       15.81         4.50        15.91        14.07        17.75        24.92 
TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS 
        8.94        13.91         7.73         2.10         3.12        20.98 
TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 
        2.20         7.36        10.92        11.31        11.31         7.63 
TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATO TCGA-GU-AATP 
       27.09        20.05         5.62         4.73        10.65        32.98 
TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF 
        7.00        14.27        21.34        19.10        19.82        20.28 
TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA 
        8.48        10.59        27.35         8.58        19.07        22.72 
TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE 
        1.51        19.40        38.60         3.06         9.01         8.22 
TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R 
       25.02         3.45        21.24         2.76         9.14        27.68 
TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P 
        9.07        11.70         1.74         1.81        15.42         6.38 
TCGA-K4-AAQO TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X 
       11.80        15.32        15.58        12.23        16.67        14.24 
TCGA-S5-A6DX TCGA-S5-AA26 TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L 
        1.84         3.75        12.43        31.56        17.62        37.05 
TCGA-UY-A78M TCGA-UY-A78N TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A9PA TCGA-UY-A9PB 
       22.68        86.83        76.01        65.75        35.24        29.56 
TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG 
       17.82         4.54         1.64         1.87        17.88        48.62 
TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SL TCGA-XF-A9SV TCGA-XF-A9SW 
       64.80        79.66         3.22        66.41        12.76        11.90 
TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 
       23.64        21.04        28.24        26.27        18.90         2.24 
TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMF 
       16.27        66.64         2.10        13.74        92.98        10.82 
TCGA-XF-AAMG TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR 
      110.60        11.31        54.90         7.63        71.57        91.73 
TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN0 
        2.96         8.32         6.77        98.99        44.32        56.48 
TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN7 
       30.94        61.45        86.30        27.06        75.39        18.81 
TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R0 
        3.88         9.63         0.66        11.97        13.64        18.64 
TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R7 
        7.36        21.11        24.13        30.28        27.19        21.86 
TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RL 
       74.56        13.41         3.48        52.73        52.60        82.49 
TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4U 
       47.84        20.22         2.89        34.06        19.69         8.61 
TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA53 TCGA-ZF-AA54 
       60.16        63.02        38.73        35.41        57.90        19.40 
TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-ZF-AA5P 
        8.52        47.15        19.17         5.52        10.13 

  HORMAD1 MUTATED HORMAD1 WILD-TYPE 
             0.66              0.10 
  HORMAD1 MUTATED HORMAD1 WILD-TYPE 
           112.44            166.03 
  HORMAD1 MUTATED HORMAD1 WILD-TYPE 
            28.41             15.42 
[1] "0.7 - 112.4 (28.4)" "0.1 - 166.0 (15.4)"
[1] "hr=" "3.1"
D117V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  HORMAD1 MUTATED         0        3         5        3
  HORMAD1 WILD-TYPE       4      114       117      125
D117V3, multiclass
           clus
vv          HORMAD1 MUTATED HORMAD1 WILD-TYPE
  STAGE I                 0                 4
  STAGE II                3               114
  STAGE III               5               117
  STAGE IV                3               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"
                   vv
clus                T0+T1+T2  T3  T4
  HORMAD1 MUTATED          1   8   1
  HORMAD1 WILD-TYPE      113 171  51
D117V4, multiclass
          clus
vv         HORMAD1 MUTATED HORMAD1 WILD-TYPE
  T0+T1+T2               1               113
  T3                     8               171
  T4                     1                51
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  HORMAD1 MUTATED     7   0   3   0
  HORMAD1 WILD-TYPE 206  41  72   8
D117V5, multiclass
    clus
vv   HORMAD1 MUTATED HORMAD1 WILD-TYPE
  N0               7               206
  N1               0                41
  N2               3                72
  N3               0                 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"
D117V6, binary
                   cls
clus                  0   1
  HORMAD1 MUTATED     8   0
  HORMAD1 WILD-TYPE 174  10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  HORMAD1 MUTATED      8    0
  HORMAD1 WILD-TYPE  174   10
   clus
vv  HORMAD1 MUTATED HORMAD1 WILD-TYPE
  0               8               174
  1               0                10
[1] 2 2
[1] FALSE
D117V7, binary
                   cls
clus                  0   1
  HORMAD1 MUTATED     1  10
  HORMAD1 WILD-TYPE  95 270
[1] "tbl2"
                   cls
clus                [,1] [,2]
  HORMAD1 MUTATED      1   10
  HORMAD1 WILD-TYPE   95  270
        clus
vv       HORMAD1 MUTATED HORMAD1 WILD-TYPE
  FEMALE               1                95
  MALE                10               270
[1] 2 2
[1] FALSE
D117V8, continuous
D117V9, continuous
D117V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  HORMAD1 MUTATED       2                         0     9
  HORMAD1 WILD-TYPE    36                        21   292
D117V11, multiclass
                           clus
vv                          HORMAD1 MUTATED HORMAD1 WILD-TYPE
  ASIAN                                   2                36
  BLACK OR AFRICAN AMERICAN               0                21
  WHITE                                   9               292
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D117V12, binary
                   cls
clus                  0   1
  HORMAD1 MUTATED     0  10
  HORMAD1 WILD-TYPE   8 328
[1] "tbl2"
                   cls
clus                [,1] [,2]
  HORMAD1 MUTATED      0   10
  HORMAD1 WILD-TYPE    8  328
                        clus
vv                       HORMAD1 MUTATED HORMAD1 WILD-TYPE
  HISPANIC OR LATINO                   0                 8
  NOT HISPANIC OR LATINO              10               328
[1] 2 2
[1] FALSE

Clustering(118) Variable = SND1 MUTATION ANALYSIS
D118V1, survival
                sevent
clus2              0   1
  SND1 MUTATED     5   3
  SND1 WILD-TYPE 214 148
  SND1 MUTATED SND1 WILD-TYPE 
             8            362 
  SND1 MUTATED SND1 WILD-TYPE 
             3            148 
$`SND1 MUTATED`
TCGA-BT-A3PJ TCGA-BT-A42E TCGA-CF-A1HR TCGA-DK-A1A3 TCGA-DK-A3X1 TCGA-DK-A6AW 
       12.82        24.26         0.46        21.86        48.00        41.56 
TCGA-FD-A6TH TCGA-GU-A762 
        4.31         7.63 

$`SND1 WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        91.63       103.50       105.70         8.35 
TCGA-4Z-AA7M TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7S 
       16.27        44.94        16.83        16.77        17.16        34.98 
TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 
       27.62        49.12         0.62        41.75        51.16        66.54 
TCGA-4Z-AA84 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BL-A13I 
       15.12        10.22        47.80        33.83        40.08         7.33 
TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J 
        2.66         6.74        12.39         6.58        13.15        19.04 
TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T 
       32.84        12.16        17.88        19.50         5.06        14.89 
TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB 
       14.96         5.06         8.35         8.25        17.16        16.18 
TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42F 
       20.48         4.67         9.96        17.56        28.70        28.41 
TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-C4-A0F6 TCGA-C4-A0F7 TCGA-CF-A1HS 
        8.98         1.94         2.93        23.01         2.04         0.43 
TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X 
        0.69        10.95        12.66        12.46        12.10        12.62 
TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A9FF TCGA-CF-A9FM 
       12.26        13.12        12.00        12.10        11.87        13.08 
TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL 
       12.92         4.90         7.20         5.46         5.19        16.31 
TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA 
        1.84        13.58         2.14        66.41        18.41        19.00 
TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG 
       16.70       130.88       112.44        16.14        17.62        15.62 
TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK 
        1.81        10.59         7.79       123.85        87.32         2.20 
TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT 
       13.58         7.82         8.22        17.72        50.27        21.30 
TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X2 
       23.21         9.67        20.81        10.55       140.81        17.98 
TCGA-DK-A6AV TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 
       64.18        76.60        67.36        15.68        41.06        30.67 
TCGA-DK-AA6L TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6U 
       38.24        15.02        13.58       166.03        12.36        10.49 
TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA76 TCGA-DK-AA77 
        8.65         7.53        13.64        43.50        12.03        10.62 
TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ 
       43.59        15.35        38.83        24.66         0.10         0.49 
TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 
        2.24        16.70        17.39         0.56         0.66        14.56 
TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7DV TCGA-E7-A7PW 
       13.97        12.99        14.33         0.92         1.22        13.68 
TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 
       14.07        12.95        14.37         8.09        32.02        16.77 
TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 
        8.94        33.04         4.01        12.62        22.52        27.98 
TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO 
       60.66        24.30        23.41        17.98        29.16         5.52 
TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P 
       25.74        46.78        19.79        12.85        22.98        27.35 
TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT 
       14.96        20.91         3.62        26.73        53.88        11.01 
TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 
       19.33         5.36         5.69         8.25        27.45        18.08 
TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA 
       58.92         2.70         7.10         6.28        13.35        62.86 
TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TG 
       18.81         6.15        12.69        12.36         2.27         3.06 
TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF 
        9.67        10.85        31.07         7.13        10.65        17.23 
TCGA-FJ-A871 TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EC TCGA-G2-A2EF TCGA-G2-A2EJ 
        8.94         3.25         6.48        22.88        61.94        30.61 
TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE 
       15.95        26.93        35.24        33.01         7.23        20.12 
TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3BM 
       17.62        66.02         6.94        64.44        19.46        21.40 
TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC 
        2.24        15.81         4.50        15.91        14.07        17.75 
TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ 
       24.92         8.94        13.91         7.73         2.10         3.12 
TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R 
       20.98         2.20         7.36        10.92        11.31        11.31 
TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATO TCGA-GU-AATP 
       27.09        20.05         5.62         4.73        10.65        32.98 
TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF 
        7.00        14.27        21.34        19.10        19.82        20.28 
TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA 
        8.48        10.59        27.35         8.58        19.07        22.72 
TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE 
        1.51        19.40        38.60         3.06         9.01         8.22 
TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R 
       25.02         3.45        21.24         2.76         9.14        27.68 
TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P 
        9.07        11.70         1.74         1.81        15.42         6.38 
TCGA-K4-AAQO TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN 
       11.80        15.32        15.58        13.48        12.23        16.67 
TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78K 
       14.24         1.84         3.75        12.43        31.56        17.62 
TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78N TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A9PA 
       37.05        22.68        86.83        76.01        65.75        35.24 
TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HH TCGA-XF-A8HI 
       29.56        17.82         4.54         1.64         1.87        17.88 
TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SL TCGA-XF-A9SV 
       48.62        64.80        79.66         3.22        66.41        12.76 
TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 
       11.90        23.64        21.04        28.24        26.27        18.90 
TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAME 
        2.24        16.27        66.64         2.10        13.74        92.98 
TCGA-XF-AAMF TCGA-XF-AAMG TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ 
       10.82       110.60        11.31        54.90         7.63        71.57 
TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAMZ 
       91.73         2.96         8.32         6.77        98.99        44.32 
TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN5 
       56.48        30.94        61.45        86.30        27.06        75.39 
TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-YF-AA3M 
       18.81         3.88         9.63         0.66        11.97        13.64 
TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R5 
       18.64         7.36        21.11        24.13        30.28        27.19 
TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RF 
       21.86        28.41        74.56        13.41         3.48        52.73 
TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4R 
       52.60        82.49        47.84        20.22         2.89        34.06 
TCGA-ZF-AA4T TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA51 
       19.69         8.61        59.38        60.16        63.02        38.73 
TCGA-ZF-AA52 TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H 
       35.41        57.90        19.40         8.52        47.15        19.17 
TCGA-ZF-AA5N TCGA-ZF-AA5P 
        5.52        10.13 

  SND1 MUTATED SND1 WILD-TYPE 
          0.46           0.10 
  SND1 MUTATED SND1 WILD-TYPE 
         48.00         166.03 
  SND1 MUTATED SND1 WILD-TYPE 
         17.34          15.65 
[1] "0.5 - 48.0 (17.3)"  "0.1 - 166.0 (15.6)"
[1] "hr=" "1"  
D118V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  SND1 MUTATED         0        1         3        3
  SND1 WILD-TYPE       4      116       119      125
D118V3, multiclass
           clus
vv          SND1 MUTATED SND1 WILD-TYPE
  STAGE I              0              4
  STAGE II             1            116
  STAGE III            3            119
  STAGE IV             3            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"
                vv
clus             T0+T1+T2  T3  T4
  SND1 MUTATED          1   6   1
  SND1 WILD-TYPE      113 173  51
D118V4, multiclass
          clus
vv         SND1 MUTATED SND1 WILD-TYPE
  T0+T1+T2            1            113
  T3                  6            173
  T4                  1             51
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  SND1 MUTATED     4   0   3   1
  SND1 WILD-TYPE 209  41  72   7
D118V5, multiclass
    clus
vv   SND1 MUTATED SND1 WILD-TYPE
  N0            4            209
  N1            0             41
  N2            3             72
  N3            1              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"
D118V6, binary
                cls
clus               0   1
  SND1 MUTATED     6   0
  SND1 WILD-TYPE 176  10
[1] "tbl2"
                cls
clus             [,1] [,2]
  SND1 MUTATED      6    0
  SND1 WILD-TYPE  176   10
   clus
vv  SND1 MUTATED SND1 WILD-TYPE
  0            6            176
  1            0             10
[1] 2 2
[1] FALSE
D118V7, binary
                cls
clus               0   1
  SND1 MUTATED     1   7
  SND1 WILD-TYPE  95 273
[1] "tbl2"
                cls
clus             [,1] [,2]
  SND1 MUTATED      1    7
  SND1 WILD-TYPE   95  273
        clus
vv       SND1 MUTATED SND1 WILD-TYPE
  FEMALE            1             95
  MALE              7            273
[1] 2 2
[1] FALSE
D118V8, continuous
D118V9, continuous
D118V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SND1 MUTATED       1                         0     7
  SND1 WILD-TYPE    37                        21   294
D118V11, multiclass
                           clus
vv                          SND1 MUTATED SND1 WILD-TYPE
  ASIAN                                1             37
  BLACK OR AFRICAN AMERICAN            0             21
  WHITE                                7            294
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D118V12, binary
                cls
clus               0   1
  SND1 MUTATED     0   8
  SND1 WILD-TYPE   8 330
[1] "tbl2"
                cls
clus             [,1] [,2]
  SND1 MUTATED      0    8
  SND1 WILD-TYPE    8  330
                        clus
vv                       SND1 MUTATED SND1 WILD-TYPE
  HISPANIC OR LATINO                0              8
  NOT HISPANIC OR LATINO            8            330
[1] 2 2
[1] FALSE
