[1] "terrence_modification_tag"
[1] TRUE
[1] "nver"         "-nVNozzle.R1"
[1] "nfn"                                 "/xchip/tcga/Tools/Nozzle/v1.current"
[1] "Nozzle.R1"
[1] "successfully load Nozzle.R1"
[1] "ofn"        "-oTSKCM-TM"
[1] "opt"       "-OPMUTSIG"
[1] "tl" ""  
[1] "dx" ""  
[1] "opt"    "MUTSIG"
[1] "dx" ""  
[1] "cfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/SKCM-TM/10006254/SKCM-TM.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/SKCM-TM/10689408/transformed.cor.cli.txt"

nPatients in clinical file=295, in cluster file=278, common to both=268
[1] 147 268
[1] "NRAS MUTATION ANALYSIS"
[1] 3
  NRAS MUTATED NRAS WILD-TYPE 
            82            186 
  NRAS MUTATED NRAS WILD-TYPE 
            82            186 
[1] "TP53 MUTATION ANALYSIS"
[1] 3
  TP53 MUTATED TP53 WILD-TYPE 
            46            222 
  TP53 MUTATED TP53 WILD-TYPE 
            46            222 
[1] "CDKN2A MUTATION ANALYSIS"
[1] 3
  CDKN2A MUTATED CDKN2A WILD-TYPE 
              38              230 
  CDKN2A MUTATED CDKN2A WILD-TYPE 
              38              230 
[1] "RPS27 MUTATION ANALYSIS"
[1] 3
  RPS27 MUTATED RPS27 WILD-TYPE 
             21             247 
  RPS27 MUTATED RPS27 WILD-TYPE 
             21             247 
[1] "MRPS31 MUTATION ANALYSIS"
[1] 3
  MRPS31 MUTATED MRPS31 WILD-TYPE 
              19              249 
  MRPS31 MUTATED MRPS31 WILD-TYPE 
              19              249 
[1] "NF1 MUTATION ANALYSIS"
[1] 3
  NF1 MUTATED NF1 WILD-TYPE 
           38           230 
  NF1 MUTATED NF1 WILD-TYPE 
           38           230 
[1] "RAC1 MUTATION ANALYSIS"
[1] 3
  RAC1 MUTATED RAC1 WILD-TYPE 
            20            248 
  RAC1 MUTATED RAC1 WILD-TYPE 
            20            248 
[1] "ARID2 MUTATION ANALYSIS"
[1] 3
  ARID2 MUTATED ARID2 WILD-TYPE 
             35             233 
  ARID2 MUTATED ARID2 WILD-TYPE 
             35             233 
[1] "C15ORF23 MUTATION ANALYSIS"
[1] 3
  C15ORF23 MUTATED C15ORF23 WILD-TYPE 
                18                250 
  C15ORF23 MUTATED C15ORF23 WILD-TYPE 
                18                250 
[1] "PTEN MUTATION ANALYSIS"
[1] 3
  PTEN MUTATED PTEN WILD-TYPE 
            22            246 
  PTEN MUTATED PTEN WILD-TYPE 
            22            246 
[1] "NOTCH2NL MUTATION ANALYSIS"
[1] 3
  NOTCH2NL MUTATED NOTCH2NL WILD-TYPE 
                15                253 
  NOTCH2NL MUTATED NOTCH2NL WILD-TYPE 
                15                253 
[1] "MAP2K1 MUTATION ANALYSIS"
[1] 3
  MAP2K1 MUTATED MAP2K1 WILD-TYPE 
              11              257 
  MAP2K1 MUTATED MAP2K1 WILD-TYPE 
              11              257 
[1] "PPP6C MUTATION ANALYSIS"
[1] 3
  PPP6C MUTATED PPP6C WILD-TYPE 
             20             248 
  PPP6C MUTATED PPP6C WILD-TYPE 
             20             248 
[1] "IDH1 MUTATION ANALYSIS"
[1] 3
  IDH1 MUTATED IDH1 WILD-TYPE 
            13            255 
  IDH1 MUTATED IDH1 WILD-TYPE 
            13            255 
[1] "PDE1A MUTATION ANALYSIS"
[1] 3
  PDE1A MUTATED PDE1A WILD-TYPE 
             38             230 
  PDE1A MUTATED PDE1A WILD-TYPE 
             38             230 
[1] "HMGCR MUTATION ANALYSIS"
[1] 3
  HMGCR MUTATED HMGCR WILD-TYPE 
             11             257 
  HMGCR MUTATED HMGCR WILD-TYPE 
             11             257 
[1] "PHGDH MUTATION ANALYSIS"
[1] 3
  PHGDH MUTATED PHGDH WILD-TYPE 
             10             258 
  PHGDH MUTATED PHGDH WILD-TYPE 
             10             258 
[1] "SLC38A4 MUTATION ANALYSIS"
[1] 3
  SLC38A4 MUTATED SLC38A4 WILD-TYPE 
               32               236 
  SLC38A4 MUTATED SLC38A4 WILD-TYPE 
               32               236 
[1] "CDK4 MUTATION ANALYSIS"
[1] 3
  CDK4 MUTATED CDK4 WILD-TYPE 
             7            261 
  CDK4 MUTATED CDK4 WILD-TYPE 
             7            261 
[1] "FAM58A MUTATION ANALYSIS"
[1] 3
  FAM58A MUTATED FAM58A WILD-TYPE 
               5              263 
  FAM58A MUTATED FAM58A WILD-TYPE 
               5              263 
[1] "EMG1 MUTATION ANALYSIS"
[1] 3
  EMG1 MUTATED EMG1 WILD-TYPE 
             8            260 
  EMG1 MUTATED EMG1 WILD-TYPE 
             8            260 
[1] "RQCD1 MUTATION ANALYSIS"
[1] 3
  RQCD1 MUTATED RQCD1 WILD-TYPE 
              8             260 
  RQCD1 MUTATED RQCD1 WILD-TYPE 
              8             260 
[1] "HSD11B1 MUTATION ANALYSIS"
[1] 3
  HSD11B1 MUTATED HSD11B1 WILD-TYPE 
               14               254 
  HSD11B1 MUTATED HSD11B1 WILD-TYPE 
               14               254 
[1] "DMC1 MUTATION ANALYSIS"
[1] 3
  DMC1 MUTATED DMC1 WILD-TYPE 
            12            256 
  DMC1 MUTATED DMC1 WILD-TYPE 
            12            256 
[1] "NRK MUTATION ANALYSIS"
[1] 3
  NRK MUTATED NRK WILD-TYPE 
           41           227 
  NRK MUTATED NRK WILD-TYPE 
           41           227 
[1] "TAF1A MUTATION ANALYSIS"
[1] 3
  TAF1A MUTATED TAF1A WILD-TYPE 
             13             255 
  TAF1A MUTATED TAF1A WILD-TYPE 
             13             255 
[1] "OXA1L MUTATION ANALYSIS"
[1] 3
  OXA1L MUTATED OXA1L WILD-TYPE 
              8             260 
  OXA1L MUTATED OXA1L WILD-TYPE 
              8             260 
[1] "COL3A1 MUTATION ANALYSIS"
[1] 3
  COL3A1 MUTATED COL3A1 WILD-TYPE 
              53              215 
  COL3A1 MUTATED COL3A1 WILD-TYPE 
              53              215 
[1] "TCHHL1 MUTATION ANALYSIS"
[1] 3
  TCHHL1 MUTATED TCHHL1 WILD-TYPE 
              38              230 
  TCHHL1 MUTATED TCHHL1 WILD-TYPE 
              38              230 
[1] "IL5RA MUTATION ANALYSIS"
[1] 3
  IL5RA MUTATED IL5RA WILD-TYPE 
             17             251 
  IL5RA MUTATED IL5RA WILD-TYPE 
             17             251 
[1] "NBPF7 MUTATION ANALYSIS"
[1] 3
  NBPF7 MUTATED NBPF7 WILD-TYPE 
             13             255 
  NBPF7 MUTATED NBPF7 WILD-TYPE 
             13             255 
[1] "KEL MUTATION ANALYSIS"
[1] 3
  KEL MUTATED KEL WILD-TYPE 
           35           233 
  KEL MUTATED KEL WILD-TYPE 
           35           233 
[1] "C7ORF58 MUTATION ANALYSIS"
[1] 3
  C7ORF58 MUTATED C7ORF58 WILD-TYPE 
               32               236 
  C7ORF58 MUTATED C7ORF58 WILD-TYPE 
               32               236 
[1] "NBPF1 MUTATION ANALYSIS"
[1] 3
  NBPF1 MUTATED NBPF1 WILD-TYPE 
             38             230 
  NBPF1 MUTATED NBPF1 WILD-TYPE 
             38             230 
[1] "TMEM216 MUTATION ANALYSIS"
[1] 3
  TMEM216 MUTATED TMEM216 WILD-TYPE 
                8               260 
  TMEM216 MUTATED TMEM216 WILD-TYPE 
                8               260 
[1] "DOM3Z MUTATION ANALYSIS"
[1] 3
  DOM3Z MUTATED DOM3Z WILD-TYPE 
              7             261 
  DOM3Z MUTATED DOM3Z WILD-TYPE 
              7             261 
[1] "BCLAF1 MUTATION ANALYSIS"
[1] 3
  BCLAF1 MUTATED BCLAF1 WILD-TYPE 
              46              222 
  BCLAF1 MUTATED BCLAF1 WILD-TYPE 
              46              222 
[1] "ZFX MUTATION ANALYSIS"
[1] 3
  ZFX MUTATED ZFX WILD-TYPE 
           13           255 
  ZFX MUTATED ZFX WILD-TYPE 
           13           255 
[1] "BRAF MUTATION ANALYSIS"
[1] 3
  BRAF MUTATED BRAF WILD-TYPE 
           136            132 
  BRAF MUTATED BRAF WILD-TYPE 
           136            132 
[1] "SAG MUTATION ANALYSIS"
[1] 3
  SAG MUTATED SAG WILD-TYPE 
           11           257 
  SAG MUTATED SAG WILD-TYPE 
           11           257 
[1] "OR51S1 MUTATION ANALYSIS"
[1] 3
  OR51S1 MUTATED OR51S1 WILD-TYPE 
              29              239 
  OR51S1 MUTATED OR51S1 WILD-TYPE 
              29              239 
[1] "USP17L2 MUTATION ANALYSIS"
[1] 3
  USP17L2 MUTATED USP17L2 WILD-TYPE 
               21               247 
  USP17L2 MUTATED USP17L2 WILD-TYPE 
               21               247 
[1] "LRPPRC MUTATION ANALYSIS"
[1] 3
  LRPPRC MUTATED LRPPRC WILD-TYPE 
              14              254 
  LRPPRC MUTATED LRPPRC WILD-TYPE 
              14              254 
[1] "BTK MUTATION ANALYSIS"
[1] 3
  BTK MUTATED BTK WILD-TYPE 
           15           253 
  BTK MUTATED BTK WILD-TYPE 
           15           253 
[1] "DSG3 MUTATION ANALYSIS"
[1] 3
  DSG3 MUTATED DSG3 WILD-TYPE 
            46            222 
  DSG3 MUTATED DSG3 WILD-TYPE 
            46            222 
[1] "C1QTNF9 MUTATION ANALYSIS"
[1] 3
  C1QTNF9 MUTATED C1QTNF9 WILD-TYPE 
               16               252 
  C1QTNF9 MUTATED C1QTNF9 WILD-TYPE 
               16               252 
[1] "BLM MUTATION ANALYSIS"
[1] 3
  BLM MUTATED BLM WILD-TYPE 
           15           253 
  BLM MUTATED BLM WILD-TYPE 
           15           253 
[1] "ACSM2B MUTATION ANALYSIS"
[1] 3
  ACSM2B MUTATED ACSM2B WILD-TYPE 
              42              226 
  ACSM2B MUTATED ACSM2B WILD-TYPE 
              42              226 
[1] "PARM1 MUTATION ANALYSIS"
[1] 3
  PARM1 MUTATED PARM1 WILD-TYPE 
             18             250 
  PARM1 MUTATED PARM1 WILD-TYPE 
             18             250 
[1] "TP63 MUTATION ANALYSIS"
[1] 3
  TP63 MUTATED TP63 WILD-TYPE 
            46            222 
  TP63 MUTATED TP63 WILD-TYPE 
            46            222 
[1] "NGF MUTATION ANALYSIS"
[1] 3
  NGF MUTATED NGF WILD-TYPE 
            9           259 
  NGF MUTATED NGF WILD-TYPE 
            9           259 
[1] "ANO4 MUTATION ANALYSIS"
[1] 3
  ANO4 MUTATED ANO4 WILD-TYPE 
            41            227 
  ANO4 MUTATED ANO4 WILD-TYPE 
            41            227 
[1] "PCDH18 MUTATION ANALYSIS"
[1] 3
  PCDH18 MUTATED PCDH18 WILD-TYPE 
              47              221 
  PCDH18 MUTATED PCDH18 WILD-TYPE 
              47              221 
[1] "NMS MUTATION ANALYSIS"
[1] 3
  NMS MUTATED NMS WILD-TYPE 
           13           255 
  NMS MUTATED NMS WILD-TYPE 
           13           255 
[1] "C12ORF43 MUTATION ANALYSIS"
[1] 3
  C12ORF43 MUTATED C12ORF43 WILD-TYPE 
                 5                263 
  C12ORF43 MUTATED C12ORF43 WILD-TYPE 
                 5                263 
[1] "XIRP2 MUTATION ANALYSIS"
[1] 3
  XIRP2 MUTATED XIRP2 WILD-TYPE 
             89             179 
  XIRP2 MUTATED XIRP2 WILD-TYPE 
             89             179 
[1] "USH2A MUTATION ANALYSIS"
[1] 3
  USH2A MUTATED USH2A WILD-TYPE 
             89             179 
  USH2A MUTATED USH2A WILD-TYPE 
             89             179 
[1] "DDX3X MUTATION ANALYSIS"
[1] 3
  DDX3X MUTATED DDX3X WILD-TYPE 
             19             249 
  DDX3X MUTATED DDX3X WILD-TYPE 
             19             249 
[1] "PTPN22 MUTATION ANALYSIS"
[1] 3
  PTPN22 MUTATED PTPN22 WILD-TYPE 
              21              247 
  PTPN22 MUTATED PTPN22 WILD-TYPE 
              21              247 
[1] "C3ORF71 MUTATION ANALYSIS"
[1] 3
  C3ORF71 MUTATED C3ORF71 WILD-TYPE 
                4               264 
  C3ORF71 MUTATED C3ORF71 WILD-TYPE 
                4               264 
[1] "CEACAM6 MUTATION ANALYSIS"
[1] 3
  CEACAM6 MUTATED CEACAM6 WILD-TYPE 
               15               253 
  CEACAM6 MUTATED CEACAM6 WILD-TYPE 
               15               253 
[1] "MUC7 MUTATION ANALYSIS"
[1] 3
  MUC7 MUTATED MUC7 WILD-TYPE 
            16            252 
  MUC7 MUTATED MUC7 WILD-TYPE 
            16            252 
[1] "SELP MUTATION ANALYSIS"
[1] 3
  SELP MUTATED SELP WILD-TYPE 
            33            235 
  SELP MUTATED SELP WILD-TYPE 
            33            235 
[1] "LIPH MUTATION ANALYSIS"
[1] 3
  LIPH MUTATED LIPH WILD-TYPE 
            13            255 
  LIPH MUTATED LIPH WILD-TYPE 
            13            255 
[1] "MMP1 MUTATION ANALYSIS"
[1] 3
  MMP1 MUTATED MMP1 WILD-TYPE 
            14            254 
  MMP1 MUTATED MMP1 WILD-TYPE 
            14            254 
[1] "KLF11 MUTATION ANALYSIS"
[1] 3
  KLF11 MUTATED KLF11 WILD-TYPE 
              9             259 
  KLF11 MUTATED KLF11 WILD-TYPE 
              9             259 
[1] "USP9X MUTATION ANALYSIS"
[1] 3
  USP9X MUTATED USP9X WILD-TYPE 
             14             254 
  USP9X MUTATED USP9X WILD-TYPE 
             14             254 
[1] "PTK7 MUTATION ANALYSIS"
[1] 3
  PTK7 MUTATED PTK7 WILD-TYPE 
            16            252 
  PTK7 MUTATED PTK7 WILD-TYPE 
            16            252 
[1] "SLC14A1 MUTATION ANALYSIS"
[1] 3
  SLC14A1 MUTATED SLC14A1 WILD-TYPE 
               17               251 
  SLC14A1 MUTATED SLC14A1 WILD-TYPE 
               17               251 
[1] "PROX2 MUTATION ANALYSIS"
[1] 3
  PROX2 MUTATED PROX2 WILD-TYPE 
             13             255 
  PROX2 MUTATED PROX2 WILD-TYPE 
             13             255 
[1] "DNMBP MUTATION ANALYSIS"
[1] 3
  DNMBP MUTATED DNMBP WILD-TYPE 
             19             249 
  DNMBP MUTATED DNMBP WILD-TYPE 
             19             249 
[1] "MPP7 MUTATION ANALYSIS"
[1] 3
  MPP7 MUTATED MPP7 WILD-TYPE 
            30            238 
  MPP7 MUTATED MPP7 WILD-TYPE 
            30            238 
[1] "IFNGR2 MUTATION ANALYSIS"
[1] 3
  IFNGR2 MUTATED IFNGR2 WILD-TYPE 
               4              264 
  IFNGR2 MUTATED IFNGR2 WILD-TYPE 
               4              264 
[1] "ASNSD1 MUTATION ANALYSIS"
[1] 3
  ASNSD1 MUTATED ASNSD1 WILD-TYPE 
               7              261 
  ASNSD1 MUTATED ASNSD1 WILD-TYPE 
               7              261 
[1] "RB1 MUTATION ANALYSIS"
[1] 3
  RB1 MUTATED RB1 WILD-TYPE 
            9           259 
  RB1 MUTATED RB1 WILD-TYPE 
            9           259 
[1] "CCK MUTATION ANALYSIS"
[1] 3
  CCK MUTATED CCK WILD-TYPE 
            5           263 
  CCK MUTATED CCK WILD-TYPE 
            5           263 
[1] "ZNF780B MUTATION ANALYSIS"
[1] 3
  ZNF780B MUTATED ZNF780B WILD-TYPE 
                9               259 
  ZNF780B MUTATED ZNF780B WILD-TYPE 
                9               259 
[1] "ATP5F1 MUTATION ANALYSIS"
[1] 3
  ATP5F1 MUTATED ATP5F1 WILD-TYPE 
               7              261 
  ATP5F1 MUTATED ATP5F1 WILD-TYPE 
               7              261 
[1] "LOC728819 MUTATION ANALYSIS"
[1] 3
  LOC728819 MUTATED LOC728819 WILD-TYPE 
                  7                 261 
  LOC728819 MUTATED LOC728819 WILD-TYPE 
                  7                 261 
[1] "LACRT MUTATION ANALYSIS"
[1] 3
  LACRT MUTATED LACRT WILD-TYPE 
              9             259 
  LACRT MUTATED LACRT WILD-TYPE 
              9             259 
[1] "RPGRIP1 MUTATION ANALYSIS"
[1] 3
  RPGRIP1 MUTATED RPGRIP1 WILD-TYPE 
               23               245 
  RPGRIP1 MUTATED RPGRIP1 WILD-TYPE 
               23               245 
[1] "THEMIS MUTATION ANALYSIS"
[1] 3
  THEMIS MUTATED THEMIS WILD-TYPE 
              32              236 
  THEMIS MUTATED THEMIS WILD-TYPE 
              32              236 
[1] "PTPRT MUTATION ANALYSIS"
[1] 3
  PTPRT MUTATED PTPRT WILD-TYPE 
             76             192 
  PTPRT MUTATED PTPRT WILD-TYPE 
             76             192 
[1] "SELPLG MUTATION ANALYSIS"
[1] 3
  SELPLG MUTATED SELPLG WILD-TYPE 
               9              259 
  SELPLG MUTATED SELPLG WILD-TYPE 
               9              259 
[1] "CSN3 MUTATION ANALYSIS"
[1] 3
  CSN3 MUTATED CSN3 WILD-TYPE 
             4            264 
  CSN3 MUTATED CSN3 WILD-TYPE 
             4            264 
[1] "SLC7A11 MUTATION ANALYSIS"
[1] 3
  SLC7A11 MUTATED SLC7A11 WILD-TYPE 
               11               257 
  SLC7A11 MUTATED SLC7A11 WILD-TYPE 
               11               257 
[1] "SYNE1 MUTATION ANALYSIS"
[1] 3
  SYNE1 MUTATED SYNE1 WILD-TYPE 
             69             199 
  SYNE1 MUTATED SYNE1 WILD-TYPE 
             69             199 
[1] "NFASC MUTATION ANALYSIS"
[1] 3
  NFASC MUTATED NFASC WILD-TYPE 
             22             246 
  NFASC MUTATED NFASC WILD-TYPE 
             22             246 
[1] "CCDC11 MUTATION ANALYSIS"
[1] 3
  CCDC11 MUTATED CCDC11 WILD-TYPE 
              17              251 
  CCDC11 MUTATED CCDC11 WILD-TYPE 
              17              251 
[1] "IL31RA MUTATION ANALYSIS"
[1] 3
  IL31RA MUTATED IL31RA WILD-TYPE 
              17              251 
  IL31RA MUTATED IL31RA WILD-TYPE 
              17              251 
[1] "MLL MUTATION ANALYSIS"
[1] 3
  MLL MUTATED MLL WILD-TYPE 
           37           231 
  MLL MUTATED MLL WILD-TYPE 
           37           231 
[1] "DIRC2 MUTATION ANALYSIS"
[1] 3
  DIRC2 MUTATED DIRC2 WILD-TYPE 
              4             264 
  DIRC2 MUTATED DIRC2 WILD-TYPE 
              4             264 
[1] "ADAM22 MUTATION ANALYSIS"
[1] 3
  ADAM22 MUTATED ADAM22 WILD-TYPE 
              19              249 
  ADAM22 MUTATED ADAM22 WILD-TYPE 
              19              249 
[1] "PLCXD2 MUTATION ANALYSIS"
[1] 3
  PLCXD2 MUTATED PLCXD2 WILD-TYPE 
               9              259 
  PLCXD2 MUTATED PLCXD2 WILD-TYPE 
               9              259 
[1] "EDN1 MUTATION ANALYSIS"
[1] 3
  EDN1 MUTATED EDN1 WILD-TYPE 
             9            259 
  EDN1 MUTATED EDN1 WILD-TYPE 
             9            259 
[1] "HTR7 MUTATION ANALYSIS"
[1] 3
  HTR7 MUTATED HTR7 WILD-TYPE 
             9            259 
  HTR7 MUTATED HTR7 WILD-TYPE 
             9            259 
[1] "TLR9 MUTATION ANALYSIS"
[1] 3
  TLR9 MUTATED TLR9 WILD-TYPE 
            18            250 
  TLR9 MUTATED TLR9 WILD-TYPE 
            18            250 
[1] "MYH1 MUTATION ANALYSIS"
[1] 3
  MYH1 MUTATED MYH1 WILD-TYPE 
            63            205 
  MYH1 MUTATED MYH1 WILD-TYPE 
            63            205 
[1] "EPHA3 MUTATION ANALYSIS"
[1] 3
  EPHA3 MUTATED EPHA3 WILD-TYPE 
             28             240 
  EPHA3 MUTATED EPHA3 WILD-TYPE 
             28             240 
[1] "ARL16 MUTATION ANALYSIS"
[1] 3
  ARL16 MUTATED ARL16 WILD-TYPE 
              7             261 
  ARL16 MUTATED ARL16 WILD-TYPE 
              7             261 
[1] "DDX17 MUTATION ANALYSIS"
[1] 3
  DDX17 MUTATED DDX17 WILD-TYPE 
             11             257 
  DDX17 MUTATED DDX17 WILD-TYPE 
             11             257 
[1] "MAN1A1 MUTATION ANALYSIS"
[1] 3
  MAN1A1 MUTATED MAN1A1 WILD-TYPE 
              12              256 
  MAN1A1 MUTATED MAN1A1 WILD-TYPE 
              12              256 
[1] "ADAM30 MUTATION ANALYSIS"
[1] 3
  ADAM30 MUTATED ADAM30 WILD-TYPE 
              26              242 
  ADAM30 MUTATED ADAM30 WILD-TYPE 
              26              242 
[1] "NBEAL1 MUTATION ANALYSIS"
[1] 3
  NBEAL1 MUTATED NBEAL1 WILD-TYPE 
              30              238 
  NBEAL1 MUTATED NBEAL1 WILD-TYPE 
              30              238 
[1] "WDR65 MUTATION ANALYSIS"
[1] 3
  WDR65 MUTATED WDR65 WILD-TYPE 
             21             247 
  WDR65 MUTATED WDR65 WILD-TYPE 
             21             247 
[1] "C6ORF165 MUTATION ANALYSIS"
[1] 3
  C6ORF165 MUTATED C6ORF165 WILD-TYPE 
                16                252 
  C6ORF165 MUTATED C6ORF165 WILD-TYPE 
                16                252 
[1] "RNF133 MUTATION ANALYSIS"
[1] 3
  RNF133 MUTATED RNF133 WILD-TYPE 
               8              260 
  RNF133 MUTATED RNF133 WILD-TYPE 
               8              260 
[1] "GTPBP4 MUTATION ANALYSIS"
[1] 3
  GTPBP4 MUTATED GTPBP4 WILD-TYPE 
               8              260 
  GTPBP4 MUTATED GTPBP4 WILD-TYPE 
               8              260 
[1] "ACSBG1 MUTATION ANALYSIS"
[1] 3
  ACSBG1 MUTATED ACSBG1 WILD-TYPE 
              10              258 
  ACSBG1 MUTATED ACSBG1 WILD-TYPE 
              10              258 
[1] "TPTE MUTATION ANALYSIS"
[1] 3
  TPTE MUTATED TPTE WILD-TYPE 
            58            210 
  TPTE MUTATED TPTE WILD-TYPE 
            58            210 
[1] "CLCC1 MUTATION ANALYSIS"
[1] 3
  CLCC1 MUTATED CLCC1 WILD-TYPE 
             13             255 
  CLCC1 MUTATED CLCC1 WILD-TYPE 
             13             255 
[1] "PPAP2B MUTATION ANALYSIS"
[1] 3
  PPAP2B MUTATED PPAP2B WILD-TYPE 
               9              259 
  PPAP2B MUTATED PPAP2B WILD-TYPE 
               9              259 
[1] "CD300E MUTATION ANALYSIS"
[1] 3
  CD300E MUTATED CD300E WILD-TYPE 
               8              260 
  CD300E MUTATED CD300E WILD-TYPE 
               8              260 
[1] "ALDH5A1 MUTATION ANALYSIS"
[1] 3
  ALDH5A1 MUTATED ALDH5A1 WILD-TYPE 
               10               258 
  ALDH5A1 MUTATED ALDH5A1 WILD-TYPE 
               10               258 
[1] "SPRYD3 MUTATION ANALYSIS"
[1] 3
  SPRYD3 MUTATED SPRYD3 WILD-TYPE 
               7              261 
  SPRYD3 MUTATED SPRYD3 WILD-TYPE 
               7              261 
[1] "MAP3K5 MUTATION ANALYSIS"
[1] 3
  MAP3K5 MUTATED MAP3K5 WILD-TYPE 
              17              251 
  MAP3K5 MUTATED MAP3K5 WILD-TYPE 
              17              251 
[1] "CASP8 MUTATION ANALYSIS"
[1] 3
  CASP8 MUTATED CASP8 WILD-TYPE 
              8             260 
  CASP8 MUTATED CASP8 WILD-TYPE 
              8             260 
[1] "SNCAIP MUTATION ANALYSIS"
[1] 3
  SNCAIP MUTATED SNCAIP WILD-TYPE 
              46              222 
  SNCAIP MUTATED SNCAIP WILD-TYPE 
              46              222 
[1] "HLA-DRA MUTATION ANALYSIS"
[1] 3
  HLA-DRA MUTATED HLA-DRA WILD-TYPE 
               11               257 
  HLA-DRA MUTATED HLA-DRA WILD-TYPE 
               11               257 
[1] "ACTC1 MUTATION ANALYSIS"
[1] 3
  ACTC1 MUTATED ACTC1 WILD-TYPE 
             15             253 
  ACTC1 MUTATED ACTC1 WILD-TYPE 
             15             253 
[1] "ELOVL3 MUTATION ANALYSIS"
[1] 3
  ELOVL3 MUTATED ELOVL3 WILD-TYPE 
               5              263 
  ELOVL3 MUTATED ELOVL3 WILD-TYPE 
               5              263 
[1] "THSD7B MUTATION ANALYSIS"
[1] 3
  THSD7B MUTATED THSD7B WILD-TYPE 
              83              185 
  THSD7B MUTATED THSD7B WILD-TYPE 
              83              185 
[1] "SLC27A5 MUTATION ANALYSIS"
[1] 3
  SLC27A5 MUTATED SLC27A5 WILD-TYPE 
                8               260 
  SLC27A5 MUTATED SLC27A5 WILD-TYPE 
                8               260 
[1] "PDE4DIP MUTATION ANALYSIS"
[1] 3
  PDE4DIP MUTATED PDE4DIP WILD-TYPE 
               42               226 
  PDE4DIP MUTATED PDE4DIP WILD-TYPE 
               42               226 
[1] "KANK3 MUTATION ANALYSIS"
[1] 3
  KANK3 MUTATED KANK3 WILD-TYPE 
              7             261 
  KANK3 MUTATED KANK3 WILD-TYPE 
              7             261 
[1] "RUNX1T1 MUTATION ANALYSIS"
[1] 3
  RUNX1T1 MUTATED RUNX1T1 WILD-TYPE 
               33               235 
  RUNX1T1 MUTATED RUNX1T1 WILD-TYPE 
               33               235 
[1] "WDR12 MUTATION ANALYSIS"
[1] 3
  WDR12 MUTATED WDR12 WILD-TYPE 
             11             257 
  WDR12 MUTATED WDR12 WILD-TYPE 
             11             257 
[1] "POTEG MUTATION ANALYSIS"
[1] 3
  POTEG MUTATED POTEG WILD-TYPE 
             29             239 
  POTEG MUTATED POTEG WILD-TYPE 
             29             239 
[1] "ITPR2 MUTATION ANALYSIS"
[1] 3
  ITPR2 MUTATED ITPR2 WILD-TYPE 
             15             253 
  ITPR2 MUTATED ITPR2 WILD-TYPE 
             15             253 
[1] "CRNKL1 MUTATION ANALYSIS"
[1] 3
  CRNKL1 MUTATED CRNKL1 WILD-TYPE 
              12              256 
  CRNKL1 MUTATED CRNKL1 WILD-TYPE 
              12              256 
[1] "DSP MUTATION ANALYSIS"
[1] 3
  DSP MUTATED DSP WILD-TYPE 
           56           212 
  DSP MUTATED DSP WILD-TYPE 
           56           212 
[1] "SF3B1 MUTATION ANALYSIS"
[1] 3
  SF3B1 MUTATED SF3B1 WILD-TYPE 
             13             255 
  SF3B1 MUTATED SF3B1 WILD-TYPE 
             13             255 
[1] "CAGE1 MUTATION ANALYSIS"
[1] 3
  CAGE1 MUTATED CAGE1 WILD-TYPE 
             11             257 
  CAGE1 MUTATED CAGE1 WILD-TYPE 
             11             257 
[1] "DDX43 MUTATION ANALYSIS"
[1] 3
  DDX43 MUTATED DDX43 WILD-TYPE 
             11             257 
  DDX43 MUTATED DDX43 WILD-TYPE 
             11             257 
[1] "CYP3A7 MUTATION ANALYSIS"
[1] 3
  CYP3A7 MUTATED CYP3A7 WILD-TYPE 
              23              245 
  CYP3A7 MUTATED CYP3A7 WILD-TYPE 
              23              245 
[1] "VGLL1 MUTATION ANALYSIS"
[1] 3
  VGLL1 MUTATED VGLL1 WILD-TYPE 
              6             262 
  VGLL1 MUTATED VGLL1 WILD-TYPE 
              6             262 
[1] "GML MUTATION ANALYSIS"
[1] 3
  GML MUTATED GML WILD-TYPE 
           10           258 
  GML MUTATED GML WILD-TYPE 
           10           258 
[1] "GZMA MUTATION ANALYSIS"
[1] 3
  GZMA MUTATED GZMA WILD-TYPE 
            11            257 
  GZMA MUTATED GZMA WILD-TYPE 
            11            257 
[1] "NPTX1 MUTATION ANALYSIS"
[1] 3
  NPTX1 MUTATED NPTX1 WILD-TYPE 
              8             260 
  NPTX1 MUTATED NPTX1 WILD-TYPE 
              8             260 
[1] "DACT1 MUTATION ANALYSIS"
[1] 3
  DACT1 MUTATED DACT1 WILD-TYPE 
             11             257 
  DACT1 MUTATED DACT1 WILD-TYPE 
             11             257 
[1] "STK19 MUTATION ANALYSIS"
[1] 3
  STK19 MUTATED STK19 WILD-TYPE 
             12             256 
  STK19 MUTATED STK19 WILD-TYPE 
             12             256 
[1] "STK31 MUTATION ANALYSIS"
[1] 3
  STK31 MUTATED STK31 WILD-TYPE 
             34             234 
  STK31 MUTATED STK31 WILD-TYPE 
             34             234 
[1] "ROS1 MUTATION ANALYSIS"
[1] 3
  ROS1 MUTATED ROS1 WILD-TYPE 
            54            214 
  ROS1 MUTATED ROS1 WILD-TYPE 
            54            214 
[1] "KCNB2 MUTATION ANALYSIS"
[1] 3
  KCNB2 MUTATED KCNB2 WILD-TYPE 
             57             211 
  KCNB2 MUTATED KCNB2 WILD-TYPE 
             57             211 
[1] "ART3 MUTATION ANALYSIS"
[1] 3
  ART3 MUTATED ART3 WILD-TYPE 
            12            256 
  ART3 MUTATED ART3 WILD-TYPE 
            12            256 
[1] "CLDN4 MUTATION ANALYSIS"
[1] 3
  CLDN4 MUTATED CLDN4 WILD-TYPE 
             10             258 
  CLDN4 MUTATED CLDN4 WILD-TYPE 
             10             258 
[1] "RAG2 MUTATION ANALYSIS"
[1] 3
  RAG2 MUTATED RAG2 WILD-TYPE 
            18            250 
  RAG2 MUTATED RAG2 WILD-TYPE 
            18            250 
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                          
 [2] "VITALSTATUS"                           
 [3] "DAYSTODEATH"                           
 [4] "DAYSTOLASTFOLLOWUP"                    
 [5] "DAYSTOSUBMITTEDSPECIMENDX"             
 [6] "PRIMARYSITEOFDESEASE"                  
 [7] "NEOPLASM.DISEASESTAGE"                 
 [8] "PATHOLOGY.T.STAGE"                     
 [9] "PATHOLOGY.N.STAGE"                     
[10] "PATHOLOGY.M.STAGE"                     
[11] "MELANOMA.ULCERATION"                   
[12] "MELANOMA.PRIMARY.KNOWN"                
[13] "BRESLOW.THICKNESS"                     
[14] "DCCUPLOADDATE"                         
[15] "GENDER"                                
[16] "DATEOFINITIALPATHOLOGICDIAGNOSIS"      
[17] "RADIATIONTHERAPY"                      
[18] "RADIATIONS.RADIATION.REGIMENINDICATION"
[19] "RACE"                                  
[20] "ETHNICITY"                             
[21] "BATCHNUMBER"                           

Input Data has 21 rows and 268 columns.

[1] "Batch" "21"   
[1] "Last Follow UP"
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
          NA           NA         3408           NA           NA         4053 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
          NA           NA         2765         2912           NA           NA 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
          NA           NA         3514           NA         2126           NA 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
        1483           NA         1280           NA         5219         1709 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C1 TCGA-D3-A3C3 TCGA-D3-A3C6 
        2010         1372         3976           NA           NA           NA 
TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF 
        1429         1409         5065         2644           NA           NA 
TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E 
          NA           NA         3151         1209          653         4923 
TCGA-D3-A51F TCGA-D3-A51G TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N 
        1329           NA         1221         4012          559          305 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS 
        1572          458         4129         4195         5055          226 
TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 
        3808         4609         1663          111          195          345 
TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1HW 
          99          301          766         2015         1487           NA 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 
        3565           NA         5926           NA           NA         3265 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
        1861           NA           NA          713           NA          870 
TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG 
          NA         6553          477          422          309         1372 
TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z 
        1065          108         1582           NA           NA           NA 
TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 
          NA           NA           NA           NA           NA           NA 
TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A 
        3335           NA         2399           NA           NA           NA 
TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H 
        2452         1455           NA         1205           NA          979 
TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R 
          NA         1349           NA         1716         1136          440 
TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 
        1701           NA         5218           NA           NA         3130 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD 
         743           NA         1787         1446         2051         9568 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
        4135         6328         1482         2717         1665         2423 
TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS 
        2296         2767         3101           NA          435         1691 
TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 
        1365         2884           NA         3932           NA           NA 
TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI 
          NA           NA           NA           NA           NA           NA 
TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP 
          NA         4403         6176           NA           NA         7563 
TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA 
          NA         3150         4151         1265         1620         3781 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG 
        3733          786          112         1658           NA          714 
TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 
          NA           NA           NA           NA         1949           NA 
TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 
          NA           NA         1016         3096         4504           NA 
TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B 
          NA           NA           NA           NA         2365           NA 
TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H 
          NA           NA           NA           NA         8180           NA 
TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19O TCGA-ER-A19P 
          NA           NA           NA         1340           NA           NA 
TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
          NA         1133           NA         2433           NA           NA 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET 
          NA          498          951          975           NA         2443 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A3YO TCGA-FR-A44A TCGA-FR-A69P 
        1429         1010         2828           NA         5299          149 
TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 
          NA           NA           NA           NA           NA           NA 
TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE 
          NA           NA           NA           NA           NA         1225 
TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM 
          NA           NA           NA           NA           NA         3080 
TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU 
          NA           NA           NA         4526         1617           NA 
TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 
        1505           NA           NA         2367           NA           NA 
TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 
          NA          378           NA         1504         2369            6 
TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
         697         1446            5           73          301          220 
TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 
         427         3664           NA         2577           NA           NA 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS 
          NA           NA         1204          203 
Variable 1:'AGE':	nDistinctValues=66,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=130,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=137,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 5:'DAYSTOSUBMITTEDSPECIMENDX':	nDistinctValues=212,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 6:'PRIMARY.SITE.OF.DISEASE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'NEOPLASM.DISEASESTAGE':	nDistinctValues=14,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY.T.STAGE':	nDistinctValues=15,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY.N.STAGE':	nDistinctValues=10,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'PATHOLOGY.M.STAGE':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'MELANOMA.ULCERATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'MELANOMA.PRIMARY.KNOWN':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 13:'BRESLOW.THICKNESS':	nDistinctValues=109,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 14:'DCCUPLOADDAY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 15:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=27,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 17:'RADIATION.THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 18:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 19:'RACE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 20:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 21:'BATCH.NUMBER':	nDistinctValues=9,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
 [1] "AGE"                     "PRIMARY.SITE.OF.DISEASE"
 [3] "NEOPLASM.DISEASESTAGE"   "PATHOLOGY.T.STAGE"      
 [5] "PATHOLOGY.N.STAGE"       "PATHOLOGY.M.STAGE"      
 [7] "MELANOMA.ULCERATION"     "MELANOMA.PRIMARY.KNOWN" 
 [9] "BRESLOW.THICKNESS"       "GENDER"                 
[11] "RACE"                    "ETHNICITY"              
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T" "4"          
[1] "PATHOLOGY.N" "5"          
Output Data has 268 columns, 2 survival variables, and 12 non-survival variables.
AGE, nv=66, binary=FALSE, numeric=TRUE
PRIMARY.SITE.OF.DISEASE, nv=4, binary=FALSE, numeric=FALSE
NEOPLASM.DISEASESTAGE, nv=14, binary=FALSE, numeric=FALSE
PATHOLOGY.T.STAGE, nv=5, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
T0 T1 T2 T3 T4 
21 30 58 53 55 
[1] "table(vv)"
vv
T0+T1    T2    T3    T4 
   51    58    53    55 
$ClinVariableName
[1] "PATHOLOGY.T.STAGE"

$Table
vv
T0 T1 T2 T3 T4 
21 30 58 53 55 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


T0+T1    T2    T3    T4 
   51    58    53    55 
PATHOLOGY.N.STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
 N0  N1  N2  N3 
138  48  32  33 
[1] "table(vv)"
vv
 N0  N1  N2  N3 
138  48  32  33 
$ClinVariableName
[1] "PATHOLOGY.N.STAGE"

$Table
vv
 N0  N1  N2  N3 
138  48  32  33 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 N0  N1  N2  N3 
138  48  32  33 
PATHOLOGY.M.STAGE, nv=5, binary=FALSE, numeric=FALSE
MELANOMA.ULCERATION, nv=2, binary=FALSE, numeric=FALSE
MELANOMA.PRIMARY.KNOWN, nv=2, binary=FALSE, numeric=FALSE
BRESLOW.THICKNESS, nv=109, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
RACE, nv=3, binary=FALSE, numeric=FALSE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = NRAS MUTATION ANALYSIS
D1V1, survival
                sevent
clus2             0  1
  NRAS MUTATED   37 43
  NRAS WILD-TYPE 91 87
  NRAS MUTATED NRAS WILD-TYPE 
            80            178 
  NRAS MUTATED NRAS WILD-TYPE 
            43             87 
$`NRAS MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q8 TCGA-D3-A1QB TCGA-D3-A2J8 TCGA-D3-A2JL TCGA-D3-A2JO 
       16.47        28.08        81.24         8.38        92.42        64.44 
TCGA-D3-A3ML TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51R TCGA-D3-A5GO TCGA-D9-A3Z1 
        6.31         5.39        80.22        20.48        47.87         4.01 
TCGA-D9-A6EA TCGA-DA-A1HV TCGA-DA-A1I1 TCGA-DA-A3F3 TCGA-EB-A44Q TCGA-EB-A44R 
       11.31        48.79        39.19         7.00        13.15         0.20 
TCGA-EB-A5SG TCGA-EE-A17X TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20C TCGA-EE-A29G 
        0.00        11.57         5.13         4.31         4.34         8.55 
TCGA-EE-A29L TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29X 
        1.08         8.09         8.84         9.99         2.43         8.09 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2GD TCGA-EE-A2GJ TCGA-EE-A2GL 
       49.22        23.90         9.67        17.98        19.43        35.54 
TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GU TCGA-EE-A2MC TCGA-EE-A2MD 
       28.31        33.83         5.42        36.33        47.51         9.53 
TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MU TCGA-EE-A3AC TCGA-EE-A3J7 
      111.91        56.02        25.08         5.56        25.84        21.60 
TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A199 TCGA-ER-A19D 
       16.14        22.22        33.60        18.61         5.72         3.52 
TCGA-ER-A19N TCGA-ER-A19W TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NH TCGA-FR-A3YN 
       42.84        17.72        11.80         1.51        11.74        18.41 
TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1ZA TCGA-FS-A1ZB 
        4.90        64.47        23.80        14.24         7.30         3.39 
TCGA-FS-A1ZE TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZT TCGA-FS-A1ZW TCGA-FS-A1ZY 
       19.53        52.08         8.65        40.64        27.39         0.82 
TCGA-FS-A1ZZ TCGA-FS-A4F5 TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FS-A4FD TCGA-GF-A3OT 
        5.23        28.73        10.78         6.41         2.27         9.90 
TCGA-GN-A267 TCGA-GN-A268 
       16.24        15.42 

$`NRAS WILD-TYPE`
TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q9 
        8.52       111.09        32.42        70.16       110.79        22.55 
TCGA-D3-A1QA TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB 
       45.83        10.29        85.32        21.14        88.50        68.22 
TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK 
       69.90        11.41        30.87         7.50        36.16         6.31 
TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 
       56.19        45.11       114.67        15.25        46.98        46.32 
TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MR 
       82.29        61.38        13.32        24.00         9.34       103.59 
TCGA-D3-A3MU TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N 
       26.37        42.71        15.09        41.10        17.72         8.84 
TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z3 
       13.94        52.01         1.55         6.97        23.11         2.89 
TCGA-D9-A6E9 TCGA-D9-A6EC TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I2 
        9.90        13.22        35.80        51.12        10.03        13.68 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB 
        9.99        44.52        36.69        25.15         4.93        22.36 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A5SH TCGA-EB-A5UN 
        6.64        19.36        17.56        14.83         0.00        13.22 
TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 
       10.55         6.31         8.12         1.12         1.35        12.20 
TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B 
       36.07         5.13         9.21         1.18         7.99         9.90 
TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29N 
       37.97        11.15        38.63         4.41        27.12         9.50 
TCGA-EE-A29P TCGA-EE-A29W TCGA-EE-A2A0 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC 
       12.03         8.68        11.31         8.94        39.39        34.29 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GK TCGA-EE-A2GO TCGA-EE-A2GR 
       34.92        47.21        30.08        16.01        30.84         1.15 
TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 
       13.02        34.98         8.84        98.27         2.70         6.18 
TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK 
       29.46        44.25         7.96        14.56        63.42       111.78 
TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AA 
       26.99        21.60        29.65        27.16        23.05       124.31 
TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH 
      122.73         3.68        30.15        13.81        15.95        12.72 
TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH 
        3.22        22.92        21.60        27.35         0.46        13.94 
TCGA-ER-A193 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C 
       31.40        12.95        38.40        76.41        25.18         3.78 
TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L 
       11.90        11.11       114.15        34.88         4.21        13.45 
TCGA-ER-A19M TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A1A1 TCGA-ER-A2ND 
       28.60        34.68         9.57        36.07        78.44         1.87 
TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL 
       13.08        12.62         9.04         6.58        22.49         1.71 
TCGA-FR-A44A TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZC 
       85.74         3.45        11.01        15.52         7.33        20.38 
TCGA-FS-A1ZD TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK 
        8.22        11.08         7.17        30.87        12.92        12.89 
TCGA-FS-A1ZM TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZU TCGA-FS-A4F0 TCGA-FS-A4F4 
       47.38         8.81        49.15         8.68        53.85         7.36 
TCGA-FS-A4F8 TCGA-FS-A4FB TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV 
       14.20         5.98         0.20         0.99         0.13         0.16 
TCGA-FW-A5DY TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        0.43         7.23        12.85        24.85        31.33        84.72 
TCGA-GN-A266 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS 
       10.13        12.16        14.70         5.79 

  NRAS MUTATED NRAS WILD-TYPE 
             0              0 
  NRAS MUTATED NRAS WILD-TYPE 
        111.91         124.31 
  NRAS MUTATED NRAS WILD-TYPE 
        14.830         14.765 
[1] "0.0 - 111.9 (14.8)" "0.0 - 124.3 (14.8)"
[1] "hr=" "1.3"
D1V2, survival
                sevent
clus2             0  1
  NRAS MUTATED   38 43
  NRAS WILD-TYPE 94 88
  NRAS MUTATED NRAS WILD-TYPE 
            81            182 
  NRAS MUTATED NRAS WILD-TYPE 
            43             88 
$`NRAS MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q8 TCGA-D3-A1QB TCGA-D3-A2J8 TCGA-D3-A2JL TCGA-D3-A2JO 
       16.57        28.08        95.74        65.49       171.58        66.08 
TCGA-D3-A3ML TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51R TCGA-D3-A5GO TCGA-D9-A3Z1 
       13.87        21.47       161.85        51.68       137.92        11.34 
TCGA-D9-A6EA TCGA-DA-A1HV TCGA-DA-A1I1 TCGA-DA-A3F3 TCGA-EB-A44Q TCGA-EB-A44R 
       25.18        48.89       194.83        10.49        13.87        10.16 
TCGA-EB-A5SG TCGA-EB-A5UL TCGA-EE-A17X TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20C 
       45.11         3.55        29.82        68.15         4.96       151.27 
TCGA-EE-A29G TCGA-EE-A29L TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V 
       72.07         2.60        37.35        14.47        55.92        25.87 
TCGA-EE-A29X TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2GD TCGA-EE-A2GJ 
       17.92       102.90        24.43        39.29       314.56        89.33 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GU TCGA-EE-A2MC 
       79.66        75.48        90.97        13.91        94.82        61.51 
TCGA-EE-A2MD TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MU TCGA-EE-A3AC 
       47.28       203.05       167.90        47.54        53.26        25.84 
TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A199 
       64.08        34.32        53.19       148.08        35.44         9.17 
TCGA-ER-A19D TCGA-ER-A19N TCGA-ER-A19W TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NH 
       12.59        44.05       148.18        43.82        20.15        32.05 
TCGA-FR-A3YN TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1ZA 
       92.98         4.90       216.92       202.65        20.91        27.72 
TCGA-FS-A1ZB TCGA-FS-A1ZE TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZT TCGA-FS-A1ZW 
       48.85        40.27        74.73       133.55        53.16        49.48 
TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F5 TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FS-A4FD 
       27.09        27.02        28.73        12.43        49.45        77.88 
TCGA-GF-A3OT TCGA-GN-A267 TCGA-GN-A268 
        9.90        64.44        62.79 

$`NRAS WILD-TYPE`
TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q9 
       16.67       112.04       112.57        71.80       133.25        31.59 
TCGA-D3-A1QA TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB 
       90.90        43.43       103.10        23.77       115.53       168.00 
TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK 
       69.90        11.87        48.76       113.52        42.08        12.10 
TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 
       56.19        45.11       130.72        58.06        46.98        46.32 
TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MR 
      166.52        86.93        60.23        24.53         9.34       103.59 
TCGA-D3-A3MU TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N 
       39.75        43.69        40.14       131.90        18.38        10.03 
TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 
       15.06       135.75       166.19         7.43       125.19       151.53 
TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EC 
       54.67         3.65         6.41         3.25         9.90        66.25 
TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 
       36.03       117.21        20.38       176.55        35.93       107.34 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
       61.18        53.92        65.92        23.44        68.09        28.60 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EE-A17Y TCGA-EE-A17Z 
      215.44        15.68        35.01        52.01        27.22         8.65 
TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A20B TCGA-EE-A20F 
       94.98        33.73        14.70        26.89       109.64        78.87 
TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D 
      168.26        13.55        63.35        80.61        47.84        13.97 
TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29W 
       39.62        32.19        44.35        18.61        56.42       171.55 
TCGA-EE-A2A0 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GE TCGA-EE-A2GH 
       46.82        58.75        47.54        67.43       135.95       208.04 
TCGA-EE-A2GI TCGA-EE-A2GK TCGA-EE-A2GO TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT 
       48.72        54.74       101.95        14.30        55.59        44.88 
TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2ME TCGA-EE-A2MG 
       21.67       129.27        28.83        19.76       103.27       103.20 
TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2MP TCGA-EE-A2MQ 
       16.96       204.66        96.23       144.76       248.65        43.23 
TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AD 
      103.56       136.47        41.59       124.31       122.73         3.68 
TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 
       54.51        13.81        23.47       138.81       172.18       127.20 
TCGA-EE-A3J5 TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A197 
       36.95        27.35        33.40       101.79        31.40        13.94 
TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19E TCGA-ER-A19F 
       50.76        77.75        98.40        48.89        13.02        26.37 
TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19P 
      268.93       152.35         6.44       131.51        61.05       162.08 
TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A1A1 TCGA-ER-A2ND TCGA-ER-A2NF TCGA-ER-A2NG 
       50.89        37.25        79.99        23.34        16.37        31.27 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A44A TCGA-FS-A1YX 
      247.04        80.32        46.98        33.21       174.21        48.59 
TCGA-FS-A1YY TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZF 
      228.59        28.08         7.79       357.37        53.52        15.45 
TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZR 
        9.70        32.75        47.38        23.93       101.26        11.41 
TCGA-FS-A1ZS TCGA-FS-A1ZU TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4FB 
      148.80        26.56        77.82        66.67       174.84        26.73 
TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A4EO 
        0.20        22.92        47.54         0.16         2.40         7.23 
TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A26A 
       14.04       120.46       117.93        84.72        10.13        32.48 
TCGA-GN-A26D TCGA-QB-A6FS 
       39.58         6.67 

  NRAS MUTATED NRAS WILD-TYPE 
          2.60           0.16 
  NRAS MUTATED NRAS WILD-TYPE 
        314.56         357.37 
  NRAS MUTATED NRAS WILD-TYPE 
        47.540         48.655 
[1] "2.6 - 314.6 (47.5)" "0.2 - 357.4 (48.7)"
[1] "hr=" "1.2"
D1V3, continuous
                vv
clus             DISTANT METASTASIS PRIMARY TUMOR
  NRAS MUTATED                   15             1
  NRAS WILD-TYPE                 20             3
                vv
clus             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  NRAS MUTATED                                          19                  47
  NRAS WILD-TYPE                                        39                 123
D1V4, multiclass
                                           clus
vv                                          NRAS MUTATED NRAS WILD-TYPE
  DISTANT METASTASIS                                  15             20
  PRIMARY TUMOR                                        1              3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE           19             39
  REGIONAL LYMPH NODE                                 47            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             I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  NRAS MUTATED             3       3       5        5       11        5
  NRAS WILD-TYPE           7       3      17        5       13       12
                vv
clus             STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  NRAS MUTATED           5         5         2         4          4          7
  NRAS WILD-TYPE         5         9         7        27          9         15
                vv
clus             STAGE IIIC STAGE IV
  NRAS MUTATED           17        2
  NRAS WILD-TYPE         27       10
D1V5, multiclass
             clus
vv            NRAS MUTATED NRAS WILD-TYPE
  I OR II NOS            3              7
  STAGE 0                3              3
  STAGE I                5             17
  STAGE IA               5              5
  STAGE IB              11             13
  STAGE II               5             12
  STAGE IIA              5              5
  STAGE IIB              5              9
  STAGE IIC              2              7
  STAGE III              4             27
  STAGE IIIA             4              9
  STAGE IIIB             7             15
  STAGE IIIC            17             27
  STAGE IV               2             10
[1] 14  2
[1] 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      13 22 15 17
  NRAS WILD-TYPE    38 36 38 38
D1V6, multiclass
       clus
vv      NRAS MUTATED NRAS WILD-TYPE
  T0+T1           13             38
  T2              22             36
  T3              15             38
  T4              17             38
[1] 4 2
[1] TRUE
[1] "dimension 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   46  9  9 15
  NRAS WILD-TYPE 92 39 23 18
D1V7, multiclass
    clus
vv   NRAS MUTATED NRAS WILD-TYPE
  N0           46             92
  N1            9             39
  N2            9             23
  N3           15             18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              M0  M1 M1A M1B M1C
  NRAS MUTATED    76   1   0   1   0
  NRAS WILD-TYPE 164   3   2   1   5
D1V8, multiclass
     clus
vv    NRAS MUTATED NRAS WILD-TYPE
  M0            76            164
  M1             1              3
  M1A            0              2
  M1B            1              1
  M1C            0              5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V9, binary
                cls
clus              0  1
  NRAS MUTATED   35 22
  NRAS WILD-TYPE 67 45
[1] "tbl2"
                cls
clus             [,1] [,2]
  NRAS MUTATED     35   22
  NRAS WILD-TYPE   67   45
     clus
vv    NRAS MUTATED NRAS WILD-TYPE
  NO            35             67
  YES           22             45
[1] 2 2
[1] FALSE
D1V10, binary
                cls
clus               0   1
  NRAS MUTATED     9  73
  NRAS WILD-TYPE  24 162
[1] "tbl2"
                cls
clus             [,1] [,2]
  NRAS MUTATED      9   73
  NRAS WILD-TYPE   24  162
     clus
vv    NRAS MUTATED NRAS WILD-TYPE
  NO             9             24
  YES           73            162
[1] 2 2
[1] FALSE
D1V11, continuous
D1V12, binary
                cls
clus               0   1
  NRAS MUTATED    30  52
  NRAS WILD-TYPE  73 113
[1] "tbl2"
                cls
clus             [,1] [,2]
  NRAS MUTATED     30   52
  NRAS WILD-TYPE   73  113
        clus
vv       NRAS MUTATED NRAS WILD-TYPE
  FEMALE           30             73
  MALE             52            113
[1] 2 2
[1] FALSE
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  NRAS MUTATED       2                         0    80
  NRAS WILD-TYPE     1                         1   184
D1V13, multiclass
                           clus
vv                          NRAS MUTATED NRAS WILD-TYPE
  ASIAN                                2              1
  BLACK OR AFRICAN AMERICAN            0              1
  WHITE                               80            184
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V14, binary
                cls
clus               0   1
  NRAS MUTATED     1  80
  NRAS WILD-TYPE   2 181
[1] "tbl2"
                cls
clus             [,1] [,2]
  NRAS MUTATED      1   80
  NRAS WILD-TYPE    2  181
                        clus
vv                       NRAS MUTATED NRAS WILD-TYPE
  HISPANIC OR LATINO                1              2
  NOT HISPANIC OR LATINO           80            181
[1] 2 2
[1] FALSE

Clustering(2) Variable = TP53 MUTATION ANALYSIS
D2V1, survival
                sevent
clus2              0   1
  TP53 MUTATED    27  18
  TP53 WILD-TYPE 101 112
  TP53 MUTATED TP53 WILD-TYPE 
            45            213 
  TP53 MUTATED TP53 WILD-TYPE 
            18            112 
$`TP53 MUTATED`
TCGA-D3-A1QA TCGA-D3-A2JA TCGA-D3-A3C8 TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO 
       45.83        88.50        46.32        13.94        52.01        47.87 
TCGA-D3-A5GR TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1I5 
        1.55        11.31        13.22        48.79        35.80        44.52 
TCGA-EE-A181 TCGA-EE-A29E TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29V TCGA-EE-A29X 
        1.12        38.63         1.08        27.12         2.43         8.09 
TCGA-EE-A2A2 TCGA-EE-A2GC TCGA-EE-A2GJ TCGA-EE-A2GP TCGA-EE-A2GT TCGA-EE-A2MG 
       23.90        34.29        19.43         5.42        34.98        44.25 
TCGA-EE-A2MM TCGA-EE-A2MQ TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AD TCGA-EE-A3AE 
       56.02        21.60         5.56       124.31         3.68        30.15 
TCGA-EE-A3AG TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JD TCGA-EE-A3JI 
       15.95        21.60        21.60        16.14        27.35        33.60 
TCGA-ER-A199 TCGA-ER-A19E TCGA-ER-A3ET TCGA-FS-A1Z4 TCGA-FS-A1ZW TCGA-FS-A4F9 
        5.72        11.90         6.58        15.52        27.39        10.78 
TCGA-FW-A3R5 TCGA-GF-A6C8 TCGA-GN-A266 
        0.99        12.85        10.13 

$`TP53 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.47         8.52       111.09        32.42        70.16       110.79 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 
       28.08        22.55        81.24        10.29        85.32         8.38 
TCGA-D3-A2J9 TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JG 
       21.14        68.22        69.90        11.41        30.87         7.50 
TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP 
       36.16         6.31        92.42        56.19        64.44        45.11 
TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE 
      114.67        15.25        46.98        82.29        61.38        13.32 
TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV 
       24.00         6.31         9.34       103.59        26.37         5.39 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N 
       80.22        42.71        15.09        41.10        17.72         8.84 
TCGA-D3-A51R TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 
       20.48         6.97        23.11         4.01         2.89         9.90 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I7 
       51.12        10.03        39.19        13.68         9.99        36.69 
TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 
       25.15         4.93        22.36         6.64        19.36         7.00 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH 
       17.56        14.83        13.15         0.20         0.00         0.00 
TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A182 
       13.22        11.57        10.55         6.31         8.12         1.35 
TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F 
       12.20         5.13         4.31        36.07         4.34         5.13 
TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D 
        9.21         1.18         7.99         9.90        37.97        11.15 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R 
        8.55         4.41         9.50        12.03         8.09         8.84 
TCGA-EE-A29S TCGA-EE-A29W TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A5 TCGA-EE-A2A6 
        9.99         8.68        11.31        49.22         9.67         8.94 
TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GK 
       39.39        17.98        34.92        47.21        30.08        16.01 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GR TCGA-EE-A2GS 
       35.54        28.31        33.83        30.84         1.15        13.02 
TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC 
       36.33         8.84        98.27         2.70         6.18        47.51 
TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK 
        9.53        29.46         7.96        14.56        63.42       111.78 
TCGA-EE-A2ML TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT 
      111.91        25.08        26.99        29.65        27.16        23.05 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AF TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 
      122.73        25.84        13.81        12.72         3.22        22.92 
TCGA-EE-A3JA TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 
       22.22         0.46        13.94        31.40        18.61        12.95 
TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19F 
       38.40        76.41        25.18         3.78         3.52        11.11 
TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N 
      114.15        34.88         4.21        13.45        28.60        42.84 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
       34.68         9.57        36.07        17.72        78.44        11.80 
TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES 
        1.87         1.51        13.08        12.62        11.74         9.04 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW 
       22.49         1.71        18.41        85.74         4.90        64.47 
TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z7 TCGA-FS-A1ZA 
        3.45        11.01        23.80        14.24         7.33         7.30 
TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG 
        3.39        20.38         8.22        19.53        11.08         7.17 
TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ 
       30.87        12.92        12.89        47.38        52.08         8.65 
TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZY TCGA-FS-A1ZZ 
        8.81        49.15        40.64         8.68         0.82         5.23 
TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4FB TCGA-FS-A4FC 
       53.85         7.36        28.73        14.20         5.98         6.41 
TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
        2.27         0.20         0.13         0.16         0.43         9.90 
TCGA-GF-A4EO TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 
        7.23        24.85        31.33        84.72        16.24        15.42 
TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS 
       12.16        14.70         5.79 

  TP53 MUTATED TP53 WILD-TYPE 
          0.99           0.00 
  TP53 MUTATED TP53 WILD-TYPE 
        124.31         122.73 
  TP53 MUTATED TP53 WILD-TYPE 
         21.60          13.94 
[1] "1.0 - 124.3 (21.6)" "0.0 - 122.7 (13.9)"
[1] "hr=" "1.4"
D2V2, survival
                sevent
clus2              0   1
  TP53 MUTATED    27  18
  TP53 WILD-TYPE 105 113
  TP53 MUTATED TP53 WILD-TYPE 
            45            218 
  TP53 MUTATED TP53 WILD-TYPE 
            18            113 
$`TP53 MUTATED`
TCGA-D3-A1QA TCGA-D3-A2JA TCGA-D3-A3C8 TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO 
       90.90       115.53        46.32        15.06       135.75       137.92 
TCGA-D3-A5GR TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1I5 
      166.19        25.18        66.25        48.89        36.03       107.34 
TCGA-EE-A181 TCGA-EE-A29E TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29V TCGA-EE-A29X 
       33.73        39.62         2.60        44.35        25.87        17.92 
TCGA-EE-A2A2 TCGA-EE-A2GC TCGA-EE-A2GJ TCGA-EE-A2GP TCGA-EE-A2GT TCGA-EE-A2MG 
       24.43        67.43        89.33        13.91        44.88       103.20 
TCGA-EE-A2MM TCGA-EE-A2MQ TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AD TCGA-EE-A3AE 
      167.90        43.23        53.26       124.31         3.68        54.51 
TCGA-EE-A3AG TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JD TCGA-EE-A3JI 
       23.47        36.95        64.08        34.32        27.35       148.08 
TCGA-ER-A199 TCGA-ER-A19E TCGA-ER-A3ET TCGA-FS-A1Z4 TCGA-FS-A1ZW TCGA-FS-A4F9 
        9.17        13.02        80.32        28.08        49.48        12.43 
TCGA-FW-A3R5 TCGA-GF-A6C8 TCGA-GN-A266 
       22.92        14.04        10.13 

$`TP53 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.57        16.67       112.04       112.57        71.80       133.25 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 
       28.08        31.59        95.74        43.43       103.10        65.49 
TCGA-D3-A2J9 TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JG 
       23.77       168.00        69.90        11.87        48.76       113.52 
TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP 
       42.08        12.10       171.58        56.19        66.08        45.11 
TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE 
      130.72        58.06        46.98       166.52        86.93        60.23 
TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV 
       24.53        13.87         9.34       103.59        39.75        21.47 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N 
      161.85        43.69        40.14       131.90        18.38        10.03 
TCGA-D3-A51R TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW 
       51.68         7.43       125.19       151.53        54.67         3.65 
TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-DA-A1HY TCGA-DA-A1I0 
        6.41        11.34         3.25         9.90       117.21        20.38 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA 
      194.83       176.55        35.93        61.18        53.92        65.92 
TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 
       23.44        68.09        28.60        10.49       215.44        15.68 
TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN 
       13.87        10.16        45.11        35.01         3.55        52.01 
TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A182 TCGA-EE-A183 
       29.82        27.22         8.65        94.98        14.70        26.89 
TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H 
       68.15         4.96       109.64       151.27        78.87       168.26 
TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29G 
       13.55        63.35        80.61        47.84        13.97        72.07 
TCGA-EE-A29H TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S 
       32.19        18.61        56.42        37.35        14.47        55.92 
TCGA-EE-A29W TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB 
      171.55        46.82       102.90        39.29        58.75        47.54 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GK TCGA-EE-A2GL 
      314.56       135.95       208.04        48.72        54.74        79.66 
TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU 
       75.48        90.97       101.95        14.30        55.59        94.82 
TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD 
       21.67       129.27        28.83        19.76        61.51        47.28 
TCGA-EE-A2ME TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML 
      103.27        16.96       204.66        96.23       144.76       203.05 
TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AB 
       47.54       248.65       103.56       136.47        41.59       122.73 
TCGA-EE-A3AC TCGA-EE-A3AF TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3JA 
       25.84        13.81       138.81       172.18       127.20        53.19 
TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 
       33.40       101.79        31.40        35.44        13.94        50.76 
TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19G 
       77.75        98.40        48.89        12.59        26.37       268.93 
TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P 
      152.35         6.44       131.51        61.05        44.05       162.08 
TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
       50.89        37.25       148.18        79.99        43.82        23.34 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3EV 
       20.15        16.37        31.27        32.05       247.04        46.98 
TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX 
       33.21        92.98       174.21         4.90       216.92        48.59 
TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB 
      228.59       202.65        20.91         7.79        27.72        48.85 
TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH 
      357.37        53.52        40.27        15.45         9.70        32.75 
TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR 
       47.38        23.93       101.26        74.73       133.55        11.41 
TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 
      148.80        53.16        26.56        27.09        27.02        77.82 
TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD 
       66.67        28.73       174.84        26.73        49.45        77.88 
TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
        0.20        47.54         0.16         2.40         9.90         7.23 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
      120.46       117.93        84.72        64.44        62.79        32.48 
TCGA-GN-A26D TCGA-QB-A6FS 
       39.58         6.67 

  TP53 MUTATED TP53 WILD-TYPE 
          2.60           0.16 
  TP53 MUTATED TP53 WILD-TYPE 
        167.90         357.37 
  TP53 MUTATED TP53 WILD-TYPE 
         43.23          48.87 
[1] "2.6 - 167.9 (43.2)" "0.2 - 357.4 (48.9)"
[1] "hr=" "1"  
D2V3, continuous
                vv
clus             DISTANT METASTASIS PRIMARY TUMOR
  TP53 MUTATED                    3             2
  TP53 WILD-TYPE                 32             2
                vv
clus             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  TP53 MUTATED                                          11                  30
  TP53 WILD-TYPE                                        47                 140
D2V4, multiclass
                                           clus
vv                                          TP53 MUTATED TP53 WILD-TYPE
  DISTANT METASTASIS                                   3             32
  PRIMARY TUMOR                                        2              2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE           11             47
  REGIONAL LYMPH NODE                                 30            140
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  TP53 MUTATED             0       1       6        3        4        2
  TP53 WILD-TYPE          10       5      16        7       20       15
                vv
clus             STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  TP53 MUTATED           1         2         0         7          5          5
  TP53 WILD-TYPE         9        12         9        24          8         17
                vv
clus             STAGE IIIC STAGE IV
  TP53 MUTATED            8        1
  TP53 WILD-TYPE         36       11
D2V5, multiclass
             clus
vv            TP53 MUTATED TP53 WILD-TYPE
  I OR II NOS            0             10
  STAGE 0                1              5
  STAGE I                6             16
  STAGE IA               3              7
  STAGE IB               4             20
  STAGE II               2             15
  STAGE IIA              1              9
  STAGE IIB              2             12
  STAGE IIC              0              9
  STAGE III              7             24
  STAGE IIIA             5              8
  STAGE IIIB             5             17
  STAGE IIIC             8             36
  STAGE IV               1             11
[1] 14  2
[1] 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      12 10  9 10
  TP53 WILD-TYPE    39 48 44 45
D2V6, multiclass
       clus
vv      TP53 MUTATED TP53 WILD-TYPE
  T0+T1           12             39
  T2              10             48
  T3               9             44
  T4              10             45
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  TP53 MUTATED    19  15   5   5
  TP53 WILD-TYPE 119  33  27  28
D2V7, multiclass
    clus
vv   TP53 MUTATED TP53 WILD-TYPE
  N0           19            119
  N1           15             33
  N2            5             27
  N3            5             28
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              M0  M1 M1A M1B M1C
  TP53 MUTATED    44   0   0   0   1
  TP53 WILD-TYPE 196   4   2   2   4
D2V8, multiclass
     clus
vv    TP53 MUTATED TP53 WILD-TYPE
  M0            44            196
  M1             0              4
  M1A            0              2
  M1B            0              2
  M1C            1              4
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V9, binary
                cls
clus              0  1
  TP53 MUTATED   19 11
  TP53 WILD-TYPE 83 56
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED     19   11
  TP53 WILD-TYPE   83   56
     clus
vv    TP53 MUTATED TP53 WILD-TYPE
  NO            19             83
  YES           11             56
[1] 2 2
[1] FALSE
D2V10, binary
                cls
clus               0   1
  TP53 MUTATED     6  40
  TP53 WILD-TYPE  27 195
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED      6   40
  TP53 WILD-TYPE   27  195
     clus
vv    TP53 MUTATED TP53 WILD-TYPE
  NO             6             27
  YES           40            195
[1] 2 2
[1] FALSE
D2V11, continuous
D2V12, binary
                cls
clus               0   1
  TP53 MUTATED    18  28
  TP53 WILD-TYPE  85 137
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED     18   28
  TP53 WILD-TYPE   85  137
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  FEMALE           18             85
  MALE             28            137
[1] 2 2
[1] FALSE
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TP53 MUTATED       0                         0    46
  TP53 WILD-TYPE     3                         1   218
D2V13, multiclass
                           clus
vv                          TP53 MUTATED TP53 WILD-TYPE
  ASIAN                                0              3
  BLACK OR AFRICAN AMERICAN            0              1
  WHITE                               46            218
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V14, binary
                cls
clus               0   1
  TP53 MUTATED     0  46
  TP53 WILD-TYPE   3 215
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED      0   46
  TP53 WILD-TYPE    3  215
                        clus
vv                       TP53 MUTATED TP53 WILD-TYPE
  HISPANIC OR LATINO                0              3
  NOT HISPANIC OR LATINO           46            215
[1] 2 2
[1] FALSE

Clustering(3) Variable = CDKN2A MUTATION ANALYSIS
D3V1, survival
                  sevent
clus2                0   1
  CDKN2A MUTATED    20  17
  CDKN2A WILD-TYPE 108 113
  CDKN2A MUTATED CDKN2A WILD-TYPE 
              37              221 
  CDKN2A MUTATED CDKN2A WILD-TYPE 
              17              113 
$`CDKN2A MUTATED`
TCGA-D3-A1Q4 TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JK TCGA-D3-A3CB TCGA-D3-A3MV 
      111.09        11.41        30.87         6.31        82.29         5.39 
TCGA-D3-A51J TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D9-A3Z1 TCGA-D9-A6EC 
       41.10        52.01         1.55         6.97         4.01        13.22 
TCGA-DA-A1HV TCGA-DA-A1HY TCGA-EE-A181 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A29E 
       48.79        51.12         1.12         4.31        36.07        38.63 
TCGA-EE-A29V TCGA-EE-A2A6 TCGA-EE-A2GC TCGA-EE-A2GM TCGA-EE-A2GP TCGA-EE-A2M5 
        2.43         8.94        34.29        28.31         5.42         8.84 
TCGA-EE-A2MD TCGA-EE-A3AE TCGA-EE-A3AG TCGA-EE-A3J7 TCGA-EE-A3JD TCGA-ER-A19D 
        9.53        30.15        15.95        21.60        27.35         3.52 
TCGA-ER-A19L TCGA-ER-A19P TCGA-FS-A1YW TCGA-FS-A1ZQ TCGA-FS-A1ZW TCGA-GF-A4EO 
       13.45        34.68        64.47         8.65        27.39         7.23 
TCGA-GN-A26A 
       12.16 

$`CDKN2A WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       16.47         8.52        32.42        70.16       110.79        28.08 
TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 
       22.55        45.83        81.24        10.29        85.32         8.38 
TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JG TCGA-D3-A2JH 
       21.14        88.50        68.22        69.90         7.50        36.16 
TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 
       92.42        56.19        64.44        45.11       114.67        15.25 
TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML 
       46.98        46.32        61.38        13.32        24.00         6.31 
TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H 
        9.34       103.59        26.37        80.22        42.71        15.09 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GO TCGA-D3-A5GU 
       17.72         8.84        20.48        13.94        47.87        23.11 
TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-DA-A1HW TCGA-DA-A1I0 TCGA-DA-A1I1 
        2.89         9.90        11.31        35.80        10.03        39.19 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA 
       13.68         9.99        44.52        36.69        25.15         4.93 
TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 
       22.36         6.64        19.36         7.00        17.56        14.83 
TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EE-A17X 
       13.15         0.20         0.00         0.00        13.22        11.57 
TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 
       10.55         6.31         8.12         1.35        12.20         5.13 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B 
        4.34         5.13         9.21         1.18         7.99         9.90 
TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M 
       37.97        11.15         8.55         4.41         1.08        27.12 
TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29W 
        9.50        12.03         8.09         8.84         9.99         8.68 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2GB 
        8.09        11.31        49.22        23.90         9.67        39.39 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK 
       17.98        34.92        47.21        30.08        19.43        16.01 
TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT 
       35.54        33.83        30.84         1.15        13.02        34.98 
TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2ME 
       36.33        98.27         2.70         6.18        47.51        29.46 
TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML 
       44.25         7.96        14.56        63.42       111.78       111.91 
TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS 
       56.02        25.08        26.99        21.60        29.65        27.16 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD 
       23.05         5.56       124.31       122.73        25.84         3.68 
TCGA-EE-A3AF TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J8 
       13.81        12.72         3.22        22.92        21.60        16.14 
TCGA-EE-A3JA TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 
       22.22         0.46        13.94        33.60        31.40        18.61 
TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C 
       12.95        38.40         5.72        76.41        25.18         3.78 
TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19M 
       11.90        11.11       114.15        34.88         4.21        28.60 
TCGA-ER-A19N TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
       42.84         9.57        36.07        17.72        78.44        11.80 
TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES 
        1.87         1.51        13.08        12.62        11.74         9.04 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
        6.58        22.49         1.71        18.41        85.74         4.90 
TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 
        3.45        11.01        23.80        14.24        15.52         7.33 
TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF 
        7.30         3.39        20.38         8.22        19.53        11.08 
TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP 
        7.17        30.87        12.92        12.89        47.38        52.08 
TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZY TCGA-FS-A1ZZ 
        8.81        49.15        40.64         8.68         0.82         5.23 
TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB 
       53.85         7.36        28.73        14.20        10.78         5.98 
TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV 
        6.41         2.27         0.20         0.99         0.13         0.16 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        0.43         9.90        12.85        24.85        31.33        84.72 
TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26D TCGA-QB-A6FS 
       10.13        16.24        15.42        14.70         5.79 

  CDKN2A MUTATED CDKN2A WILD-TYPE 
            1.12             0.00 
  CDKN2A MUTATED CDKN2A WILD-TYPE 
          111.09           124.31 
  CDKN2A MUTATED CDKN2A WILD-TYPE 
           13.45            14.83 
[1] "1.1 - 111.1 (13.4)" "0.0 - 124.3 (14.8)"
[1] "hr=" "1.1"
D3V2, survival
                  sevent
clus2                0   1
  CDKN2A MUTATED    20  17
  CDKN2A WILD-TYPE 112 114
  CDKN2A MUTATED CDKN2A WILD-TYPE 
              37              226 
  CDKN2A MUTATED CDKN2A WILD-TYPE 
              17              114 
$`CDKN2A MUTATED`
TCGA-D3-A1Q4 TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JK TCGA-D3-A3CB TCGA-D3-A3MV 
      112.04        11.87        48.76        12.10       166.52        21.47 
TCGA-D3-A51J TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D9-A3Z1 TCGA-D9-A6EC 
      131.90       135.75       166.19         7.43        11.34        66.25 
TCGA-DA-A1HV TCGA-DA-A1HY TCGA-EE-A181 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A29E 
       48.89       117.21        33.73         4.96       109.64        39.62 
TCGA-EE-A29V TCGA-EE-A2A6 TCGA-EE-A2GC TCGA-EE-A2GM TCGA-EE-A2GP TCGA-EE-A2M5 
       25.87        58.75        67.43        75.48        13.91        21.67 
TCGA-EE-A2MD TCGA-EE-A3AE TCGA-EE-A3AG TCGA-EE-A3J7 TCGA-EE-A3JD TCGA-ER-A19D 
       47.28        54.51        23.47        64.08        27.35        12.59 
TCGA-ER-A19L TCGA-ER-A19P TCGA-FS-A1YW TCGA-FS-A1ZQ TCGA-FS-A1ZW TCGA-GF-A4EO 
      131.51       162.08       216.92       133.55        49.48         7.23 
TCGA-GN-A26A 
       32.48 

$`CDKN2A WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       16.57        16.67       112.57        71.80       133.25        28.08 
TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 
       31.59        90.90        95.74        43.43       103.10        65.49 
TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JG TCGA-D3-A2JH 
       23.77       115.53       168.00        69.90       113.52        42.08 
TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 
      171.58        56.19        66.08        45.11       130.72        58.06 
TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML 
       46.98        46.32        86.93        60.23        24.53        13.87 
TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H 
        9.34       103.59        39.75       161.85        43.69        40.14 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GO TCGA-D3-A5GU 
       18.38        10.03        51.68        15.06       137.92       125.19 
TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z3 TCGA-D9-A6E9 
      151.53        54.67         3.65         6.41         3.25         9.90 
TCGA-D9-A6EA TCGA-DA-A1HW TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 
       25.18        36.03        20.38       194.83       176.55        35.93 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC 
      107.34        61.18        53.92        65.92        23.44        68.09 
TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R 
       28.60        10.49       215.44        15.68        13.87        10.16 
TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y 
       45.11        35.01         3.55        52.01        29.82        27.22 
TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A20C 
        8.65        94.98        14.70        26.89        68.15       151.27 
TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C 
       78.87       168.26        13.55        63.35        80.61        47.84 
TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N 
       13.97        72.07        32.19         2.60        44.35        18.61 
TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29W TCGA-EE-A29X 
       56.42        37.35        14.47        55.92       171.55        17.92 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2GB TCGA-EE-A2GD 
       46.82       102.90        24.43        39.29        47.54       314.56 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
      135.95       208.04        48.72        89.33        54.74        79.66 
TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU 
       90.97       101.95        14.30        55.59        44.88        94.82 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2ME TCGA-EE-A2MG 
      129.27        28.83        19.76        61.51       103.27       103.20 
TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM 
       16.96       204.66        96.23       144.76       203.05       167.90 
TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT 
       47.54       248.65        43.23       103.56       136.47        41.59 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AF 
       53.26       124.31       122.73        25.84         3.68        13.81 
TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J8 TCGA-EE-A3JA 
      138.81       172.18       127.20        36.95        34.32        53.19 
TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 
       33.40       101.79       148.08        31.40        35.44        13.94 
TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19E 
       50.76         9.17        77.75        98.40        48.89        13.02 
TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19M TCGA-ER-A19N 
       26.37       268.93       152.35         6.44        61.05        44.05 
TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
       50.89        37.25       148.18        79.99        43.82        23.34 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET 
       20.15        16.37        31.27        32.05       247.04        80.32 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YX 
       46.98        33.21        92.98       174.21         4.90        48.59 
TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA 
      228.59       202.65        20.91        28.08         7.79        27.72 
TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG 
       48.85       357.37        53.52        40.27        15.45         9.70 
TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZR 
       32.75        47.38        23.93       101.26        74.73        11.41 
TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 
      148.80        53.16        26.56        27.09        27.02        77.82 
TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC 
       66.67        28.73       174.84        12.43        26.73        49.45 
TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY 
       77.88         0.20        22.92        47.54         0.16         2.40 
TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 
        9.90        14.04       120.46       117.93        84.72        10.13 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26D TCGA-QB-A6FS 
       64.44        62.79        39.58         6.67 

  CDKN2A MUTATED CDKN2A WILD-TYPE 
            4.96             0.16 
  CDKN2A MUTATED CDKN2A WILD-TYPE 
          216.92           357.37 
  CDKN2A MUTATED CDKN2A WILD-TYPE 
           48.89            47.69 
[1] "5.0 - 216.9 (48.9)" "0.2 - 357.4 (47.7)"
[1] "hr=" "1"  
D3V3, continuous
                  vv
clus               DISTANT METASTASIS PRIMARY TUMOR
  CDKN2A MUTATED                    4             1
  CDKN2A WILD-TYPE                 31             3
                  vv
clus               REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  CDKN2A MUTATED                                           9
  CDKN2A WILD-TYPE                                        49
                  vv
clus               REGIONAL LYMPH NODE
  CDKN2A MUTATED                    24
  CDKN2A WILD-TYPE                 146
D3V4, multiclass
                                           clus
vv                                          CDKN2A MUTATED CDKN2A WILD-TYPE
  DISTANT METASTASIS                                     4               31
  PRIMARY TUMOR                                          1                3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE              9               49
  REGIONAL LYMPH NODE                                   24              146
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  CDKN2A MUTATED             3       0       3        3        2        3
  CDKN2A WILD-TYPE           7       6      19        7       22       14
                  vv
clus               STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  CDKN2A MUTATED           0         1         1         4          2
  CDKN2A WILD-TYPE        10        13         8        27         11
                  vv
clus               STAGE IIIB STAGE IIIC STAGE IV
  CDKN2A MUTATED            5          7        1
  CDKN2A WILD-TYPE         17         37       11
D3V5, multiclass
             clus
vv            CDKN2A MUTATED CDKN2A WILD-TYPE
  I OR II NOS              3                7
  STAGE 0                  0                6
  STAGE I                  3               19
  STAGE IA                 3                7
  STAGE IB                 2               22
  STAGE II                 3               14
  STAGE IIA                0               10
  STAGE IIB                1               13
  STAGE IIC                1                8
  STAGE III                4               27
  STAGE IIIA               2               11
  STAGE IIIB               5               17
  STAGE IIIC               7               37
  STAGE IV                 1               11
[1] 14  2
[1] 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      10 10  8  5
  CDKN2A WILD-TYPE    41 48 45 50
D3V6, multiclass
       clus
vv      CDKN2A MUTATED CDKN2A WILD-TYPE
  T0+T1             10               41
  T2                10               48
  T3                 8               45
  T4                 5               50
[1] 4 2
[1] TRUE
[1] "dimension 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    17  11   5   3
  CDKN2A WILD-TYPE 121  37  27  30
D3V7, multiclass
    clus
vv   CDKN2A MUTATED CDKN2A WILD-TYPE
  N0             17              121
  N1             11               37
  N2              5               27
  N3              3               30
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                M0  M1 M1A M1B M1C
  CDKN2A MUTATED    35   0   0   0   1
  CDKN2A WILD-TYPE 205   4   2   2   4
D3V8, multiclass
     clus
vv    CDKN2A MUTATED CDKN2A WILD-TYPE
  M0              35              205
  M1               0                4
  M1A              0                2
  M1B              0                2
  M1C              1                4
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V9, binary
                  cls
clus                0  1
  CDKN2A MUTATED   10 13
  CDKN2A WILD-TYPE 92 54
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CDKN2A MUTATED     10   13
  CDKN2A WILD-TYPE   92   54
     clus
vv    CDKN2A MUTATED CDKN2A WILD-TYPE
  NO              10               92
  YES             13               54
[1] 2 2
[1] FALSE
D3V10, binary
                  cls
clus                 0   1
  CDKN2A MUTATED     5  33
  CDKN2A WILD-TYPE  28 202
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CDKN2A MUTATED      5   33
  CDKN2A WILD-TYPE   28  202
     clus
vv    CDKN2A MUTATED CDKN2A WILD-TYPE
  NO               5               28
  YES             33              202
[1] 2 2
[1] FALSE
D3V11, continuous
D3V12, binary
                  cls
clus                 0   1
  CDKN2A MUTATED    16  22
  CDKN2A WILD-TYPE  87 143
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CDKN2A MUTATED     16   22
  CDKN2A WILD-TYPE   87  143
        clus
vv       CDKN2A MUTATED CDKN2A WILD-TYPE
  FEMALE             16               87
  MALE               22              143
[1] 2 2
[1] FALSE
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CDKN2A MUTATED       0                         0    38
  CDKN2A WILD-TYPE     3                         1   226
D3V13, multiclass
                           clus
vv                          CDKN2A MUTATED CDKN2A WILD-TYPE
  ASIAN                                  0                3
  BLACK OR AFRICAN AMERICAN              0                1
  WHITE                                 38              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"
D3V14, binary
                  cls
clus                 0   1
  CDKN2A MUTATED     0  38
  CDKN2A WILD-TYPE   3 223
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CDKN2A MUTATED      0   38
  CDKN2A WILD-TYPE    3  223
                        clus
vv                       CDKN2A MUTATED CDKN2A WILD-TYPE
  HISPANIC OR LATINO                  0                3
  NOT HISPANIC OR LATINO             38              223
[1] 2 2
[1] FALSE

Clustering(4) Variable = RPS27 MUTATION ANALYSIS
D4V1, survival
                 sevent
clus2               0   1
  RPS27 MUTATED    13   8
  RPS27 WILD-TYPE 115 122
  RPS27 MUTATED RPS27 WILD-TYPE 
             21             237 
  RPS27 MUTATED RPS27 WILD-TYPE 
              8             122 
$`RPS27 MUTATED`
TCGA-D3-A1QB TCGA-D3-A3MR TCGA-D9-A6EC TCGA-DA-A1HV TCGA-EE-A20C TCGA-EE-A20F 
       81.24       103.59        13.22        48.79         4.34         5.13 
TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29R TCGA-EE-A2A2 TCGA-EE-A2GO TCGA-EE-A2GR 
       38.63         8.55         8.84        23.90        30.84         1.15 
TCGA-EE-A2MJ TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3J3 TCGA-EE-A3JA TCGA-ER-A193 
       63.42       122.73        25.84         3.22        22.22        31.40 
TCGA-FS-A1ZF TCGA-FS-A1ZK TCGA-FW-A3TU 
       11.08        12.89         0.13 

$`RPS27 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.47         8.52       111.09        32.42        70.16       110.79 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 
       28.08        22.55        45.83        10.29        85.32         8.38 
TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF 
       21.14        88.50        68.22        69.90        11.41        30.87 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO 
        7.50        36.16         6.31        92.42        56.19        64.44 
TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB 
       45.11       114.67        15.25        46.98        46.32        82.29 
TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MU 
       61.38        13.32        24.00         6.31         9.34        26.37 
TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K 
        5.39        80.22        42.71        15.09        41.10        17.72 
TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR 
        8.84        20.48        13.94        52.01        47.87         1.55 
TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA 
        6.97        23.11         4.01         2.89         9.90        11.31 
TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 
       35.80        51.12        10.03        39.19        13.68         9.99 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC 
       44.52        36.69        25.15         4.93        22.36         6.64 
TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R 
       19.36         7.00        17.56        14.83        13.15         0.20 
TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z 
        0.00         0.00        13.22        11.57        10.55         6.31 
TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 
        8.12         1.12         1.35        12.20         5.13         4.31 
TCGA-EE-A20B TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C 
       36.07         9.21         1.18         7.99         9.90        37.97 
TCGA-EE-A29D TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P 
       11.15         4.41         1.08        27.12         9.50        12.03 
TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 
        8.09         9.99         2.43         8.68         8.09        11.31 
TCGA-EE-A2A1 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD 
       49.22         9.67         8.94        39.39        34.29        17.98 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
       34.92        47.21        30.08        19.43        16.01        35.54 
TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU 
       28.31        33.83         5.42        13.02        34.98        36.33 
TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD 
        8.84        98.27         2.70         6.18        47.51         9.53 
TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2ML 
       29.46        44.25         7.96        14.56       111.78       111.91 
TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS 
       56.02        25.08        26.99        21.60        29.65        27.16 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF 
       23.05         5.56       124.31         3.68        30.15        13.81 
TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 
       15.95        12.72        22.92        21.60        21.60        16.14 
TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 
       27.35         0.46        13.94        33.60        18.61        12.95 
TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D 
       38.40         5.72        76.41        25.18         3.78         3.52 
TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L 
       11.90        11.11       114.15        34.88         4.21        13.45 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W 
       28.60        42.84        34.68         9.57        36.07        17.72 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG 
       78.44        11.80         1.87         1.51        13.08        12.62 
TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN 
       11.74         9.04         6.58        22.49         1.71        18.41 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 
       85.74         4.90        64.47         3.45        11.01        23.80 
TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC 
       14.24        15.52         7.33         7.30         3.39        20.38 
TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZM 
        8.22        19.53         7.17        30.87        12.92        47.38 
TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU 
       52.08         8.65         8.81        49.15        40.64         8.68 
TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 
       27.39         0.82         5.23        53.85         7.36        28.73 
TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 
       14.20        10.78         5.98         6.41         2.27         0.20 
TCGA-FW-A3R5 TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 
        0.99         0.16         0.43         9.90         7.23        12.85 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 
       24.85        31.33        84.72        10.13        16.24        15.42 
TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS 
       12.16        14.70         5.79 

  RPS27 MUTATED RPS27 WILD-TYPE 
           0.13            0.00 
  RPS27 MUTATED RPS27 WILD-TYPE 
         122.73          124.31 
  RPS27 MUTATED RPS27 WILD-TYPE 
          22.22           14.70 
[1] "0.1 - 122.7 (22.2)" "0.0 - 124.3 (14.7)"
[1] "hr=" "1.5"
D4V2, survival
                 sevent
clus2               0   1
  RPS27 MUTATED    13   8
  RPS27 WILD-TYPE 119 123
  RPS27 MUTATED RPS27 WILD-TYPE 
             21             242 
  RPS27 MUTATED RPS27 WILD-TYPE 
              8             123 
$`RPS27 MUTATED`
TCGA-D3-A1QB TCGA-D3-A3MR TCGA-D9-A6EC TCGA-DA-A1HV TCGA-EE-A20C TCGA-EE-A20F 
       95.74       103.59        66.25        48.89       151.27        78.87 
TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29R TCGA-EE-A2A2 TCGA-EE-A2GO TCGA-EE-A2GR 
       39.62        72.07        14.47        24.43       101.95        14.30 
TCGA-EE-A2MJ TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3J3 TCGA-EE-A3JA TCGA-ER-A193 
       96.23       122.73        25.84       172.18        53.19        31.40 
TCGA-FS-A1ZF TCGA-FS-A1ZK TCGA-FW-A3TU 
       15.45        23.93        47.54 

$`RPS27 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.57        16.67       112.04       112.57        71.80       133.25 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 
       28.08        31.59        90.90        43.43       103.10        65.49 
TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF 
       23.77       115.53       168.00        69.90        11.87        48.76 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO 
      113.52        42.08        12.10       171.58        56.19        66.08 
TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB 
       45.11       130.72        58.06        46.98        46.32       166.52 
TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MU 
       86.93        60.23        24.53        13.87         9.34        39.75 
TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K 
       21.47       161.85        43.69        40.14       131.90        18.38 
TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR 
       10.03        51.68        15.06       135.75       137.92       166.19 
TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX 
        7.43       125.19       151.53        54.67         3.65         6.41 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-DA-A1HW TCGA-DA-A1HY 
       11.34         3.25         9.90        25.18        36.03       117.21 
TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 
       20.38       194.83       176.55        35.93       107.34        61.18 
TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 
       53.92        65.92        23.44        68.09        28.60        10.49 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH 
      215.44        15.68        13.87        10.16        45.11        35.01 
TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 
        3.55        52.01        29.82        27.22         8.65        94.98 
TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B 
       33.73        14.70        26.89        68.15         4.96       109.64 
TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D 
      168.26        13.55        63.35        80.61        47.84        13.97 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
       32.19         2.60        44.35        18.61        56.42        37.35 
TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 
       55.92        25.87       171.55        17.92        46.82       102.90 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE 
       39.29        58.75        47.54        67.43       314.56       135.95 
TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM 
      208.04        48.72        89.33        54.74        79.66        75.48 
TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 
       90.97        13.91        55.59        44.88        94.82        21.67 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME 
      129.27        28.83        19.76        61.51        47.28       103.27 
TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM 
      103.20        16.96       204.66       144.76       203.05       167.90 
TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT 
       47.54       248.65        43.23       103.56       136.47        41.59 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG 
       53.26       124.31         3.68        54.51        13.81        23.47 
TCGA-EE-A3AH TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JD 
      138.81       127.20        36.95        64.08        34.32        27.35 
TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 
       33.40       101.79       148.08        35.44        13.94        50.76 
TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E 
        9.17        77.75        98.40        48.89        12.59        13.02 
TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M 
       26.37       268.93       152.35         6.44       131.51        61.05 
TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 
       44.05       162.08        50.89        37.25       148.18        79.99 
TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH 
       43.82        23.34        20.15        16.37        31.27        32.05 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A 
      247.04        80.32        46.98        33.21        92.98       174.21 
TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
        4.90       216.92        48.59       228.59       202.65        20.91 
TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD 
       28.08         7.79        27.72        48.85       357.37        53.52 
TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZP 
       40.27         9.70        32.75        47.38       101.26        74.73 
TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW 
      133.55        11.41       148.80        53.16        26.56        49.48 
TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 
       27.09        27.02        77.82        66.67        28.73       174.84 
TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 
       12.43        26.73        49.45        77.88         0.20        22.92 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 
        0.16         2.40         9.90         7.23        14.04       120.46 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
      117.93        84.72        10.13        64.44        62.79        32.48 
TCGA-GN-A26D TCGA-QB-A6FS 
       39.58         6.67 

  RPS27 MUTATED RPS27 WILD-TYPE 
          14.30            0.16 
  RPS27 MUTATED RPS27 WILD-TYPE 
         172.18          357.37 
  RPS27 MUTATED RPS27 WILD-TYPE 
          53.19           47.69 
[1] "14.3 - 172.2 (53.2)" "0.2 - 357.4 (47.7)" 
[1] "hr=" "1.3"
D4V3, continuous
                 vv
clus              DISTANT METASTASIS PRIMARY TUMOR
  RPS27 MUTATED                    4             1
  RPS27 WILD-TYPE                 31             3
                 vv
clus              REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  RPS27 MUTATED                                           5                  11
  RPS27 WILD-TYPE                                        53                 159
D4V4, multiclass
                                           clus
vv                                          RPS27 MUTATED RPS27 WILD-TYPE
  DISTANT METASTASIS                                    4              31
  PRIMARY TUMOR                                         1               3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE             5              53
  REGIONAL LYMPH NODE                                  11             159
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  RPS27 MUTATED             0       1       1        0        2        3
  RPS27 WILD-TYPE          10       5      21       10       22       14
                 vv
clus              STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  RPS27 MUTATED           0         1         1         5          2          2
  RPS27 WILD-TYPE        10        13         8        26         11         20
                 vv
clus              STAGE IIIC STAGE IV
  RPS27 MUTATED            2        0
  RPS27 WILD-TYPE         42       12
D4V5, multiclass
             clus
vv            RPS27 MUTATED RPS27 WILD-TYPE
  I OR II NOS             0              10
  STAGE 0                 1               5
  STAGE I                 1              21
  STAGE IA                0              10
  STAGE IB                2              22
  STAGE II                3              14
  STAGE IIA               0              10
  STAGE IIB               1              13
  STAGE IIC               1               8
  STAGE III               5              26
  STAGE IIIA              2              11
  STAGE IIIB              2              20
  STAGE IIIC              2              42
  STAGE IV                0              12
[1] 14  2
[1] 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
  RPS27 MUTATED       6  2  5  6
  RPS27 WILD-TYPE    45 56 48 49
D4V6, multiclass
       clus
vv      RPS27 MUTATED RPS27 WILD-TYPE
  T0+T1             6              45
  T2                2              56
  T3                5              48
  T4                6              49
[1] 4 2
[1] TRUE
[1] "dimension 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
  RPS27 MUTATED    10   5   5   0
  RPS27 WILD-TYPE 128  43  27  33
D4V7, multiclass
    clus
vv   RPS27 MUTATED RPS27 WILD-TYPE
  N0            10             128
  N1             5              43
  N2             5              27
  N3             0              33
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               M0  M1 M1A M1B M1C
  RPS27 MUTATED    20   0   0   0   0
  RPS27 WILD-TYPE 220   4   2   2   5
D4V8, multiclass
     clus
vv    RPS27 MUTATED RPS27 WILD-TYPE
  M0             20             220
  M1              0               4
  M1A             0               2
  M1B             0               2
  M1C             0               5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V9, binary
                 cls
clus               0  1
  RPS27 MUTATED    7  3
  RPS27 WILD-TYPE 95 64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RPS27 MUTATED      7    3
  RPS27 WILD-TYPE   95   64
     clus
vv    RPS27 MUTATED RPS27 WILD-TYPE
  NO              7              95
  YES             3              64
[1] 2 2
[1] FALSE
D4V10, binary
                 cls
clus                0   1
  RPS27 MUTATED     5  16
  RPS27 WILD-TYPE  28 219
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RPS27 MUTATED      5   16
  RPS27 WILD-TYPE   28  219
     clus
vv    RPS27 MUTATED RPS27 WILD-TYPE
  NO              5              28
  YES            16             219
[1] 2 2
[1] FALSE
D4V11, continuous
D4V12, binary
                 cls
clus                0   1
  RPS27 MUTATED     7  14
  RPS27 WILD-TYPE  96 151
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RPS27 MUTATED      7   14
  RPS27 WILD-TYPE   96  151
        clus
vv       RPS27 MUTATED RPS27 WILD-TYPE
  FEMALE             7              96
  MALE              14             151
[1] 2 2
[1] FALSE
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RPS27 MUTATED       0                         0    21
  RPS27 WILD-TYPE     3                         1   243
D4V13, multiclass
                           clus
vv                          RPS27 MUTATED RPS27 WILD-TYPE
  ASIAN                                 0               3
  BLACK OR AFRICAN AMERICAN             0               1
  WHITE                                21             243
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V14, binary
                 cls
clus                0   1
  RPS27 MUTATED     0  21
  RPS27 WILD-TYPE   3 240
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RPS27 MUTATED      0   21
  RPS27 WILD-TYPE    3  240
                        clus
vv                       RPS27 MUTATED RPS27 WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO            21             240
[1] 2 2
[1] FALSE

Clustering(5) Variable = MRPS31 MUTATION ANALYSIS
D5V1, survival
                  sevent
clus2                0   1
  MRPS31 MUTATED     9  10
  MRPS31 WILD-TYPE 119 120
  MRPS31 MUTATED MRPS31 WILD-TYPE 
              19              239 
  MRPS31 MUTATED MRPS31 WILD-TYPE 
              10              120 
$`MRPS31 MUTATED`
TCGA-D9-A6EC TCGA-DA-A1I0 TCGA-DA-A1I7 TCGA-EE-A20H TCGA-EE-A29D TCGA-EE-A29L 
       13.22        10.03        36.69         9.21        11.15         1.08 
TCGA-EE-A29V TCGA-EE-A2GC TCGA-EE-A2GJ TCGA-EE-A2MI TCGA-EE-A2MM TCGA-EE-A2MQ 
        2.43        34.29        19.43        14.56        56.02        21.60 
TCGA-EE-A3JI TCGA-FS-A1Z3 TCGA-FS-A1ZP TCGA-FS-A1ZT TCGA-FS-A4F9 TCGA-FW-A3R5 
       33.60        14.24        52.08        40.64        10.78         0.99 
TCGA-FW-A3TU 
        0.13 

$`MRPS31 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.47         8.52       111.09        32.42        70.16       110.79 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       28.08        22.55        45.83        81.24        10.29        85.32 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
        8.38        21.14        88.50        68.22        69.90        11.41 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       30.87         7.50        36.16         6.31        92.42        56.19 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 
       64.44        45.11       114.67        15.25        46.98        46.32 
TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO 
       82.29        61.38        13.32        24.00         6.31         9.34 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H 
      103.59        26.37         5.39        80.22        42.71        15.09 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN 
       41.10        17.72         8.84        20.48        13.94        52.01 
TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 
       47.87         1.55         6.97        23.11         4.01         2.89 
TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I1 
        9.90        11.31        48.79        35.80        51.12        39.19 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB 
       13.68         9.99        44.52        25.15         4.93        22.36 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q 
        6.64        19.36         7.00        17.56        14.83        13.15 
TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y 
        0.20         0.00         0.00        13.22        11.57        10.55 
TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 
        6.31         8.12         1.12         1.35        12.20         5.13 
TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29A 
        4.31        36.07         4.34         5.13         1.18         7.99 
TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M 
        9.90        37.97        38.63         8.55         4.41        27.12 
TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29W 
        9.50        12.03         8.09         8.84         9.99         8.68 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 
        8.09        11.31        49.22        23.90         9.67         8.94 
TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GK 
       39.39        17.98        34.92        47.21        30.08        16.01 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR 
       35.54        28.31        33.83        30.84         5.42         1.15 
TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 
       13.02        34.98        36.33         8.84        98.27         2.70 
TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH 
        6.18        47.51         9.53        29.46        44.25         7.96 
TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MR 
       63.42       111.78       111.91        25.08        26.99        29.65 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC 
       27.16        23.05         5.56       124.31       122.73        25.84 
TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 
        3.68        30.15        13.81        15.95        12.72         3.22 
TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JD 
       22.92        21.60        21.60        16.14        22.22        27.35 
TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 
        0.46        13.94        31.40        18.61        12.95        38.40 
TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E 
        5.72        76.41        25.18         3.78         3.52        11.90 
TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M 
       11.11       114.15        34.88         4.21        13.45        28.60 
TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 
       42.84        34.68         9.57        36.07        17.72        78.44 
TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH 
       11.80         1.87         1.51        13.08        12.62        11.74 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A 
        9.04         6.58        22.49         1.71        18.41        85.74 
TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z4 
        4.90        64.47         3.45        11.01        23.80        15.52 
TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE 
        7.33         7.30         3.39        20.38         8.22        19.53 
TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM 
       11.08         7.17        30.87        12.92        12.89        47.38 
TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY 
        8.65         8.81        49.15         8.68        27.39         0.82 
TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4FB 
        5.23        53.85         7.36        28.73        14.20         5.98 
TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
        6.41         2.27         0.20         0.16         0.43         9.90 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 
        7.23        12.85        24.85        31.33        84.72        10.13 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS 
       16.24        15.42        12.16        14.70         5.79 

  MRPS31 MUTATED MRPS31 WILD-TYPE 
            0.13             0.00 
  MRPS31 MUTATED MRPS31 WILD-TYPE 
           56.02           124.31 
  MRPS31 MUTATED MRPS31 WILD-TYPE 
           14.24            15.09 
[1] "0.1 - 56.0 (14.2)"  "0.0 - 124.3 (15.1)"
[1] "hr=" "1.2"
D5V2, survival
                  sevent
clus2                0   1
  MRPS31 MUTATED     9  10
  MRPS31 WILD-TYPE 123 121
  MRPS31 MUTATED MRPS31 WILD-TYPE 
              19              244 
  MRPS31 MUTATED MRPS31 WILD-TYPE 
              10              121 
$`MRPS31 MUTATED`
TCGA-D9-A6EC TCGA-DA-A1I0 TCGA-DA-A1I7 TCGA-EE-A20H TCGA-EE-A29D TCGA-EE-A29L 
       66.25        20.38        61.18       168.26        13.97         2.60 
TCGA-EE-A29V TCGA-EE-A2GC TCGA-EE-A2GJ TCGA-EE-A2MI TCGA-EE-A2MM TCGA-EE-A2MQ 
       25.87        67.43        89.33       204.66       167.90        43.23 
TCGA-EE-A3JI TCGA-FS-A1Z3 TCGA-FS-A1ZP TCGA-FS-A1ZT TCGA-FS-A4F9 TCGA-FW-A3R5 
      148.08        20.91        74.73        53.16        12.43        22.92 
TCGA-FW-A3TU 
       47.54 

$`MRPS31 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.57        16.67       112.04       112.57        71.80       133.25 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       28.08        31.59        90.90        95.74        43.43       103.10 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
       65.49        23.77       115.53       168.00        69.90        11.87 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       48.76       113.52        42.08        12.10       171.58        56.19 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 
       66.08        45.11       130.72        58.06        46.98        46.32 
TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO 
      166.52        86.93        60.23        24.53        13.87         9.34 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H 
      103.59        39.75        21.47       161.85        43.69        40.14 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN 
      131.90        18.38        10.03        51.68        15.06       135.75 
TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 
      137.92       166.19         7.43       125.19       151.53        54.67 
TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA 
        3.65         6.41        11.34         3.25         9.90        25.18 
TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 
       48.89        36.03       117.21       194.83       176.55        35.93 
TCGA-DA-A1I5 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
      107.34        53.92        65.92        23.44        68.09        28.60 
TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG 
       10.49       215.44        15.68        13.87        10.16        45.11 
TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z 
       35.01         3.55        52.01        29.82        27.22         8.65 
TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 
       94.98        33.73        14.70        26.89        68.15         4.96 
TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B 
      109.64       151.27        78.87        13.55        63.35        80.61 
TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29N 
       47.84        39.62        72.07        32.19        44.35        18.61 
TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29W TCGA-EE-A29X 
       56.42        37.35        14.47        55.92       171.55        17.92 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB 
       46.82       102.90        24.43        39.29        58.75        47.54 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GK TCGA-EE-A2GL 
      314.56       135.95       208.04        48.72        54.74        79.66 
TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS 
       75.48        90.97       101.95        13.91        14.30        55.59 
TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 
       44.88        94.82        21.67       129.27        28.83        19.76 
TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MJ 
       61.51        47.28       103.27       103.20        16.96        96.23 
TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MR TCGA-EE-A2MS 
      144.76       203.05        47.54       248.65       103.56       136.47 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD 
       41.59        53.26       124.31       122.73        25.84         3.68 
TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 
       54.51        13.81        23.47       138.81       172.18       127.20 
TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE 
       36.95        64.08        34.32        53.19        27.35        33.40 
TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 
      101.79        31.40        35.44        13.94        50.76         9.17 
TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F 
       77.75        98.40        48.89        12.59        13.02        26.37 
TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N 
      268.93       152.35         6.44       131.51        61.05        44.05 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
      162.08        50.89        37.25       148.18        79.99        43.82 
TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES 
       23.34        20.15        16.37        31.27        32.05       247.04 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
       80.32        46.98        33.21        92.98       174.21         4.90 
TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1Z7 
      216.92        48.59       228.59       202.65        28.08         7.79 
TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF 
       27.72        48.85       357.37        53.52        40.27        15.45 
TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZQ 
        9.70        32.75        47.38        23.93       101.26       133.55 
TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ 
       11.41       148.80        26.56        49.48        27.09        27.02 
TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4FB TCGA-FS-A4FC 
       77.82        66.67        28.73       174.84        26.73        49.45 
TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
       77.88         0.20         0.16         2.40         9.90         7.23 
TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 
       14.04       120.46       117.93        84.72        10.13        64.44 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS 
       62.79        32.48        39.58         6.67 

  MRPS31 MUTATED MRPS31 WILD-TYPE 
            2.60             0.16 
  MRPS31 MUTATED MRPS31 WILD-TYPE 
          204.66           357.37 
  MRPS31 MUTATED MRPS31 WILD-TYPE 
          53.160           48.215 
[1] "2.6 - 204.7 (53.2)" "0.2 - 357.4 (48.2)"
[1] "hr=" "1"  
D5V3, continuous
                  vv
clus               DISTANT METASTASIS PRIMARY TUMOR
  MRPS31 MUTATED                    5             1
  MRPS31 WILD-TYPE                 30             3
                  vv
clus               REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  MRPS31 MUTATED                                           2
  MRPS31 WILD-TYPE                                        56
                  vv
clus               REGIONAL LYMPH NODE
  MRPS31 MUTATED                    11
  MRPS31 WILD-TYPE                 159
D5V4, multiclass
                                           clus
vv                                          MRPS31 MUTATED MRPS31 WILD-TYPE
  DISTANT METASTASIS                                     5               30
  PRIMARY TUMOR                                          1                3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE              2               56
  REGIONAL LYMPH NODE                                   11              159
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  MRPS31 MUTATED             0       0       3        1        0        1
  MRPS31 WILD-TYPE          10       6      19        9       24       16
                  vv
clus               STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  MRPS31 MUTATED           0         2         0         2          2
  MRPS31 WILD-TYPE        10        12         9        29         11
                  vv
clus               STAGE IIIB STAGE IIIC STAGE IV
  MRPS31 MUTATED            1          4        2
  MRPS31 WILD-TYPE         21         40       10
D5V5, multiclass
             clus
vv            MRPS31 MUTATED MRPS31 WILD-TYPE
  I OR II NOS              0               10
  STAGE 0                  0                6
  STAGE I                  3               19
  STAGE IA                 1                9
  STAGE IB                 0               24
  STAGE II                 1               16
  STAGE IIA                0               10
  STAGE IIB                2               12
  STAGE IIC                0                9
  STAGE III                2               29
  STAGE IIIA               2               11
  STAGE IIIB               1               21
  STAGE IIIC               4               40
  STAGE IV                 2               10
[1] 14  2
[1] 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
  MRPS31 MUTATED       2  4  6  4
  MRPS31 WILD-TYPE    49 54 47 51
D5V6, multiclass
       clus
vv      MRPS31 MUTATED MRPS31 WILD-TYPE
  T0+T1              2               49
  T2                 4               54
  T3                 6               47
  T4                 4               51
[1] 4 2
[1] TRUE
[1] "dimension 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
  MRPS31 MUTATED     8   4   3   3
  MRPS31 WILD-TYPE 130  44  29  30
D5V7, multiclass
    clus
vv   MRPS31 MUTATED MRPS31 WILD-TYPE
  N0              8              130
  N1              4               44
  N2              3               29
  N3              3               30
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                M0  M1 M1A M1B M1C
  MRPS31 MUTATED    16   1   1   0   0
  MRPS31 WILD-TYPE 224   3   1   2   5
D5V8, multiclass
     clus
vv    MRPS31 MUTATED MRPS31 WILD-TYPE
  M0              16              224
  M1               1                3
  M1A              1                1
  M1B              0                2
  M1C              0                5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V9, binary
                  cls
clus                0  1
  MRPS31 MUTATED    4  6
  MRPS31 WILD-TYPE 98 61
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MRPS31 MUTATED      4    6
  MRPS31 WILD-TYPE   98   61
     clus
vv    MRPS31 MUTATED MRPS31 WILD-TYPE
  NO               4               98
  YES              6               61
[1] 2 2
[1] FALSE
D5V10, binary
                  cls
clus                 0   1
  MRPS31 MUTATED     2  17
  MRPS31 WILD-TYPE  31 218
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MRPS31 MUTATED      2   17
  MRPS31 WILD-TYPE   31  218
     clus
vv    MRPS31 MUTATED MRPS31 WILD-TYPE
  NO               2               31
  YES             17              218
[1] 2 2
[1] FALSE
D5V11, continuous
D5V12, binary
                  cls
clus                 0   1
  MRPS31 MUTATED     5  14
  MRPS31 WILD-TYPE  98 151
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MRPS31 MUTATED      5   14
  MRPS31 WILD-TYPE   98  151
        clus
vv       MRPS31 MUTATED MRPS31 WILD-TYPE
  FEMALE              5               98
  MALE               14              151
[1] 2 2
[1] FALSE
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MRPS31 MUTATED       0                         0    19
  MRPS31 WILD-TYPE     3                         1   245
D5V13, multiclass
                           clus
vv                          MRPS31 MUTATED MRPS31 WILD-TYPE
  ASIAN                                  0                3
  BLACK OR AFRICAN AMERICAN              0                1
  WHITE                                 19              245
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V14, binary
                  cls
clus                 0   1
  MRPS31 MUTATED     0  19
  MRPS31 WILD-TYPE   3 242
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MRPS31 MUTATED      0   19
  MRPS31 WILD-TYPE    3  242
                        clus
vv                       MRPS31 MUTATED MRPS31 WILD-TYPE
  HISPANIC OR LATINO                  0                3
  NOT HISPANIC OR LATINO             19              242
[1] 2 2
[1] FALSE

Clustering(6) Variable = NF1 MUTATION ANALYSIS
D6V1, survival
               sevent
clus2             0   1
  NF1 MUTATED    17  21
  NF1 WILD-TYPE 111 109
  NF1 MUTATED NF1 WILD-TYPE 
           38           220 
  NF1 MUTATED NF1 WILD-TYPE 
           21           109 
$`NF1 MUTATED`
TCGA-D3-A2JA TCGA-D3-A2JF TCGA-D3-A51R TCGA-D9-A6EC TCGA-DA-A1I0 TCGA-DA-A1IC 
       88.50        30.87        20.48        13.22        10.03         6.64 
TCGA-EE-A17X TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A20C TCGA-EE-A29L 
       11.57         8.12         1.12         1.35         4.34         1.08 
TCGA-EE-A29N TCGA-EE-A29V TCGA-EE-A2A2 TCGA-EE-A2GC TCGA-EE-A2GI TCGA-EE-A2GO 
        9.50         2.43        23.90        34.29        30.08        30.84 
TCGA-EE-A2GR TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AE 
        1.15        14.56        63.42        27.16        23.05        30.15 
TCGA-EE-A3J5 TCGA-EE-A3JD TCGA-ER-A19A TCGA-ER-A19F TCGA-FS-A1Z3 TCGA-FS-A1ZA 
       21.60        27.35        76.41        11.11        14.24         7.30 
TCGA-FS-A1ZP TCGA-FS-A1ZZ TCGA-FS-A4F4 TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU 
       52.08         5.23         7.36         0.20         0.99         0.13 
TCGA-GF-A4EO TCGA-GN-A266 
        7.23        10.13 

$`NF1 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.47         8.52       111.09        32.42        70.16       110.79 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       28.08        22.55        45.83        81.24        10.29        85.32 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JG 
        8.38        21.14        68.22        69.90        11.41         7.50 
TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP 
       36.16         6.31        92.42        56.19        64.44        45.11 
TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC 
      114.67        15.25        46.98        46.32        82.29        61.38 
TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU 
       13.32        24.00         6.31         9.34       103.59        26.37 
TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K 
        5.39        80.22        42.71        15.09        41.10        17.72 
TCGA-D3-A51N TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS 
        8.84        13.94        52.01        47.87         1.55         6.97 
TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-DA-A1HV 
       23.11         4.01         2.89         9.90        11.31        48.79 
TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 
       35.80        51.12        39.19        13.68         9.99        44.52 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A3F2 TCGA-DA-A3F3 
       36.69        25.15         4.93        22.36        19.36         7.00 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH 
       17.56        14.83        13.15         0.20         0.00         0.00 
TCGA-EB-A5UN TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 
       13.22        10.55         6.31        12.20         5.13         4.31 
TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B 
       36.07         5.13         9.21         1.18         7.99         9.90 
TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M 
       37.97        11.15        38.63         8.55         4.41        27.12 
TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29W TCGA-EE-A29X 
       12.03         8.09         8.84         9.99         8.68         8.09 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD 
       11.31        49.22         9.67         8.94        39.39        17.98 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM 
       34.92        47.21        19.43        16.01        35.54        28.31 
TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 
       33.83         5.42        13.02        34.98        36.33         8.84 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME 
       98.27         2.70         6.18        47.51         9.53        29.46 
TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN 
       44.25         7.96       111.78       111.91        56.02        25.08 
TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB 
       26.99        21.60        29.65         5.56       124.31       122.73 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 
       25.84         3.68        13.81        15.95        12.72         3.22 
TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JE TCGA-EE-A3JH 
       22.92        21.60        16.14        22.22         0.46        13.94 
TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 
       33.60        31.40        18.61        12.95        38.40         5.72 
TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19G TCGA-ER-A19H 
       25.18         3.78         3.52        11.90       114.15        34.88 
TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q 
        4.21        13.45        28.60        42.84        34.68         9.57 
TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE 
       36.07        17.72        78.44        11.80         1.87         1.51 
TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV 
       13.08        12.62        11.74         9.04         6.58        22.49 
TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX 
        1.71        18.41        85.74         4.90        64.47         3.45 
TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZB TCGA-FS-A1ZC 
       11.01        23.80        15.52         7.33         3.39        20.38 
TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ 
        8.22        19.53        11.08         7.17        30.87        12.92 
TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT 
       12.89        47.38         8.65         8.81        49.15        40.64 
TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A4F0 TCGA-FS-A4F5 TCGA-FS-A4F8 
        8.68        27.39         0.82        53.85        28.73        14.20 
TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3TV TCGA-FW-A5DY 
       10.78         5.98         6.41         2.27         0.16         0.43 
TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 
        9.90        12.85        24.85        31.33        84.72        16.24 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS 
       15.42        12.16        14.70         5.79 

  NF1 MUTATED NF1 WILD-TYPE 
         0.13          0.00 
  NF1 MUTATED NF1 WILD-TYPE 
        88.50        124.31 
  NF1 MUTATED NF1 WILD-TYPE 
        11.34         15.47 
[1] "0.1 - 88.5 (11.3)"  "0.0 - 124.3 (15.5)"
[1] "hr=" "1.4"
D6V2, survival
               sevent
clus2             0   1
  NF1 MUTATED    17  21
  NF1 WILD-TYPE 115 110
  NF1 MUTATED NF1 WILD-TYPE 
           38           225 
  NF1 MUTATED NF1 WILD-TYPE 
           21           110 
$`NF1 MUTATED`
TCGA-D3-A2JA TCGA-D3-A2JF TCGA-D3-A51R TCGA-D9-A6EC TCGA-DA-A1I0 TCGA-DA-A1IC 
      115.53        48.76        51.68        66.25        20.38        68.09 
TCGA-EE-A17X TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A20C TCGA-EE-A29L 
       29.82        94.98        33.73        14.70       151.27         2.60 
TCGA-EE-A29N TCGA-EE-A29V TCGA-EE-A2A2 TCGA-EE-A2GC TCGA-EE-A2GI TCGA-EE-A2GO 
       18.61        25.87        24.43        67.43        48.72       101.95 
TCGA-EE-A2GR TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AE 
       14.30       204.66        96.23       136.47        41.59        54.51 
TCGA-EE-A3J5 TCGA-EE-A3JD TCGA-ER-A19A TCGA-ER-A19F TCGA-FS-A1Z3 TCGA-FS-A1ZA 
       36.95        27.35        77.75        26.37        20.91        27.72 
TCGA-FS-A1ZP TCGA-FS-A1ZZ TCGA-FS-A4F4 TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU 
       74.73        27.02        66.67         0.20        22.92        47.54 
TCGA-GF-A4EO TCGA-GN-A266 
        7.23        10.13 

$`NF1 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.57        16.67       112.04       112.57        71.80       133.25 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       28.08        31.59        90.90        95.74        43.43       103.10 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JG 
       65.49        23.77       168.00        69.90        11.87       113.52 
TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP 
       42.08        12.10       171.58        56.19        66.08        45.11 
TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC 
      130.72        58.06        46.98        46.32       166.52        86.93 
TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU 
       60.23        24.53        13.87         9.34       103.59        39.75 
TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K 
       21.47       161.85        43.69        40.14       131.90        18.38 
TCGA-D3-A51N TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS 
       10.03        15.06       135.75       137.92       166.19         7.43 
TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 
      125.19       151.53        54.67         3.65         6.41        11.34 
TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY 
        3.25         9.90        25.18        48.89        36.03       117.21 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 
      194.83       176.55        35.93       107.34        61.18        53.92 
TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 
       65.92        23.44        28.60        10.49       215.44        15.68 
TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN 
       13.87        10.16        45.11        35.01         3.55        52.01 
TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B 
       27.22         8.65        26.89        68.15         4.96       109.64 
TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C 
       78.87       168.26        13.55        63.35        80.61        47.84 
TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29P 
       13.97        39.62        72.07        32.19        44.35        56.42 
TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 
       37.35        14.47        55.92       171.55        17.92        46.82 
TCGA-EE-A2A1 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE 
      102.90        39.29        58.75        47.54       314.56       135.95 
TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN 
      208.04        89.33        54.74        79.66        75.48        90.97 
TCGA-EE-A2GP TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 
       13.91        55.59        44.88        94.82        21.67       129.27 
TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG 
       28.83        19.76        61.51        47.28       103.27       103.20 
TCGA-EE-A2MH TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP 
       16.96       144.76       203.05       167.90        47.54       248.65 
TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC 
       43.23       103.56        53.26       124.31       122.73        25.84 
TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 
        3.68        13.81        23.47       138.81       172.18       127.20 
TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI 
       64.08        34.32        53.19        33.40       101.79       148.08 
TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19B 
       31.40        35.44        13.94        50.76         9.17        98.40 
TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J 
       48.89        12.59        13.02       268.93       152.35         6.44 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S 
      131.51        61.05        44.05       162.08        50.89        37.25 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF 
      148.18        79.99        43.82        23.34        20.15        16.37 
TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL 
       31.27        32.05       247.04        80.32        46.98        33.21 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY 
       92.98       174.21         4.90       216.92        48.59       228.59 
TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD 
      202.65        28.08         7.79        48.85       357.37        53.52 
TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK 
       40.27        15.45         9.70        32.75        47.38        23.93 
TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU 
      101.26       133.55        11.41       148.80        53.16        26.56 
TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A4F0 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 
       49.48        27.09        77.82        28.73       174.84        12.43 
TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
       26.73        49.45        77.88         0.16         2.40         9.90 
TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 
       14.04       120.46       117.93        84.72        64.44        62.79 
TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS 
       32.48        39.58         6.67 

  NF1 MUTATED NF1 WILD-TYPE 
         0.20          0.16 
  NF1 MUTATED NF1 WILD-TYPE 
       204.66        357.37 
  NF1 MUTATED NF1 WILD-TYPE 
        39.27         48.89 
[1] "0.2 - 204.7 (39.3)" "0.2 - 357.4 (48.9)"
[1] "hr=" "1.5"
D6V3, continuous
               vv
clus            DISTANT METASTASIS PRIMARY TUMOR
  NF1 MUTATED                   10             1
  NF1 WILD-TYPE                 25             3
               vv
clus            REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  NF1 MUTATED                                           9                  18
  NF1 WILD-TYPE                                        49                 152
D6V4, multiclass
                                           clus
vv                                          NF1 MUTATED NF1 WILD-TYPE
  DISTANT METASTASIS                                 10            25
  PRIMARY TUMOR                                       1             3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE           9            49
  REGIONAL LYMPH NODE                                18           152
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  NF1 MUTATED             1       1       0        4        1        5
  NF1 WILD-TYPE           9       5      22        6       23       12
               vv
clus            STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  NF1 MUTATED           2         3         0         5          2          2
  NF1 WILD-TYPE         8        11         9        26         11         20
               vv
clus            STAGE IIIC STAGE IV
  NF1 MUTATED            4        4
  NF1 WILD-TYPE         40        8
D6V5, multiclass
             clus
vv            NF1 MUTATED NF1 WILD-TYPE
  I OR II NOS           1             9
  STAGE 0               1             5
  STAGE I               0            22
  STAGE IA              4             6
  STAGE IB              1            23
  STAGE II              5            12
  STAGE IIA             2             8
  STAGE IIB             3            11
  STAGE IIC             0             9
  STAGE III             5            26
  STAGE IIIA            2            11
  STAGE IIIB            2            20
  STAGE IIIC            4            40
  STAGE IV              4             8
[1] 14  2
[1] 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
  NF1 MUTATED       4  3 10 11
  NF1 WILD-TYPE    47 55 43 44
D6V6, multiclass
       clus
vv      NF1 MUTATED NF1 WILD-TYPE
  T0+T1           4            47
  T2              3            55
  T3             10            43
  T4             11            44
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             N0  N1  N2  N3
  NF1 MUTATED    23   6   4   2
  NF1 WILD-TYPE 115  42  28  31
D6V7, multiclass
    clus
vv   NF1 MUTATED NF1 WILD-TYPE
  N0          23           115
  N1           6            42
  N2           4            28
  N3           2            31
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             M0  M1 M1A M1B M1C
  NF1 MUTATED    31   3   1   0   0
  NF1 WILD-TYPE 209   1   1   2   5
D6V8, multiclass
     clus
vv    NF1 MUTATED NF1 WILD-TYPE
  M0           31           209
  M1            3             1
  M1A           1             1
  M1B           0             2
  M1C           0             5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V9, binary
               cls
clus             0  1
  NF1 MUTATED   14  9
  NF1 WILD-TYPE 88 58
[1] "tbl2"
               cls
clus            [,1] [,2]
  NF1 MUTATED     14    9
  NF1 WILD-TYPE   88   58
     clus
vv    NF1 MUTATED NF1 WILD-TYPE
  NO           14            88
  YES           9            58
[1] 2 2
[1] FALSE
D6V10, binary
               cls
clus              0   1
  NF1 MUTATED     6  32
  NF1 WILD-TYPE  27 203
[1] "tbl2"
               cls
clus            [,1] [,2]
  NF1 MUTATED      6   32
  NF1 WILD-TYPE   27  203
     clus
vv    NF1 MUTATED NF1 WILD-TYPE
  NO            6            27
  YES          32           203
[1] 2 2
[1] FALSE
D6V11, continuous
D6V12, binary
               cls
clus              0   1
  NF1 MUTATED    11  27
  NF1 WILD-TYPE  92 138
[1] "tbl2"
               cls
clus            [,1] [,2]
  NF1 MUTATED     11   27
  NF1 WILD-TYPE   92  138
        clus
vv       NF1 MUTATED NF1 WILD-TYPE
  FEMALE          11            92
  MALE            27           138
[1] 2 2
[1] FALSE
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  NF1 MUTATED       0                         0    38
  NF1 WILD-TYPE     3                         1   226
D6V13, multiclass
                           clus
vv                          NF1 MUTATED NF1 WILD-TYPE
  ASIAN                               0             3
  BLACK OR AFRICAN AMERICAN           0             1
  WHITE                              38           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"
D6V14, binary
               cls
clus              0   1
  NF1 MUTATED     1  35
  NF1 WILD-TYPE   2 226
[1] "tbl2"
               cls
clus            [,1] [,2]
  NF1 MUTATED      1   35
  NF1 WILD-TYPE    2  226
                        clus
vv                       NF1 MUTATED NF1 WILD-TYPE
  HISPANIC OR LATINO               1             2
  NOT HISPANIC OR LATINO          35           226
[1] 2 2
[1] FALSE

Clustering(7) Variable = RAC1 MUTATION ANALYSIS
D7V1, survival
                sevent
clus2              0   1
  RAC1 MUTATED     9  11
  RAC1 WILD-TYPE 119 119
  RAC1 MUTATED RAC1 WILD-TYPE 
            20            238 
  RAC1 MUTATED RAC1 WILD-TYPE 
            11            119 
$`RAC1 MUTATED`
TCGA-D3-A2JH TCGA-D3-A3C8 TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51R TCGA-D9-A3Z1 
       36.16        46.32       103.59        26.37        20.48         4.01 
TCGA-EE-A181 TCGA-EE-A29D TCGA-EE-A2GM TCGA-EE-A2M5 TCGA-EE-A3AB TCGA-EE-A3JD 
        1.12        11.15        28.31         8.84       122.73        27.35 
TCGA-ER-A199 TCGA-ER-A1A1 TCGA-FS-A1ZA TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZU 
        5.72        78.44         7.30        12.89        52.08         8.68 
TCGA-GN-A266 TCGA-QB-A6FS 
       10.13         5.79 

$`RAC1 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.47         8.52       111.09        32.42        70.16       110.79 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       28.08        22.55        45.83        81.24        10.29        85.32 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
        8.38        21.14        88.50        68.22        69.90        11.41 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO 
       30.87         7.50         6.31        92.42        56.19        64.44 
TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3CB TCGA-D3-A3CC 
       45.11       114.67        15.25        46.98        82.29        61.38 
TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MV TCGA-D3-A51E 
       13.32        24.00         6.31         9.34         5.39        80.22 
TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51T 
       42.71        15.09        41.10        17.72         8.84        13.94 
TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z3 
       52.01        47.87         1.55         6.97        23.11         2.89 
TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY 
        9.90        11.31        13.22        48.79        35.80        51.12 
TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 
       10.03        39.19        13.68         9.99        44.52        36.69 
TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 
       25.15         4.93        22.36         6.64        19.36         7.00 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH 
       17.56        14.83        13.15         0.20         0.00         0.00 
TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A182 
       13.22        11.57        10.55         6.31         8.12         1.35 
TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F 
       12.20         5.13         4.31        36.07         4.34         5.13 
TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E 
        9.21         1.18         7.99         9.90        37.97        38.63 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P 
        8.55         4.41         1.08        27.12         9.50        12.03 
TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X 
        8.09         8.84         9.99         2.43         8.68         8.09 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB 
       11.31        49.22        23.90         9.67         8.94        39.39 
TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ 
       34.29        17.98        34.92        47.21        30.08        19.43 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR 
       16.01        35.54        33.83        30.84         5.42         1.15 
TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 
       13.02        34.98        36.33        98.27         2.70         6.18 
TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI 
       47.51         9.53        29.46        44.25         7.96        14.56 
TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP 
       63.42       111.78       111.91        56.02        25.08        26.99 
TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA 
       21.60        29.65        27.16        23.05         5.56       124.31 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH 
       25.84         3.68        30.15        13.81        15.95        12.72 
TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA 
        3.22        22.92        21.60        21.60        16.14        22.22 
TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 
        0.46        13.94        33.60        31.40        18.61        12.95 
TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E 
       38.40        76.41        25.18         3.78         3.52        11.90 
TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M 
       11.11       114.15        34.88         4.21        13.45        28.60 
TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A2NC 
       42.84        34.68         9.57        36.07        17.72        11.80 
TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES 
        1.87         1.51        13.08        12.62        11.74         9.04 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
        6.58        22.49         1.71        18.41        85.74         4.90 
TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 
       64.47         3.45        11.01        23.80        14.24        15.52 
TCGA-FS-A1Z7 TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF 
        7.33         3.39        20.38         8.22        19.53        11.08 
TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZR 
        7.17        30.87        12.92        47.38         8.65         8.81 
TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 
       49.15        40.64        27.39         0.82         5.23        53.85 
TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC 
        7.36        28.73        14.20        10.78         5.98         6.41 
TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY 
        2.27         0.20         0.99         0.13         0.16         0.43 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        9.90         7.23        12.85        24.85        31.33        84.72 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D 
       16.24        15.42        12.16        14.70 

  RAC1 MUTATED RAC1 WILD-TYPE 
          1.12           0.00 
  RAC1 MUTATED RAC1 WILD-TYPE 
        122.73         124.31 
  RAC1 MUTATED RAC1 WILD-TYPE 
        16.685         14.765 
[1] "1.1 - 122.7 (16.7)" "0.0 - 124.3 (14.8)"
[1] "hr=" "1"  
D7V2, survival
                sevent
clus2              0   1
  RAC1 MUTATED     9  11
  RAC1 WILD-TYPE 123 120
  RAC1 MUTATED RAC1 WILD-TYPE 
            20            243 
  RAC1 MUTATED RAC1 WILD-TYPE 
            11            120 
$`RAC1 MUTATED`
TCGA-D3-A2JH TCGA-D3-A3C8 TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51R TCGA-D9-A3Z1 
       42.08        46.32       103.59        39.75        51.68        11.34 
TCGA-EE-A181 TCGA-EE-A29D TCGA-EE-A2GM TCGA-EE-A2M5 TCGA-EE-A3AB TCGA-EE-A3JD 
       33.73        13.97        75.48        21.67       122.73        27.35 
TCGA-ER-A199 TCGA-ER-A1A1 TCGA-FS-A1ZA TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZU 
        9.17        79.99        27.72        23.93        74.73        26.56 
TCGA-GN-A266 TCGA-QB-A6FS 
       10.13         6.67 

$`RAC1 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.57        16.67       112.04       112.57        71.80       133.25 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       28.08        31.59        90.90        95.74        43.43       103.10 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
       65.49        23.77       115.53       168.00        69.90        11.87 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO 
       48.76       113.52        12.10       171.58        56.19        66.08 
TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3CB TCGA-D3-A3CC 
       45.11       130.72        58.06        46.98       166.52        86.93 
TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MV TCGA-D3-A51E 
       60.23        24.53        13.87         9.34        21.47       161.85 
TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51T 
       43.69        40.14       131.90        18.38        10.03        15.06 
TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 
      135.75       137.92       166.19         7.43       125.19       151.53 
TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA 
       54.67         3.65         6.41         3.25         9.90        25.18 
TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 
       66.25        48.89        36.03       117.21        20.38       194.83 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA 
      176.55        35.93       107.34        61.18        53.92        65.92 
TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 
       23.44        68.09        28.60        10.49       215.44        15.68 
TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN 
       13.87        10.16        45.11        35.01         3.55        52.01 
TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A182 TCGA-EE-A183 
       29.82        27.22         8.65        94.98        14.70        26.89 
TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H 
       68.15         4.96       109.64       151.27        78.87       168.26 
TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G 
       13.55        63.35        80.61        47.84        39.62        72.07 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
       32.19         2.60        44.35        18.61        56.42        37.35 
TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 
       14.47        55.92        25.87       171.55        17.92        46.82 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC 
      102.90        24.43        39.29        58.75        47.54        67.43 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK 
      314.56       135.95       208.04        48.72        89.33        54.74 
TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS 
       79.66        90.97       101.95        13.91        14.30        55.59 
TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC 
       44.88        94.82       129.27        28.83        19.76        61.51 
TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ 
       47.28       103.27       103.20        16.96       204.66        96.23 
TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ 
      144.76       203.05       167.90        47.54       248.65        43.23 
TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AC 
      103.56       136.47        41.59        53.26       124.31        25.84 
TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 
        3.68        54.51        13.81        23.47       138.81       172.18 
TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JE 
      127.20        36.95        64.08        34.32        53.19        33.40 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 
      101.79       148.08        31.40        35.44        13.94        50.76 
TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F 
       77.75        98.40        48.89        12.59        13.02        26.37 
TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N 
      268.93       152.35         6.44       131.51        61.05        44.05 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A2NC TCGA-ER-A2ND 
      162.08        50.89        37.25       148.18        43.82        23.34 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET 
       20.15        16.37        31.27        32.05       247.04        80.32 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW 
       46.98        33.21        92.98       174.21         4.90       216.92 
TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 
       48.59       228.59       202.65        20.91        28.08         7.79 
TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG 
       48.85       357.37        53.52        40.27        15.45         9.70 
TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS 
       32.75        47.38       101.26       133.55        11.41       148.80 
TCGA-FS-A1ZT TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 
       53.16        49.48        27.09        27.02        77.82        66.67 
TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD 
       28.73       174.84        12.43        26.73        49.45        77.88 
TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
        0.20        22.92        47.54         0.16         2.40         9.90 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 
        7.23        14.04       120.46       117.93        84.72        64.44 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D 
       62.79        32.48        39.58 

  RAC1 MUTATED RAC1 WILD-TYPE 
          6.67           0.16 
  RAC1 MUTATED RAC1 WILD-TYPE 
        122.73         357.37 
  RAC1 MUTATED RAC1 WILD-TYPE 
        30.725         48.890 
[1] "6.7 - 122.7 (30.7)" "0.2 - 357.4 (48.9)"
[1] "hr=" "1.8"
D7V3, continuous
                vv
clus             DISTANT METASTASIS PRIMARY TUMOR
  RAC1 MUTATED                    3             0
  RAC1 WILD-TYPE                 32             4
                vv
clus             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  RAC1 MUTATED                                           5                  12
  RAC1 WILD-TYPE                                        53                 158
D7V4, multiclass
                                           clus
vv                                          RAC1 MUTATED RAC1 WILD-TYPE
  DISTANT METASTASIS                                   3             32
  PRIMARY TUMOR                                        0              4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE            5             53
  REGIONAL LYMPH NODE                                 12            158
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  RAC1 MUTATED             0       0       1        0        1        3
  RAC1 WILD-TYPE          10       6      21       10       23       14
                vv
clus             STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  RAC1 MUTATED           1         0         2         3          1          1
  RAC1 WILD-TYPE         9        14         7        28         12         21
                vv
clus             STAGE IIIC STAGE IV
  RAC1 MUTATED            6        0
  RAC1 WILD-TYPE         38       12
D7V5, multiclass
             clus
vv            RAC1 MUTATED RAC1 WILD-TYPE
  I OR II NOS            0             10
  STAGE 0                0              6
  STAGE I                1             21
  STAGE IA               0             10
  STAGE IB               1             23
  STAGE II               3             14
  STAGE IIA              1              9
  STAGE IIB              0             14
  STAGE IIC              2              7
  STAGE III              3             28
  STAGE IIIA             1             12
  STAGE IIIB             1             21
  STAGE IIIC             6             38
  STAGE IV               0             12
[1] 14  2
[1] 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
  RAC1 MUTATED       4  2  5  5
  RAC1 WILD-TYPE    47 56 48 50
D7V6, multiclass
       clus
vv      RAC1 MUTATED RAC1 WILD-TYPE
  T0+T1            4             47
  T2               2             56
  T3               5             48
  T4               5             50
[1] 4 2
[1] TRUE
[1] "dimension 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
  RAC1 MUTATED     8   2   4   5
  RAC1 WILD-TYPE 130  46  28  28
D7V7, multiclass
    clus
vv   RAC1 MUTATED RAC1 WILD-TYPE
  N0            8            130
  N1            2             46
  N2            4             28
  N3            5             28
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              M0  M1 M1A M1B M1C
  RAC1 MUTATED    19   0   0   0   0
  RAC1 WILD-TYPE 221   4   2   2   5
D7V8, multiclass
     clus
vv    RAC1 MUTATED RAC1 WILD-TYPE
  M0            19            221
  M1             0              4
  M1A            0              2
  M1B            0              2
  M1C            0              5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V9, binary
                cls
clus              0  1
  RAC1 MUTATED    4  5
  RAC1 WILD-TYPE 98 62
[1] "tbl2"
                cls
clus             [,1] [,2]
  RAC1 MUTATED      4    5
  RAC1 WILD-TYPE   98   62
     clus
vv    RAC1 MUTATED RAC1 WILD-TYPE
  NO             4             98
  YES            5             62
[1] 2 2
[1] FALSE
D7V10, binary
                cls
clus               0   1
  RAC1 MUTATED     6  14
  RAC1 WILD-TYPE  27 221
[1] "tbl2"
                cls
clus             [,1] [,2]
  RAC1 MUTATED      6   14
  RAC1 WILD-TYPE   27  221
     clus
vv    RAC1 MUTATED RAC1 WILD-TYPE
  NO             6             27
  YES           14            221
[1] 2 2
[1] FALSE
D7V11, continuous
D7V12, binary
                cls
clus               0   1
  RAC1 MUTATED     6  14
  RAC1 WILD-TYPE  97 151
[1] "tbl2"
                cls
clus             [,1] [,2]
  RAC1 MUTATED      6   14
  RAC1 WILD-TYPE   97  151
        clus
vv       RAC1 MUTATED RAC1 WILD-TYPE
  FEMALE            6             97
  MALE             14            151
[1] 2 2
[1] FALSE
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RAC1 MUTATED       0                         0    20
  RAC1 WILD-TYPE     3                         1   244
D7V13, multiclass
                           clus
vv                          RAC1 MUTATED RAC1 WILD-TYPE
  ASIAN                                0              3
  BLACK OR AFRICAN AMERICAN            0              1
  WHITE                               20            244
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V14, binary
                cls
clus               0   1
  RAC1 MUTATED     0  20
  RAC1 WILD-TYPE   3 241
[1] "tbl2"
                cls
clus             [,1] [,2]
  RAC1 MUTATED      0   20
  RAC1 WILD-TYPE    3  241
                        clus
vv                       RAC1 MUTATED RAC1 WILD-TYPE
  HISPANIC OR LATINO                0              3
  NOT HISPANIC OR LATINO           20            241
[1] 2 2
[1] FALSE

Clustering(8) Variable = ARID2 MUTATION ANALYSIS
D8V1, survival
                 sevent
clus2               0   1
  ARID2 MUTATED    16  18
  ARID2 WILD-TYPE 112 112
  ARID2 MUTATED ARID2 WILD-TYPE 
             34             224 
  ARID2 MUTATED ARID2 WILD-TYPE 
             18             112 
$`ARID2 MUTATED`
TCGA-D3-A2JF TCGA-D3-A2JO TCGA-D3-A3ML TCGA-D3-A3MR TCGA-D3-A5GR TCGA-D3-A5GU 
       30.87        64.44         6.31       103.59         1.55        23.11 
TCGA-D9-A6EC TCGA-DA-A1I4 TCGA-DA-A1IC TCGA-EE-A182 TCGA-EE-A29N TCGA-EE-A29P 
       13.22         9.99         6.64         1.35         9.50        12.03 
TCGA-EE-A29S TCGA-EE-A2A2 TCGA-EE-A2GD TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2MC 
        9.99        23.90        17.98        30.08        19.43        47.51 
TCGA-EE-A2MD TCGA-EE-A3AC TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3JE TCGA-ER-A193 
        9.53        25.84        13.81        15.95         0.46        31.40 
TCGA-ER-A19E TCGA-FS-A1Z3 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZP TCGA-FS-A1ZZ 
       11.90        14.24        20.38         8.22        52.08         5.23 
TCGA-FS-A4F5 TCGA-FS-A4FC TCGA-FW-A3R5 TCGA-GN-A266 
       28.73         6.41         0.99        10.13 

$`ARID2 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.47         8.52       111.09        32.42        70.16       110.79 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       28.08        22.55        45.83        81.24        10.29        85.32 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
        8.38        21.14        88.50        68.22        69.90        11.41 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JP 
        7.50        36.16         6.31        92.42        56.19        45.11 
TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC 
      114.67        15.25        46.98        46.32        82.29        61.38 
TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E 
       13.32        24.00         9.34        26.37         5.39        80.22 
TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R 
       42.71        15.09        41.10        17.72         8.84        20.48 
TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GS TCGA-D9-A3Z1 TCGA-D9-A3Z3 
       13.94        52.01        47.87         6.97         4.01         2.89 
TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 
        9.90        11.31        48.79        35.80        51.12        10.03 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA 
       39.19        13.68        44.52        36.69        25.15         4.93 
TCGA-DA-A1IB TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q 
       22.36        19.36         7.00        17.56        14.83        13.15 
TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y 
        0.20         0.00         0.00        13.22        11.57        10.55 
TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 
        6.31         8.12         1.12        12.20         5.13         4.31 
TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A 
       36.07         4.34         5.13         9.21         1.18         7.99 
TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H 
        9.90        37.97        11.15        38.63         8.55         4.41 
TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29V TCGA-EE-A29W 
        1.08        27.12         8.09         8.84         2.43         8.68 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB 
        8.09        11.31        49.22         9.67         8.94        39.39 
TCGA-EE-A2GC TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM 
       34.29        34.92        47.21        16.01        35.54        28.31 
TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT 
       33.83        30.84         5.42         1.15        13.02        34.98 
TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2ME 
       36.33         8.84        98.27         2.70         6.18        29.46 
TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML 
       44.25         7.96        14.56        63.42       111.78       111.91 
TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS 
       56.02        25.08        26.99        21.60        29.65        27.16 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AE 
       23.05         5.56       124.31       122.73         3.68        30.15 
TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 
       12.72         3.22        22.92        21.60        21.60        16.14 
TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 
       22.22        27.35        13.94        33.60        18.61        12.95 
TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D 
       38.40         5.72        76.41        25.18         3.78         3.52 
TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M 
       11.11       114.15        34.88         4.21        13.45        28.60 
TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 
       42.84        34.68         9.57        36.07        17.72        78.44 
TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH 
       11.80         1.87         1.51        13.08        12.62        11.74 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A 
        9.04         6.58        22.49         1.71        18.41        85.74 
TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z4 
        4.90        64.47         3.45        11.01        23.80        15.52 
TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG 
        7.33         7.30         3.39        19.53        11.08         7.17 
TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZR 
       30.87        12.92        12.89        47.38         8.65         8.81 
TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A4F0 
       49.15        40.64         8.68        27.39         0.82        53.85 
TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FD TCGA-FW-A3I3 
        7.36        14.20        10.78         5.98         2.27         0.20 
TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 
        0.13         0.16         0.43         9.90         7.23        12.85 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
       24.85        31.33        84.72        16.24        15.42        12.16 
TCGA-GN-A26D TCGA-QB-A6FS 
       14.70         5.79 

  ARID2 MUTATED ARID2 WILD-TYPE 
           0.46            0.00 
  ARID2 MUTATED ARID2 WILD-TYPE 
         103.59          124.31 
  ARID2 MUTATED ARID2 WILD-TYPE 
         13.515          15.170 
[1] "0.5 - 103.6 (13.5)" "0.0 - 124.3 (15.2)"
[1] "hr=" "1.2"
D8V2, survival
                 sevent
clus2               0   1
  ARID2 MUTATED    16  18
  ARID2 WILD-TYPE 116 113
  ARID2 MUTATED ARID2 WILD-TYPE 
             34             229 
  ARID2 MUTATED ARID2 WILD-TYPE 
             18             113 
$`ARID2 MUTATED`
TCGA-D3-A2JF TCGA-D3-A2JO TCGA-D3-A3ML TCGA-D3-A3MR TCGA-D3-A5GR TCGA-D3-A5GU 
       48.76        66.08        13.87       103.59       166.19       125.19 
TCGA-D9-A6EC TCGA-DA-A1I4 TCGA-DA-A1IC TCGA-EE-A182 TCGA-EE-A29N TCGA-EE-A29P 
       66.25        35.93        68.09        14.70        18.61        56.42 
TCGA-EE-A29S TCGA-EE-A2A2 TCGA-EE-A2GD TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2MC 
       55.92        24.43       314.56        48.72        89.33        61.51 
TCGA-EE-A2MD TCGA-EE-A3AC TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3JE TCGA-ER-A193 
       47.28        25.84        13.81        23.47        33.40        31.40 
TCGA-ER-A19E TCGA-FS-A1Z3 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZP TCGA-FS-A1ZZ 
       13.02        20.91       357.37        53.52        74.73        27.02 
TCGA-FS-A4F5 TCGA-FS-A4FC TCGA-FW-A3R5 TCGA-GN-A266 
       28.73        49.45        22.92        10.13 

$`ARID2 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.57        16.67       112.04       112.57        71.80       133.25 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       28.08        31.59        90.90        95.74        43.43       103.10 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
       65.49        23.77       115.53       168.00        69.90        11.87 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JP 
      113.52        42.08        12.10       171.58        56.19        45.11 
TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC 
      130.72        58.06        46.98        46.32       166.52        86.93 
TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E 
       60.23        24.53         9.34        39.75        21.47       161.85 
TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R 
       43.69        40.14       131.90        18.38        10.03        51.68 
TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GS TCGA-D9-A148 TCGA-D9-A149 
       15.06       135.75       137.92         7.43       151.53        54.67 
TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA 
        3.65         6.41        11.34         3.25         9.90        25.18 
TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 
       48.89        36.03       117.21        20.38       194.83       176.55 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A3F2 
      107.34        61.18        53.92        65.92        23.44        28.60 
TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG 
       10.49       215.44        15.68        13.87        10.16        45.11 
TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z 
       35.01         3.55        52.01        29.82        27.22         8.65 
TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B 
       94.98        33.73        26.89        68.15         4.96       109.64 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B 
      151.27        78.87       168.26        13.55        63.35        80.61 
TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L 
       47.84        13.97        39.62        72.07        32.19         2.60 
TCGA-EE-A29M TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X 
       44.35        37.35        14.47        25.87       171.55        17.92 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC 
       46.82       102.90        39.29        58.75        47.54        67.43 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN 
      135.95       208.04        54.74        79.66        75.48        90.97 
TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU 
      101.95        13.91        14.30        55.59        44.88        94.82 
TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2ME TCGA-EE-A2MG 
       21.67       129.27        28.83        19.76       103.27       103.20 
TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM 
       16.96       204.66        96.23       144.76       203.05       167.90 
TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT 
       47.54       248.65        43.23       103.56       136.47        41.59 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AH 
       53.26       124.31       122.73         3.68        54.51       138.81 
TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA 
      172.18       127.20        36.95        64.08        34.32        53.19 
TCGA-EE-A3JD TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 
       27.35       101.79       148.08        35.44        13.94        50.76 
TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19F 
        9.17        77.75        98.40        48.89        12.59        26.37 
TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N 
      268.93       152.35         6.44       131.51        61.05        44.05 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
      162.08        50.89        37.25       148.18        79.99        43.82 
TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES 
       23.34        20.15        16.37        31.27        32.05       247.04 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
       80.32        46.98        33.21        92.98       174.21         4.90 
TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1Z7 
      216.92        48.59       228.59       202.65        28.08         7.79 
TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH 
       27.72        48.85        40.27        15.45         9.70        32.75 
TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS 
       47.38        23.93       101.26       133.55        11.41       148.80 
TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A4F0 TCGA-FS-A4F4 
       53.16        26.56        49.48        27.09        77.82        66.67 
TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU 
      174.84        12.43        26.73        77.88         0.20        47.54 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 
        0.16         2.40         9.90         7.23        14.04       120.46 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D 
      117.93        84.72        64.44        62.79        32.48        39.58 
TCGA-QB-A6FS 
        6.67 

  ARID2 MUTATED ARID2 WILD-TYPE 
          10.13            0.16 
  ARID2 MUTATED ARID2 WILD-TYPE 
         357.37          268.93 
  ARID2 MUTATED ARID2 WILD-TYPE 
          48.00           48.59 
[1] "10.1 - 357.4 (48.0)" "0.2 - 268.9 (48.6)" 
[1] "hr=" "1.1"
D8V3, continuous
                 vv
clus              DISTANT METASTASIS PRIMARY TUMOR
  ARID2 MUTATED                    6             1
  ARID2 WILD-TYPE                 29             3
                 vv
clus              REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  ARID2 MUTATED                                          10                  18
  ARID2 WILD-TYPE                                        48                 152
D8V4, multiclass
                                           clus
vv                                          ARID2 MUTATED ARID2 WILD-TYPE
  DISTANT METASTASIS                                    6              29
  PRIMARY TUMOR                                         1               3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE            10              48
  REGIONAL LYMPH NODE                                  18             152
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  ARID2 MUTATED             3       0       1        3        3        2
  ARID2 WILD-TYPE           7       6      21        7       21       15
                 vv
clus              STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  ARID2 MUTATED           3         3         1         5          2          2
  ARID2 WILD-TYPE         7        11         8        26         11         20
                 vv
clus              STAGE IIIC STAGE IV
  ARID2 MUTATED            5        1
  ARID2 WILD-TYPE         39       11
D8V5, multiclass
             clus
vv            ARID2 MUTATED ARID2 WILD-TYPE
  I OR II NOS             3               7
  STAGE 0                 0               6
  STAGE I                 1              21
  STAGE IA                3               7
  STAGE IB                3              21
  STAGE II                2              15
  STAGE IIA               3               7
  STAGE IIB               3              11
  STAGE IIC               1               8
  STAGE III               5              26
  STAGE IIIA              2              11
  STAGE IIIB              2              20
  STAGE IIIC              5              39
  STAGE IV                1              11
[1] 14  2
[1] 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       9  5 11  4
  ARID2 WILD-TYPE    42 53 42 51
D8V6, multiclass
       clus
vv      ARID2 MUTATED ARID2 WILD-TYPE
  T0+T1             9              42
  T2                5              53
  T3               11              42
  T4                4              51
[1] 4 2
[1] TRUE
[1] "dimension 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    20   6   6   2
  ARID2 WILD-TYPE 118  42  26  31
D8V7, multiclass
    clus
vv   ARID2 MUTATED ARID2 WILD-TYPE
  N0            20             118
  N1             6              42
  N2             6              26
  N3             2              31
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               M0  M1 M1A M1B M1C
  ARID2 MUTATED    33   1   0   0   0
  ARID2 WILD-TYPE 207   3   2   2   5
D8V8, multiclass
     clus
vv    ARID2 MUTATED ARID2 WILD-TYPE
  M0             33             207
  M1              1               3
  M1A             0               2
  M1B             0               2
  M1C             0               5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V9, binary
                 cls
clus               0  1
  ARID2 MUTATED   13 10
  ARID2 WILD-TYPE 89 57
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ARID2 MUTATED     13   10
  ARID2 WILD-TYPE   89   57
     clus
vv    ARID2 MUTATED ARID2 WILD-TYPE
  NO             13              89
  YES            10              57
[1] 2 2
[1] FALSE
D8V10, binary
                 cls
clus                0   1
  ARID2 MUTATED     6  29
  ARID2 WILD-TYPE  27 206
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ARID2 MUTATED      6   29
  ARID2 WILD-TYPE   27  206
     clus
vv    ARID2 MUTATED ARID2 WILD-TYPE
  NO              6              27
  YES            29             206
[1] 2 2
[1] FALSE
D8V11, continuous
D8V12, binary
                 cls
clus                0   1
  ARID2 MUTATED    13  22
  ARID2 WILD-TYPE  90 143
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ARID2 MUTATED     13   22
  ARID2 WILD-TYPE   90  143
        clus
vv       ARID2 MUTATED ARID2 WILD-TYPE
  FEMALE            13              90
  MALE              22             143
[1] 2 2
[1] FALSE
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ARID2 MUTATED       0                         0    35
  ARID2 WILD-TYPE     3                         1   229
D8V13, multiclass
                           clus
vv                          ARID2 MUTATED ARID2 WILD-TYPE
  ASIAN                                 0               3
  BLACK OR AFRICAN AMERICAN             0               1
  WHITE                                35             229
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V14, binary
                 cls
clus                0   1
  ARID2 MUTATED     1  34
  ARID2 WILD-TYPE   2 227
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ARID2 MUTATED      1   34
  ARID2 WILD-TYPE    2  227
                        clus
vv                       ARID2 MUTATED ARID2 WILD-TYPE
  HISPANIC OR LATINO                 1               2
  NOT HISPANIC OR LATINO            34             227
[1] 2 2
[1] FALSE

Clustering(9) Variable = C15ORF23 MUTATION ANALYSIS
D9V1, survival
                    sevent
clus2                  0   1
  C15ORF23 MUTATED     9   9
  C15ORF23 WILD-TYPE 119 121
  C15ORF23 MUTATED C15ORF23 WILD-TYPE 
                18                240 
  C15ORF23 MUTATED C15ORF23 WILD-TYPE 
                 9                121 
$`C15ORF23 MUTATED`
TCGA-D3-A2JD TCGA-D3-A51E TCGA-D3-A5GO TCGA-DA-A1IC TCGA-EE-A181 TCGA-EE-A29G 
       11.41        80.22        47.87         6.64         1.12         8.55 
TCGA-EE-A2A2 TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2M5 TCGA-EE-A2MP TCGA-EE-A3AH 
       23.90        34.29        17.98         8.84        26.99        12.72 
TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-FS-A1ZT TCGA-FS-A4F9 TCGA-GF-A4EO TCGA-GN-A266 
       22.92        21.60        40.64        10.78         7.23        10.13 

$`C15ORF23 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.47         8.52       111.09        32.42        70.16       110.79 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       28.08        22.55        45.83        81.24        10.29        85.32 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JF 
        8.38        21.14        88.50        68.22        69.90        30.87 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO 
        7.50        36.16         6.31        92.42        56.19        64.44 
TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB 
       45.11       114.67        15.25        46.98        46.32        82.29 
TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR 
       61.38        13.32        24.00         6.31         9.34       103.59 
TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K 
       26.37         5.39        42.71        15.09        41.10        17.72 
TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS 
        8.84        20.48        13.94        52.01         1.55         6.97 
TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC 
       23.11         4.01         2.89         9.90        11.31        13.22 
TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 
       48.79        35.80        51.12        10.03        39.19        13.68 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB 
        9.99        44.52        36.69        25.15         4.93        22.36 
TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R 
       19.36         7.00        17.56        14.83        13.15         0.20 
TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z 
        0.00         0.00        13.22        11.57        10.55         6.31 
TCGA-EE-A180 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B 
        8.12         1.35        12.20         5.13         4.31        36.07 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B 
        4.34         5.13         9.21         1.18         7.99         9.90 
TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M 
       37.97        11.15        38.63         4.41         1.08        27.12 
TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V 
        9.50        12.03         8.09         8.84         9.99         2.43 
TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A5 TCGA-EE-A2A6 
        8.68         8.09        11.31        49.22         9.67         8.94 
TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK 
       39.39        34.92        47.21        30.08        19.43        16.01 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR 
       35.54        28.31        33.83        30.84         5.42         1.15 
TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 
       13.02        34.98        36.33        98.27         2.70         6.18 
TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI 
       47.51         9.53        29.46        44.25         7.96        14.56 
TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MQ 
       63.42       111.78       111.91        56.02        25.08        21.60 
TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB 
       29.65        27.16        23.05         5.56       124.31       122.73 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3J3 
       25.84         3.68        30.15        13.81        15.95         3.22 
TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH 
       21.60        16.14        22.22        27.35         0.46        13.94 
TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 
       33.60        31.40        18.61        12.95        38.40         5.72 
TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F 
       76.41        25.18         3.78         3.52        11.90        11.11 
TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N 
      114.15        34.88         4.21        13.45        28.60        42.84 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
       34.68         9.57        36.07        17.72        78.44        11.80 
TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES 
        1.87         1.51        13.08        12.62        11.74         9.04 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
        6.58        22.49         1.71        18.41        85.74         4.90 
TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 
       64.47         3.45        11.01        23.80        14.24        15.52 
TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE 
        7.33         7.30         3.39        20.38         8.22        19.53 
TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM 
       11.08         7.17        30.87        12.92        12.89        47.38 
TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZU TCGA-FS-A1ZW 
       52.08         8.65         8.81        49.15         8.68        27.39 
TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 
        0.82         5.23        53.85         7.36        28.73        14.20 
TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU 
        5.98         6.41         2.27         0.20         0.99         0.13 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 
        0.16         0.43         9.90        12.85        24.85        31.33 
TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS 
       84.72        16.24        15.42        12.16        14.70         5.79 

  C15ORF23 MUTATED C15ORF23 WILD-TYPE 
              1.12               0.00 
  C15ORF23 MUTATED C15ORF23 WILD-TYPE 
             80.22             124.31 
  C15ORF23 MUTATED C15ORF23 WILD-TYPE 
            15.350             14.765 
[1] "1.1 - 80.2 (15.4)"  "0.0 - 124.3 (14.8)"
[1] "hr=" "1"  
D9V2, survival
                    sevent
clus2                  0   1
  C15ORF23 MUTATED     9   9
  C15ORF23 WILD-TYPE 123 122
  C15ORF23 MUTATED C15ORF23 WILD-TYPE 
                18                245 
  C15ORF23 MUTATED C15ORF23 WILD-TYPE 
                 9                122 
$`C15ORF23 MUTATED`
TCGA-D3-A2JD TCGA-D3-A51E TCGA-D3-A5GO TCGA-DA-A1IC TCGA-EE-A181 TCGA-EE-A29G 
       11.87       161.85       137.92        68.09        33.73        72.07 
TCGA-EE-A2A2 TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2M5 TCGA-EE-A2MP TCGA-EE-A3AH 
       24.43        67.43       314.56        21.67       248.65       138.81 
TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-FS-A1ZT TCGA-FS-A4F9 TCGA-GF-A4EO TCGA-GN-A266 
      127.20        36.95        53.16        12.43         7.23        10.13 

$`C15ORF23 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.57        16.67       112.04       112.57        71.80       133.25 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       28.08        31.59        90.90        95.74        43.43       103.10 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JF 
       65.49        23.77       115.53       168.00        69.90        48.76 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO 
      113.52        42.08        12.10       171.58        56.19        66.08 
TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB 
       45.11       130.72        58.06        46.98        46.32       166.52 
TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR 
       86.93        60.23        24.53        13.87         9.34       103.59 
TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K 
       39.75        21.47        43.69        40.14       131.90        18.38 
TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS 
       10.03        51.68        15.06       135.75       166.19         7.43 
TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 
      125.19       151.53        54.67         3.65         6.41        11.34 
TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1HW 
        3.25         9.90        25.18        66.25        48.89        36.03 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 
      117.21        20.38       194.83       176.55        35.93       107.34 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A3F2 TCGA-DA-A3F3 
       61.18        53.92        65.92        23.44        28.60        10.49 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH 
      215.44        15.68        13.87        10.16        45.11        35.01 
TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 
        3.55        52.01        29.82        27.22         8.65        94.98 
TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C 
       14.70        26.89        68.15         4.96       109.64       151.27 
TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C 
       78.87       168.26        13.55        63.35        80.61        47.84 
TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N 
       13.97        39.62        32.19         2.60        44.35        18.61 
TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W 
       56.42        37.35        14.47        55.92        25.87       171.55 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB 
       17.92        46.82       102.90        39.29        58.75        47.54 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
      135.95       208.04        48.72        89.33        54.74        79.66 
TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS 
       75.48        90.97       101.95        13.91        14.30        55.59 
TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC 
       44.88        94.82       129.27        28.83        19.76        61.51 
TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ 
       47.28       103.27       103.20        16.96       204.66        96.23 
TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MQ TCGA-EE-A2MR 
      144.76       203.05       167.90        47.54        43.23       103.56 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC 
      136.47        41.59        53.26       124.31       122.73        25.84 
TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3J3 TCGA-EE-A3J7 
        3.68        54.51        13.81        23.47       172.18        64.08 
TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI 
       34.32        53.19        27.35        33.40       101.79       148.08 
TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A 
       31.40        35.44        13.94        50.76         9.17        77.75 
TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G 
       98.40        48.89        12.59        13.02        26.37       268.93 
TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P 
      152.35         6.44       131.51        61.05        44.05       162.08 
TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
       50.89        37.25       148.18        79.99        43.82        23.34 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET 
       20.15        16.37        31.27        32.05       247.04        80.32 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW 
       46.98        33.21        92.98       174.21         4.90       216.92 
TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 
       48.59       228.59       202.65        20.91        28.08         7.79 
TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF 
       27.72        48.85       357.37        53.52        40.27        15.45 
TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP 
        9.70        32.75        47.38        23.93       101.26        74.73 
TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY 
      133.55        11.41       148.80        26.56        49.48        27.09 
TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4FB 
       27.02        77.82        66.67        28.73       174.84        26.73 
TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV 
       49.45        77.88         0.20        22.92        47.54         0.16 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        2.40         9.90        14.04       120.46       117.93        84.72 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS 
       64.44        62.79        32.48        39.58         6.67 

  C15ORF23 MUTATED C15ORF23 WILD-TYPE 
              7.23               0.16 
  C15ORF23 MUTATED C15ORF23 WILD-TYPE 
            314.56             357.37 
  C15ORF23 MUTATED C15ORF23 WILD-TYPE 
            60.295             47.840 
[1] "7.2 - 314.6 (60.3)" "0.2 - 357.4 (47.8)"
[1] "hr=" "1.3"
D9V3, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  C15ORF23 MUTATED                    2             0
  C15ORF23 WILD-TYPE                 33             4
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  C15ORF23 MUTATED                                           7
  C15ORF23 WILD-TYPE                                        51
                    vv
clus                 REGIONAL LYMPH NODE
  C15ORF23 MUTATED                     9
  C15ORF23 WILD-TYPE                 161
D9V4, multiclass
                                           clus
vv                                          C15ORF23 MUTATED C15ORF23 WILD-TYPE
  DISTANT METASTASIS                                       2                 33
  PRIMARY TUMOR                                            0                  4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                7                 51
  REGIONAL LYMPH NODE                                      9                161
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  C15ORF23 MUTATED             1       0       2        0        0        4
  C15ORF23 WILD-TYPE           9       6      20       10       24       13
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  C15ORF23 MUTATED           0         2         0         2          1
  C15ORF23 WILD-TYPE        10        12         9        29         12
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  C15ORF23 MUTATED            1          3        0
  C15ORF23 WILD-TYPE         21         41       12
D9V5, multiclass
             clus
vv            C15ORF23 MUTATED C15ORF23 WILD-TYPE
  I OR II NOS                1                  9
  STAGE 0                    0                  6
  STAGE I                    2                 20
  STAGE IA                   0                 10
  STAGE IB                   0                 24
  STAGE II                   4                 13
  STAGE IIA                  0                 10
  STAGE IIB                  2                 12
  STAGE IIC                  0                  9
  STAGE III                  2                 29
  STAGE IIIA                 1                 12
  STAGE IIIB                 1                 21
  STAGE IIIC                 3                 41
  STAGE IV                   0                 12
[1] 14  2
[1] 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
  C15ORF23 MUTATED       0  4  5  7
  C15ORF23 WILD-TYPE    51 54 48 48
D9V6, multiclass
       clus
vv      C15ORF23 MUTATED C15ORF23 WILD-TYPE
  T0+T1                0                 51
  T2                   4                 54
  T3                   5                 48
  T4                   7                 48
[1] 4 2
[1] TRUE
[1] "dimension 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
  C15ORF23 MUTATED     9   4   2   1
  C15ORF23 WILD-TYPE 129  44  30  32
D9V7, multiclass
    clus
vv   C15ORF23 MUTATED C15ORF23 WILD-TYPE
  N0                9                129
  N1                4                 44
  N2                2                 30
  N3                1                 32
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1 M1A M1B M1C
  C15ORF23 MUTATED    16   0   0   0   0
  C15ORF23 WILD-TYPE 224   4   2   2   5
D9V8, multiclass
     clus
vv    C15ORF23 MUTATED C15ORF23 WILD-TYPE
  M0                16                224
  M1                 0                  4
  M1A                0                  2
  M1B                0                  2
  M1C                0                  5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V9, binary
                    cls
clus                  0  1
  C15ORF23 MUTATED    5  6
  C15ORF23 WILD-TYPE 97 61
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C15ORF23 MUTATED      5    6
  C15ORF23 WILD-TYPE   97   61
     clus
vv    C15ORF23 MUTATED C15ORF23 WILD-TYPE
  NO                 5                 97
  YES                6                 61
[1] 2 2
[1] FALSE
D9V10, binary
                    cls
clus                   0   1
  C15ORF23 MUTATED     2  16
  C15ORF23 WILD-TYPE  31 219
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C15ORF23 MUTATED      2   16
  C15ORF23 WILD-TYPE   31  219
     clus
vv    C15ORF23 MUTATED C15ORF23 WILD-TYPE
  NO                 2                 31
  YES               16                219
[1] 2 2
[1] FALSE
D9V11, continuous
D9V12, binary
                    cls
clus                   0   1
  C15ORF23 MUTATED     5  13
  C15ORF23 WILD-TYPE  98 152
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C15ORF23 MUTATED      5   13
  C15ORF23 WILD-TYPE   98  152
        clus
vv       C15ORF23 MUTATED C15ORF23 WILD-TYPE
  FEMALE                5                 98
  MALE                 13                152
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  C15ORF23 MUTATED       0                         0    18
  C15ORF23 WILD-TYPE     3                         1   246
D9V13, multiclass
                           clus
vv                          C15ORF23 MUTATED C15ORF23 WILD-TYPE
  ASIAN                                    0                  3
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                   18                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"
D9V14, binary
                    cls
clus                   0   1
  C15ORF23 MUTATED     0  18
  C15ORF23 WILD-TYPE   3 243
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C15ORF23 MUTATED      0   18
  C15ORF23 WILD-TYPE    3  243
                        clus
vv                       C15ORF23 MUTATED C15ORF23 WILD-TYPE
  HISPANIC OR LATINO                    0                  3
  NOT HISPANIC OR LATINO               18                243
[1] 2 2
[1] FALSE

Clustering(10) Variable = PTEN MUTATION ANALYSIS
D10V1, survival
                sevent
clus2              0   1
  PTEN MUTATED    13   9
  PTEN WILD-TYPE 115 121
  PTEN MUTATED PTEN WILD-TYPE 
            22            236 
  PTEN MUTATED PTEN WILD-TYPE 
             9            121 
$`PTEN MUTATED`
TCGA-D3-A1Q4 TCGA-D3-A1Q7 TCGA-D3-A2J8 TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3MR 
      111.09       110.79         8.38         6.31        15.25       103.59 
TCGA-D3-A51T TCGA-D3-A5GN TCGA-D9-A6EC TCGA-EE-A17Z TCGA-EE-A29P TCGA-EE-A2GN 
       13.94        52.01        13.22         6.31        12.03        33.83 
TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A3AH TCGA-EE-A3JE TCGA-ER-A19E TCGA-ER-A19J 
       13.02        36.33        12.72         0.46        11.90         4.21 
TCGA-ER-A2NE TCGA-FR-A69P TCGA-FS-A1ZD TCGA-FW-A3I3 
        1.51         4.90         8.22         0.20 

$`PTEN WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q8 TCGA-D3-A1Q9 
       16.47         8.52        32.42        70.16        28.08        22.55 
TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J9 TCGA-D3-A2JA 
       45.83        81.24        10.29        85.32        21.14        88.50 
TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH 
       68.22        69.90        11.41        30.87         7.50        36.16 
TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C7 
       92.42        56.19        64.44        45.11       114.67        46.98 
TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML 
       46.32        82.29        61.38        13.32        24.00         6.31 
TCGA-D3-A3MO TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H 
        9.34        26.37         5.39        80.22        42.71        15.09 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A5GO TCGA-D3-A5GR 
       41.10        17.72         8.84        20.48        47.87         1.55 
TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA 
        6.97        23.11         4.01         2.89         9.90        11.31 
TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 
       48.79        35.80        51.12        10.03        39.19        13.68 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB 
        9.99        44.52        36.69        25.15         4.93        22.36 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q 
        6.64        19.36         7.00        17.56        14.83        13.15 
TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y 
        0.20         0.00         0.00        13.22        11.57        10.55 
TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 
        8.12         1.12         1.35        12.20         5.13         4.31 
TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A 
       36.07         4.34         5.13         9.21         1.18         7.99 
TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H 
        9.90        37.97        11.15        38.63         8.55         4.41 
TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S 
        1.08        27.12         9.50         8.09         8.84         9.99 
TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 
        2.43         8.68         8.09        11.31        49.22        23.90 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE 
        9.67         8.94        39.39        34.29        17.98        34.92 
TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM 
       47.21        30.08        19.43        16.01        35.54        28.31 
TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GT TCGA-EE-A2M5 TCGA-EE-A2M6 
       30.84         5.42         1.15        34.98         8.84        98.27 
TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG 
        2.70         6.18        47.51         9.53        29.46        44.25 
TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM 
        7.96        14.56        63.42       111.78       111.91        56.02 
TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT 
       25.08        26.99        21.60        29.65        27.16        23.05 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE 
        5.56       124.31       122.73        25.84         3.68        30.15 
TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 
       13.81        15.95         3.22        22.92        21.60        21.60 
TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 
       16.14        22.22        27.35        13.94        33.60        31.40 
TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B 
       18.61        12.95        38.40         5.72        76.41        25.18 
TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19L 
        3.78         3.52        11.11       114.15        34.88        13.45 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W 
       28.60        42.84        34.68         9.57        36.07        17.72 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH 
       78.44        11.80         1.87        13.08        12.62        11.74 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A 
        9.04         6.58        22.49         1.71        18.41        85.74 
TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 
       64.47         3.45        11.01        23.80        14.24        15.52 
TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZE TCGA-FS-A1ZF 
        7.33         7.30         3.39        20.38        19.53        11.08 
TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP 
        7.17        30.87        12.92        12.89        47.38        52.08 
TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW 
        8.65         8.81        49.15        40.64         8.68        27.39 
TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 
        0.82         5.23        53.85         7.36        28.73        14.20 
TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3R5 TCGA-FW-A3TU 
       10.78         5.98         6.41         2.27         0.99         0.13 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 
        0.16         0.43         9.90         7.23        12.85        24.85 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
       31.33        84.72        10.13        16.24        15.42        12.16 
TCGA-GN-A26D TCGA-QB-A6FS 
       14.70         5.79 

  PTEN MUTATED PTEN WILD-TYPE 
           0.2            0.0 
  PTEN MUTATED PTEN WILD-TYPE 
        111.09         124.31 
  PTEN MUTATED PTEN WILD-TYPE 
        12.375         15.735 
[1] "0.2 - 111.1 (12.4)" "0.0 - 124.3 (15.7)"
[1] "hr=" "1.1"
D10V2, survival
                sevent
clus2              0   1
  PTEN MUTATED    13   9
  PTEN WILD-TYPE 119 122
  PTEN MUTATED PTEN WILD-TYPE 
            22            241 
  PTEN MUTATED PTEN WILD-TYPE 
             9            122 
$`PTEN MUTATED`
TCGA-D3-A1Q4 TCGA-D3-A1Q7 TCGA-D3-A2J8 TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3MR 
      112.04       133.25        65.49        12.10        58.06       103.59 
TCGA-D3-A51T TCGA-D3-A5GN TCGA-D9-A6EC TCGA-EE-A17Z TCGA-EE-A29P TCGA-EE-A2GN 
       15.06       135.75        66.25         8.65        56.42        90.97 
TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A3AH TCGA-EE-A3JE TCGA-ER-A19E TCGA-ER-A19J 
       55.59        94.82       138.81        33.40        13.02         6.44 
TCGA-ER-A2NE TCGA-FR-A69P TCGA-FS-A1ZD TCGA-FW-A3I3 
       20.15         4.90        53.52         0.20 

$`PTEN WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q8 TCGA-D3-A1Q9 
       16.57        16.67       112.57        71.80        28.08        31.59 
TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J9 TCGA-D3-A2JA 
       90.90        95.74        43.43       103.10        23.77       115.53 
TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH 
      168.00        69.90        11.87        48.76       113.52        42.08 
TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C7 
      171.58        56.19        66.08        45.11       130.72        46.98 
TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML 
       46.32       166.52        86.93        60.23        24.53        13.87 
TCGA-D3-A3MO TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H 
        9.34        39.75        21.47       161.85        43.69        40.14 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A5GO TCGA-D3-A5GR 
      131.90        18.38        10.03        51.68       137.92       166.19 
TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX 
        7.43       125.19       151.53        54.67         3.65         6.41 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-DA-A1HV TCGA-DA-A1HW 
       11.34         3.25         9.90        25.18        48.89        36.03 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 
      117.21        20.38       194.83       176.55        35.93       107.34 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
       61.18        53.92        65.92        23.44        68.09        28.60 
TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG 
       10.49       215.44        15.68        13.87        10.16        45.11 
TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A180 
       35.01         3.55        52.01        29.82        27.22        94.98 
TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B 
       33.73        14.70        26.89        68.15         4.96       109.64 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B 
      151.27        78.87       168.26        13.55        63.35        80.61 
TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L 
       47.84        13.97        39.62        72.07        32.19         2.60 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V 
       44.35        18.61        37.35        14.47        55.92        25.87 
TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 
      171.55        17.92        46.82       102.90        24.43        39.29 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH 
       58.75        47.54        67.43       314.56       135.95       208.04 
TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GO 
       48.72        89.33        54.74        79.66        75.48       101.95 
TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GT TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 
       13.91        14.30        44.88        21.67       129.27        28.83 
TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH 
       19.76        61.51        47.28       103.27       103.20        16.96 
TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN 
      204.66        96.23       144.76       203.05       167.90        47.54 
TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU 
      248.65        43.23       103.56       136.47        41.59        53.26 
TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF 
      124.31       122.73        25.84         3.68        54.51        13.81 
TCGA-EE-A3AG TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 
       23.47       172.18       127.20        36.95        64.08        34.32 
TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 
       53.19        27.35       101.79       148.08        31.40        35.44 
TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C 
       13.94        50.76         9.17        77.75        98.40        48.89 
TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M 
       12.59        26.37       268.93       152.35       131.51        61.05 
TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 
       44.05       162.08        50.89        37.25       148.18        79.99 
TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES 
       43.82        23.34        16.37        31.27        32.05       247.04 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A1YW 
       80.32        46.98        33.21        92.98       174.21       216.92 
TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 
       48.59       228.59       202.65        20.91        28.08         7.79 
TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG 
       27.72        48.85       357.37        40.27        15.45         9.70 
TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ 
       32.75        47.38        23.93       101.26        74.73       133.55 
TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY 
       11.41       148.80        53.16        26.56        49.48        27.09 
TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 
       27.02        77.82        66.67        28.73       174.84        12.43 
TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV 
       26.73        49.45        77.88        22.92        47.54         0.16 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 
        2.40         9.90         7.23        14.04       120.46       117.93 
TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D 
       84.72        10.13        64.44        62.79        32.48        39.58 
TCGA-QB-A6FS 
        6.67 

  PTEN MUTATED PTEN WILD-TYPE 
          0.20           0.16 
  PTEN MUTATED PTEN WILD-TYPE 
        138.81         357.37 
  PTEN MUTATED PTEN WILD-TYPE 
        56.005         47.540 
[1] "0.2 - 138.8 (56.0)" "0.2 - 357.4 (47.5)"
[1] "hr=" "1"  
D10V3, continuous
                vv
clus             DISTANT METASTASIS PRIMARY TUMOR
  PTEN MUTATED                    2             1
  PTEN WILD-TYPE                 33             3
                vv
clus             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  PTEN MUTATED                                           3                  16
  PTEN WILD-TYPE                                        55                 154
D10V4, multiclass
                                           clus
vv                                          PTEN MUTATED PTEN WILD-TYPE
  DISTANT METASTASIS                                   2             33
  PRIMARY TUMOR                                        1              3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE            3             55
  REGIONAL LYMPH NODE                                 16            154
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  PTEN MUTATED             0       1       1        1        5        1
  PTEN WILD-TYPE          10       5      21        9       19       16
                vv
clus             STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  PTEN MUTATED           2         1         1         1          1          1
  PTEN WILD-TYPE         8        13         8        30         12         21
                vv
clus             STAGE IIIC STAGE IV
  PTEN MUTATED            4        2
  PTEN WILD-TYPE         40       10
D10V5, multiclass
             clus
vv            PTEN MUTATED PTEN WILD-TYPE
  I OR II NOS            0             10
  STAGE 0                1              5
  STAGE I                1             21
  STAGE IA               1              9
  STAGE IB               5             19
  STAGE II               1             16
  STAGE IIA              2              8
  STAGE IIB              1             13
  STAGE IIC              1              8
  STAGE III              1             30
  STAGE IIIA             1             12
  STAGE IIIB             1             21
  STAGE IIIC             4             40
  STAGE IV               2             10
[1] 14  2
[1] 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       4  7  3  5
  PTEN WILD-TYPE    47 51 50 50
D10V6, multiclass
       clus
vv      PTEN MUTATED PTEN WILD-TYPE
  T0+T1            4             47
  T2               7             51
  T3               3             50
  T4               5             50
[1] 4 2
[1] TRUE
[1] "dimension 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    14   5   1   2
  PTEN WILD-TYPE 124  43  31  31
D10V7, multiclass
    clus
vv   PTEN MUTATED PTEN WILD-TYPE
  N0           14            124
  N1            5             43
  N2            1             31
  N3            2             31
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              M0  M1 M1A M1B M1C
  PTEN MUTATED    19   2   0   0   0
  PTEN WILD-TYPE 221   2   2   2   5
D10V8, multiclass
     clus
vv    PTEN MUTATED PTEN WILD-TYPE
  M0            19            221
  M1             2              2
  M1A            0              2
  M1B            0              2
  M1C            0              5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V9, binary
                cls
clus              0  1
  PTEN MUTATED    9  7
  PTEN WILD-TYPE 93 60
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTEN MUTATED      9    7
  PTEN WILD-TYPE   93   60
     clus
vv    PTEN MUTATED PTEN WILD-TYPE
  NO             9             93
  YES            7             60
[1] 2 2
[1] FALSE
D10V10, binary
                cls
clus               0   1
  PTEN MUTATED     4  18
  PTEN WILD-TYPE  29 217
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTEN MUTATED      4   18
  PTEN WILD-TYPE   29  217
     clus
vv    PTEN MUTATED PTEN WILD-TYPE
  NO             4             29
  YES           18            217
[1] 2 2
[1] FALSE
D10V11, continuous
D10V12, binary
                cls
clus               0   1
  PTEN MUTATED    12  10
  PTEN WILD-TYPE  91 155
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTEN MUTATED     12   10
  PTEN WILD-TYPE   91  155
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  FEMALE           12             91
  MALE             10            155
[1] 2 2
[1] FALSE
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PTEN MUTATED       0                         0    22
  PTEN WILD-TYPE     3                         1   242
D10V13, multiclass
                           clus
vv                          PTEN MUTATED PTEN WILD-TYPE
  ASIAN                                0              3
  BLACK OR AFRICAN AMERICAN            0              1
  WHITE                               22            242
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V14, binary
                cls
clus               0   1
  PTEN MUTATED     0  22
  PTEN WILD-TYPE   3 239
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTEN MUTATED      0   22
  PTEN WILD-TYPE    3  239
                        clus
vv                       PTEN MUTATED PTEN WILD-TYPE
  HISPANIC OR LATINO                0              3
  NOT HISPANIC OR LATINO           22            239
[1] 2 2
[1] FALSE

Clustering(11) Variable = NOTCH2NL MUTATION ANALYSIS
D11V1, survival
                    sevent
clus2                  0   1
  NOTCH2NL MUTATED     7   8
  NOTCH2NL WILD-TYPE 121 122
  NOTCH2NL MUTATED NOTCH2NL WILD-TYPE 
                15                243 
  NOTCH2NL MUTATED NOTCH2NL WILD-TYPE 
                 8                122 
$`NOTCH2NL MUTATED`
TCGA-D3-A1Q6 TCGA-D3-A1QA TCGA-D3-A3C7 TCGA-EE-A184 TCGA-EE-A29E TCGA-EE-A29Q 
       70.16        45.83        46.98         5.13        38.63         8.09 
TCGA-EE-A2GB TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2M5 TCGA-EE-A3AB TCGA-EE-A3AG 
       39.39        30.84         5.42         8.84       122.73        15.95 
TCGA-EE-A3AH TCGA-FS-A1Z4 TCGA-FS-A4FD 
       12.72        15.52         2.27 

$`NOTCH2NL WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       16.47         8.52       111.09        32.42       110.79        28.08 
TCGA-D3-A1Q9 TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 
       22.55        81.24        10.29        85.32         8.38        21.14 
TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JG 
       88.50        68.22        69.90        11.41        30.87         7.50 
TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP 
       36.16         6.31        92.42        56.19        64.44        45.11 
TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE 
      114.67        15.25        46.32        82.29        61.38        13.32 
TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV 
       24.00         6.31         9.34       103.59        26.37         5.39 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N 
       80.22        42.71        15.09        41.10        17.72         8.84 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS 
       20.48        13.94        52.01        47.87         1.55         6.97 
TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC 
       23.11         4.01         2.89         9.90        11.31        13.22 
TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 
       48.79        35.80        51.12        10.03        39.19        13.68 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB 
        9.99        44.52        36.69        25.15         4.93        22.36 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q 
        6.64        19.36         7.00        17.56        14.83        13.15 
TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y 
        0.20         0.00         0.00        13.22        11.57        10.55 
TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A185 
        6.31         8.12         1.12         1.35        12.20         4.31 
TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A 
       36.07         4.34         5.13         9.21         1.18         7.99 
TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L 
        9.90        37.97        11.15         8.55         4.41         1.08 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V 
       27.12         9.50        12.03         8.84         9.99         2.43 
TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 
        8.68         8.09        11.31        49.22        23.90         9.67 
TCGA-EE-A2A6 TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI 
        8.94        34.29        17.98        34.92        47.21        30.08 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GR 
       19.43        16.01        35.54        28.31        33.83         1.15 
TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 
       13.02        34.98        36.33        98.27         2.70         6.18 
TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI 
       47.51         9.53        29.46        44.25         7.96        14.56 
TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP 
       63.42       111.78       111.91        56.02        25.08        26.99 
TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA 
       21.60        29.65        27.16        23.05         5.56       124.31 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-EE-A3J4 
       25.84         3.68        30.15        13.81         3.22        22.92 
TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE 
       21.60        21.60        16.14        22.22        27.35         0.46 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 
       13.94        33.60        31.40        18.61        12.95        38.40 
TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E 
        5.72        76.41        25.18         3.78         3.52        11.90 
TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M 
       11.11       114.15        34.88         4.21        13.45        28.60 
TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 
       42.84        34.68         9.57        36.07        17.72        78.44 
TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH 
       11.80         1.87         1.51        13.08        12.62        11.74 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A 
        9.04         6.58        22.49         1.71        18.41        85.74 
TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
        4.90        64.47         3.45        11.01        23.80        14.24 
TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE 
        7.33         7.30         3.39        20.38         8.22        19.53 
TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM 
       11.08         7.17        30.87        12.92        12.89        47.38 
TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU 
       52.08         8.65         8.81        49.15        40.64         8.68 
TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 
       27.39         0.82         5.23        53.85         7.36        28.73 
TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FW-A3I3 TCGA-FW-A3R5 
       14.20        10.78         5.98         6.41         0.20         0.99 
TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 
        0.13         0.16         0.43         9.90         7.23        12.85 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 
       24.85        31.33        84.72        10.13        16.24        15.42 
TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS 
       12.16        14.70         5.79 

  NOTCH2NL MUTATED NOTCH2NL WILD-TYPE 
              2.27               0.00 
  NOTCH2NL MUTATED NOTCH2NL WILD-TYPE 
            122.73             124.31 
  NOTCH2NL MUTATED NOTCH2NL WILD-TYPE 
             15.95              14.56 
[1] "2.3 - 122.7 (15.9)" "0.0 - 124.3 (14.6)"
[1] "hr=" "1.1"
D11V2, survival
                    sevent
clus2                  0   1
  NOTCH2NL MUTATED     7   8
  NOTCH2NL WILD-TYPE 125 123
  NOTCH2NL MUTATED NOTCH2NL WILD-TYPE 
                15                248 
  NOTCH2NL MUTATED NOTCH2NL WILD-TYPE 
                 8                123 
$`NOTCH2NL MUTATED`
TCGA-D3-A1Q6 TCGA-D3-A1QA TCGA-D3-A3C7 TCGA-EE-A184 TCGA-EE-A29E TCGA-EE-A29Q 
       71.80        90.90        46.98        68.15        39.62        37.35 
TCGA-EE-A2GB TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2M5 TCGA-EE-A3AB TCGA-EE-A3AG 
       47.54       101.95        13.91        21.67       122.73        23.47 
TCGA-EE-A3AH TCGA-FS-A1Z4 TCGA-FS-A4FD 
      138.81        28.08        77.88 

$`NOTCH2NL WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       16.57        16.67       112.04       112.57       133.25        28.08 
TCGA-D3-A1Q9 TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 
       31.59        95.74        43.43       103.10        65.49        23.77 
TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JG 
      115.53       168.00        69.90        11.87        48.76       113.52 
TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP 
       42.08        12.10       171.58        56.19        66.08        45.11 
TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE 
      130.72        58.06        46.32       166.52        86.93        60.23 
TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV 
       24.53        13.87         9.34       103.59        39.75        21.47 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N 
      161.85        43.69        40.14       131.90        18.38        10.03 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS 
       51.68        15.06       135.75       137.92       166.19         7.43 
TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 
      125.19       151.53        54.67         3.65         6.41        11.34 
TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1HW 
        3.25         9.90        25.18        66.25        48.89        36.03 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 
      117.21        20.38       194.83       176.55        35.93       107.34 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
       61.18        53.92        65.92        23.44        68.09        28.60 
TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG 
       10.49       215.44        15.68        13.87        10.16        45.11 
TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z 
       35.01         3.55        52.01        29.82        27.22         8.65 
TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B 
       94.98        33.73        14.70        26.89         4.96       109.64 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B 
      151.27        78.87       168.26        13.55        63.35        80.61 
TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M 
       47.84        13.97        72.07        32.19         2.60        44.35 
TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W 
       18.61        56.42        14.47        55.92        25.87       171.55 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 
       17.92        46.82       102.90        24.43        39.29        58.75 
TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ 
       67.43       314.56       135.95       208.04        48.72        89.33 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GR TCGA-EE-A2GS 
       54.74        79.66        75.48        90.97        14.30        55.59 
TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC 
       44.88        94.82       129.27        28.83        19.76        61.51 
TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ 
       47.28       103.27       103.20        16.96       204.66        96.23 
TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ 
      144.76       203.05       167.90        47.54       248.65        43.23 
TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AC 
      103.56       136.47        41.59        53.26       124.31        25.84 
TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 
        3.68        54.51        13.81       172.18       127.20        36.95 
TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH 
       64.08        34.32        53.19        27.35        33.40       101.79 
TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 
      148.08        31.40        35.44        13.94        50.76         9.17 
TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F 
       77.75        98.40        48.89        12.59        13.02        26.37 
TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N 
      268.93       152.35         6.44       131.51        61.05        44.05 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
      162.08        50.89        37.25       148.18        79.99        43.82 
TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES 
       23.34        20.15        16.37        31.27        32.05       247.04 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
       80.32        46.98        33.21        92.98       174.21         4.90 
TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z7 
      216.92        48.59       228.59       202.65        20.91         7.79 
TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF 
       27.72        48.85       357.37        53.52        40.27        15.45 
TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP 
        9.70        32.75        47.38        23.93       101.26        74.73 
TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW 
      133.55        11.41       148.80        53.16        26.56        49.48 
TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 
       27.09        27.02        77.82        66.67        28.73       174.84 
TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU 
       12.43        26.73        49.45         0.20        22.92        47.54 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 
        0.16         2.40         9.90         7.23        14.04       120.46 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
      117.93        84.72        10.13        64.44        62.79        32.48 
TCGA-GN-A26D TCGA-QB-A6FS 
       39.58         6.67 

  NOTCH2NL MUTATED NOTCH2NL WILD-TYPE 
             13.91               0.16 
  NOTCH2NL MUTATED NOTCH2NL WILD-TYPE 
            138.81             357.37 
  NOTCH2NL MUTATED NOTCH2NL WILD-TYPE 
            47.540             48.655 
[1] "13.9 - 138.8 (47.5)" "0.2 - 357.4 (48.7)" 
[1] "hr=" "1.2"
D11V3, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  NOTCH2NL MUTATED                    1             0
  NOTCH2NL WILD-TYPE                 34             4
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  NOTCH2NL MUTATED                                           5
  NOTCH2NL WILD-TYPE                                        53
                    vv
clus                 REGIONAL LYMPH NODE
  NOTCH2NL MUTATED                     9
  NOTCH2NL WILD-TYPE                 161
D11V4, multiclass
                                           clus
vv                                          NOTCH2NL MUTATED NOTCH2NL WILD-TYPE
  DISTANT METASTASIS                                       1                 34
  PRIMARY TUMOR                                            0                  4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                5                 53
  REGIONAL LYMPH NODE                                      9                161
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  NOTCH2NL MUTATED             0       0       2        0        2        2
  NOTCH2NL WILD-TYPE          10       6      20       10       22       15
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  NOTCH2NL MUTATED           0         1         0         4          0
  NOTCH2NL WILD-TYPE        10        13         9        27         13
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  NOTCH2NL MUTATED            3          1        0
  NOTCH2NL WILD-TYPE         19         43       12
D11V5, multiclass
             clus
vv            NOTCH2NL MUTATED NOTCH2NL WILD-TYPE
  I OR II NOS                0                 10
  STAGE 0                    0                  6
  STAGE I                    2                 20
  STAGE IA                   0                 10
  STAGE IB                   2                 22
  STAGE II                   2                 15
  STAGE IIA                  0                 10
  STAGE IIB                  1                 13
  STAGE IIC                  0                  9
  STAGE III                  4                 27
  STAGE IIIA                 0                 13
  STAGE IIIB                 3                 19
  STAGE IIIC                 1                 43
  STAGE IV                   0                 12
[1] 14  2
[1] 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
  NOTCH2NL MUTATED       4  5  4  2
  NOTCH2NL WILD-TYPE    47 53 49 53
D11V6, multiclass
       clus
vv      NOTCH2NL MUTATED NOTCH2NL WILD-TYPE
  T0+T1                4                 47
  T2                   5                 53
  T3                   4                 49
  T4                   2                 53
[1] 4 2
[1] TRUE
[1] "dimension 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
  NOTCH2NL MUTATED     7   5   2   1
  NOTCH2NL WILD-TYPE 131  43  30  32
D11V7, multiclass
    clus
vv   NOTCH2NL MUTATED NOTCH2NL WILD-TYPE
  N0                7                131
  N1                5                 43
  N2                2                 30
  N3                1                 32
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1 M1A M1B M1C
  NOTCH2NL MUTATED    15   0   0   0   0
  NOTCH2NL WILD-TYPE 225   4   2   2   5
D11V8, multiclass
     clus
vv    NOTCH2NL MUTATED NOTCH2NL WILD-TYPE
  M0                15                225
  M1                 0                  4
  M1A                0                  2
  M1B                0                  2
  M1C                0                  5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V9, binary
                    cls
clus                  0  1
  NOTCH2NL MUTATED    7  3
  NOTCH2NL WILD-TYPE 95 64
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  NOTCH2NL MUTATED      7    3
  NOTCH2NL WILD-TYPE   95   64
     clus
vv    NOTCH2NL MUTATED NOTCH2NL WILD-TYPE
  NO                 7                 95
  YES                3                 64
[1] 2 2
[1] FALSE
D11V10, binary
                    cls
clus                   0   1
  NOTCH2NL MUTATED     3  12
  NOTCH2NL WILD-TYPE  30 223
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  NOTCH2NL MUTATED      3   12
  NOTCH2NL WILD-TYPE   30  223
     clus
vv    NOTCH2NL MUTATED NOTCH2NL WILD-TYPE
  NO                 3                 30
  YES               12                223
[1] 2 2
[1] FALSE
D11V11, continuous
D11V12, binary
                    cls
clus                   0   1
  NOTCH2NL MUTATED     3  12
  NOTCH2NL WILD-TYPE 100 153
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  NOTCH2NL MUTATED      3   12
  NOTCH2NL WILD-TYPE  100  153
        clus
vv       NOTCH2NL MUTATED NOTCH2NL WILD-TYPE
  FEMALE                3                100
  MALE                 12                153
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  NOTCH2NL MUTATED       0                         0    15
  NOTCH2NL WILD-TYPE     3                         1   249
D11V13, multiclass
                           clus
vv                          NOTCH2NL MUTATED NOTCH2NL WILD-TYPE
  ASIAN                                    0                  3
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                   15                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"
D11V14, binary
                    cls
clus                   0   1
  NOTCH2NL MUTATED     0  15
  NOTCH2NL WILD-TYPE   3 246
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  NOTCH2NL MUTATED      0   15
  NOTCH2NL WILD-TYPE    3  246
                        clus
vv                       NOTCH2NL MUTATED NOTCH2NL WILD-TYPE
  HISPANIC OR LATINO                    0                  3
  NOT HISPANIC OR LATINO               15                246
[1] 2 2
[1] FALSE

Clustering(12) Variable = MAP2K1 MUTATION ANALYSIS
D12V1, survival
                  sevent
clus2                0   1
  MAP2K1 MUTATED     7   3
  MAP2K1 WILD-TYPE 121 127
  MAP2K1 MUTATED MAP2K1 WILD-TYPE 
              10              248 
  MAP2K1 MUTATED MAP2K1 WILD-TYPE 
               3              127 
$`MAP2K1 MUTATED`
TCGA-D3-A1Q6 TCGA-D3-A1Q8 TCGA-D3-A3MV TCGA-D3-A51F TCGA-EB-A5UN TCGA-EE-A29M 
       70.16        28.08         5.39        42.71        13.22        27.12 
TCGA-EE-A29R TCGA-EE-A2M5 TCGA-EE-A2MU TCGA-EE-A3JH 
        8.84         8.84         5.56        13.94 

$`MAP2K1 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q9 
       16.47         8.52       111.09        32.42       110.79        22.55 
TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 
       45.83        81.24        10.29        85.32         8.38        21.14 
TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JG 
       88.50        68.22        69.90        11.41        30.87         7.50 
TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP 
       36.16         6.31        92.42        56.19        64.44        45.11 
TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC 
      114.67        15.25        46.98        46.32        82.29        61.38 
TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU 
       13.32        24.00         6.31         9.34       103.59        26.37 
TCGA-D3-A51E TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R 
       80.22        15.09        41.10        17.72         8.84        20.48 
TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU 
       13.94        52.01        47.87         1.55         6.97        23.11 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1HV 
        4.01         2.89         9.90        11.31        13.22        48.79 
TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 
       35.80        51.12        10.03        39.19        13.68         9.99 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC 
       44.52        36.69        25.15         4.93        22.36         6.64 
TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R 
       19.36         7.00        17.56        14.83        13.15         0.20 
TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 
        0.00         0.00        11.57        10.55         6.31         8.12 
TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B 
        1.12         1.35        12.20         5.13         4.31        36.07 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B 
        4.34         5.13         9.21         1.18         7.99         9.90 
TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L 
       37.97        11.15        38.63         8.55         4.41         1.08 
TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W 
        9.50        12.03         8.09         9.99         2.43         8.68 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 
        8.09        11.31        49.22        23.90         9.67         8.94 
TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI 
       39.39        34.29        17.98        34.92        47.21        30.08 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO 
       19.43        16.01        35.54        28.31        33.83        30.84 
TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M6 
        5.42         1.15        13.02        34.98        36.33        98.27 
TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG 
        2.70         6.18        47.51         9.53        29.46        44.25 
TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM 
        7.96        14.56        63.42       111.78       111.91        56.02 
TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT 
       25.08        26.99        21.60        29.65        27.16        23.05 
TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF 
      124.31       122.73        25.84         3.68        30.15        13.81 
TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 
       15.95        12.72         3.22        22.92        21.60        21.60 
TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JI TCGA-ER-A193 
       16.14        22.22        27.35         0.46        33.60        31.40 
TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B 
       18.61        12.95        38.40         5.72        76.41        25.18 
TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H 
        3.78         3.52        11.90        11.11       114.15        34.88 
TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q 
        4.21        13.45        28.60        42.84        34.68         9.57 
TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE 
       36.07        17.72        78.44        11.80         1.87         1.51 
TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV 
       13.08        12.62        11.74         9.04         6.58        22.49 
TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX 
        1.71        18.41        85.74         4.90        64.47         3.45 
TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA 
       11.01        23.80        14.24        15.52         7.33         7.30 
TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG 
        3.39        20.38         8.22        19.53        11.08         7.17 
TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ 
       30.87        12.92        12.89        47.38        52.08         8.65 
TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY 
        8.81        49.15        40.64         8.68        27.39         0.82 
TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 
        5.23        53.85         7.36        28.73        14.20        10.78 
TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU 
        5.98         6.41         2.27         0.20         0.99         0.13 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 
        0.16         0.43         9.90         7.23        12.85        24.85 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
       31.33        84.72        10.13        16.24        15.42        12.16 
TCGA-GN-A26D TCGA-QB-A6FS 
       14.70         5.79 

  MAP2K1 MUTATED MAP2K1 WILD-TYPE 
            5.39             0.00 
  MAP2K1 MUTATED MAP2K1 WILD-TYPE 
           70.16           124.31 
  MAP2K1 MUTATED MAP2K1 WILD-TYPE 
           13.58            14.96 
[1] "5.4 - 70.2 (13.6)"  "0.0 - 124.3 (15.0)"
[1] "hr=" "1.6"
D12V2, survival
                  sevent
clus2                0   1
  MAP2K1 MUTATED     8   3
  MAP2K1 WILD-TYPE 124 128
  MAP2K1 MUTATED MAP2K1 WILD-TYPE 
              11              252 
  MAP2K1 MUTATED MAP2K1 WILD-TYPE 
               3              128 
$`MAP2K1 MUTATED`
TCGA-D3-A1Q6 TCGA-D3-A1Q8 TCGA-D3-A3MV TCGA-D3-A51F TCGA-D9-A149 TCGA-EB-A5UN 
       71.80        28.08        21.47        43.69        54.67        52.01 
TCGA-EE-A29M TCGA-EE-A29R TCGA-EE-A2M5 TCGA-EE-A2MU TCGA-EE-A3JH 
       44.35        14.47        21.67        53.26       101.79 

$`MAP2K1 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q9 
       16.57        16.67       112.04       112.57       133.25        31.59 
TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 
       90.90        95.74        43.43       103.10        65.49        23.77 
TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JG 
      115.53       168.00        69.90        11.87        48.76       113.52 
TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP 
       42.08        12.10       171.58        56.19        66.08        45.11 
TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC 
      130.72        58.06        46.98        46.32       166.52        86.93 
TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU 
       60.23        24.53        13.87         9.34       103.59        39.75 
TCGA-D3-A51E TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R 
      161.85        40.14       131.90        18.38        10.03        51.68 
TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU 
       15.06       135.75       137.92       166.19         7.43       125.19 
TCGA-D9-A148 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 
      151.53         3.65         6.41        11.34         3.25         9.90 
TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 
       25.18        66.25        48.89        36.03       117.21        20.38 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 
      194.83       176.55        35.93       107.34        61.18        53.92 
TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 
       65.92        23.44        68.09        28.60        10.49       215.44 
TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL 
       15.68        13.87        10.16        45.11        35.01         3.55 
TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 
       29.82        27.22         8.65        94.98        33.73        14.70 
TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F 
       26.89        68.15         4.96       109.64       151.27        78.87 
TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D 
      168.26        13.55        63.35        80.61        47.84        13.97 
TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P 
       39.62        72.07        32.19         2.60        18.61        56.42 
TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 
       37.35        55.92        25.87       171.55        17.92        46.82 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC 
      102.90        24.43        39.29        58.75        47.54        67.43 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK 
      314.56       135.95       208.04        48.72        89.33        54.74 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR 
       79.66        75.48        90.97       101.95        13.91        14.30 
TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 
       55.59        44.88        94.82       129.27        28.83        19.76 
TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI 
       61.51        47.28       103.27       103.20        16.96       204.66 
TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP 
       96.23       144.76       203.05       167.90        47.54       248.65 
TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AB 
       43.23       103.56       136.47        41.59       124.31       122.73 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH 
       25.84         3.68        54.51        13.81        23.47       138.81 
TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA 
      172.18       127.20        36.95        64.08        34.32        53.19 
TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 
       27.35        33.40       148.08        31.40        35.44        13.94 
TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D 
       50.76         9.17        77.75        98.40        48.89        12.59 
TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L 
       13.02        26.37       268.93       152.35         6.44       131.51 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W 
       61.05        44.05       162.08        50.89        37.25       148.18 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG 
       79.99        43.82        23.34        20.15        16.37        31.27 
TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN 
       32.05       247.04        80.32        46.98        33.21        92.98 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 
      174.21         4.90       216.92        48.59       228.59       202.65 
TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC 
       20.91        28.08         7.79        27.72        48.85       357.37 
TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ 
       53.52        40.27        15.45         9.70        32.75        47.38 
TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS 
       23.93       101.26        74.73       133.55        11.41       148.80 
TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 
       53.16        26.56        49.48        27.09        27.02        77.82 
TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC 
       66.67        28.73       174.84        12.43        26.73        49.45 
TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY 
       77.88         0.20        22.92        47.54         0.16         2.40 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        9.90         7.23        14.04       120.46       117.93        84.72 
TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS 
       10.13        64.44        62.79        32.48        39.58         6.67 

  MAP2K1 MUTATED MAP2K1 WILD-TYPE 
           14.47             0.16 
  MAP2K1 MUTATED MAP2K1 WILD-TYPE 
          101.79           357.37 
  MAP2K1 MUTATED MAP2K1 WILD-TYPE 
          44.350           48.655 
[1] "14.5 - 101.8 (44.4)" "0.2 - 357.4 (48.7)" 
[1] "hr=" "1.3"
D12V3, continuous
                  vv
clus               DISTANT METASTASIS PRIMARY TUMOR
  MAP2K1 MUTATED                    1             0
  MAP2K1 WILD-TYPE                 34             4
                  vv
clus               REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  MAP2K1 MUTATED                                           4
  MAP2K1 WILD-TYPE                                        54
                  vv
clus               REGIONAL LYMPH NODE
  MAP2K1 MUTATED                     6
  MAP2K1 WILD-TYPE                 164
D12V4, multiclass
                                           clus
vv                                          MAP2K1 MUTATED MAP2K1 WILD-TYPE
  DISTANT METASTASIS                                     1               34
  PRIMARY TUMOR                                          0                4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE              4               54
  REGIONAL LYMPH NODE                                    6              164
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  MAP2K1 MUTATED             0       0       1        1        2        0
  MAP2K1 WILD-TYPE          10       6      21        9       22       17
                  vv
clus               STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  MAP2K1 MUTATED           0         0         1         1          0
  MAP2K1 WILD-TYPE        10        14         8        30         13
                  vv
clus               STAGE IIIB STAGE IIIC STAGE IV
  MAP2K1 MUTATED            1          2        1
  MAP2K1 WILD-TYPE         21         42       11
D12V5, multiclass
             clus
vv            MAP2K1 MUTATED MAP2K1 WILD-TYPE
  I OR II NOS              0               10
  STAGE 0                  0                6
  STAGE I                  1               21
  STAGE IA                 1                9
  STAGE IB                 2               22
  STAGE II                 0               17
  STAGE IIA                0               10
  STAGE IIB                0               14
  STAGE IIC                1                8
  STAGE III                1               30
  STAGE IIIA               0               13
  STAGE IIIB               1               21
  STAGE IIIC               2               42
  STAGE IV                 1               11
[1] 14  2
[1] 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
  MAP2K1 MUTATED       2  4  1  3
  MAP2K1 WILD-TYPE    49 54 52 52
D12V6, multiclass
       clus
vv      MAP2K1 MUTATED MAP2K1 WILD-TYPE
  T0+T1              2               49
  T2                 4               54
  T3                 1               52
  T4                 3               52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  MAP2K1 MUTATED     4   4   1   1
  MAP2K1 WILD-TYPE 134  44  31  32
D12V7, multiclass
    clus
vv   MAP2K1 MUTATED MAP2K1 WILD-TYPE
  N0              4              134
  N1              4               44
  N2              1               31
  N3              1               32
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                M0  M1 M1A M1B M1C
  MAP2K1 MUTATED    10   0   0   1   0
  MAP2K1 WILD-TYPE 230   4   2   1   5
D12V8, multiclass
     clus
vv    MAP2K1 MUTATED MAP2K1 WILD-TYPE
  M0              10              230
  M1               0                4
  M1A              0                2
  M1B              1                1
  M1C              0                5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V9, binary
                  cls
clus                0  1
  MAP2K1 MUTATED    4  4
  MAP2K1 WILD-TYPE 98 63
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAP2K1 MUTATED      4    4
  MAP2K1 WILD-TYPE   98   63
     clus
vv    MAP2K1 MUTATED MAP2K1 WILD-TYPE
  NO               4               98
  YES              4               63
[1] 2 2
[1] FALSE
D12V10, binary
                  cls
clus                 0   1
  MAP2K1 MUTATED     1  10
  MAP2K1 WILD-TYPE  32 225
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAP2K1 MUTATED      1   10
  MAP2K1 WILD-TYPE   32  225
     clus
vv    MAP2K1 MUTATED MAP2K1 WILD-TYPE
  NO               1               32
  YES             10              225
[1] 2 2
[1] FALSE
D12V11, continuous
D12V12, binary
                  cls
clus                 0   1
  MAP2K1 MUTATED     4   7
  MAP2K1 WILD-TYPE  99 158
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAP2K1 MUTATED      4    7
  MAP2K1 WILD-TYPE   99  158
        clus
vv       MAP2K1 MUTATED MAP2K1 WILD-TYPE
  FEMALE              4               99
  MALE                7              158
[1] 2 2
[1] FALSE
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MAP2K1 MUTATED       0                         0    11
  MAP2K1 WILD-TYPE     3                         1   253
D12V13, multiclass
                           clus
vv                          MAP2K1 MUTATED MAP2K1 WILD-TYPE
  ASIAN                                  0                3
  BLACK OR AFRICAN AMERICAN              0                1
  WHITE                                 11              253
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V14, binary
                  cls
clus                 0   1
  MAP2K1 MUTATED     0  11
  MAP2K1 WILD-TYPE   3 250
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAP2K1 MUTATED      0   11
  MAP2K1 WILD-TYPE    3  250
                        clus
vv                       MAP2K1 MUTATED MAP2K1 WILD-TYPE
  HISPANIC OR LATINO                  0                3
  NOT HISPANIC OR LATINO             11              250
[1] 2 2
[1] FALSE

Clustering(13) Variable = PPP6C MUTATION ANALYSIS
D13V1, survival
                 sevent
clus2               0   1
  PPP6C MUTATED    15   5
  PPP6C WILD-TYPE 113 125
  PPP6C MUTATED PPP6C WILD-TYPE 
             20             238 
  PPP6C MUTATED PPP6C WILD-TYPE 
              5             125 
$`PPP6C MUTATED`
TCGA-D3-A3C8 TCGA-D3-A3MV TCGA-D9-A6EC TCGA-DA-A1I1 TCGA-DA-A3F5 TCGA-DA-A3F8 
       46.32         5.39        13.22        39.19        17.56        14.83 
TCGA-EB-A5SG TCGA-EE-A29L TCGA-EE-A29R TCGA-EE-A29W TCGA-EE-A2GD TCGA-EE-A2GM 
        0.00         1.08         8.84         8.68        17.98        28.31 
TCGA-EE-A2M6 TCGA-EE-A2ML TCGA-EE-A3JI TCGA-FS-A1ZC TCGA-FS-A1ZH TCGA-FS-A1ZW 
       98.27       111.91        33.60        20.38        30.87        27.39 
TCGA-FW-A3R5 TCGA-GN-A267 
        0.99        16.24 

$`PPP6C WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.47         8.52       111.09        32.42        70.16       110.79 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       28.08        22.55        45.83        81.24        10.29        85.32 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
        8.38        21.14        88.50        68.22        69.90        11.41 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       30.87         7.50        36.16         6.31        92.42        56.19 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3CB 
       64.44        45.11       114.67        15.25        46.98        82.29 
TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR 
       61.38        13.32        24.00         6.31         9.34       103.59 
TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K 
       26.37        80.22        42.71        15.09        41.10        17.72 
TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR 
        8.84        20.48        13.94        52.01        47.87         1.55 
TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA 
        6.97        23.11         4.01         2.89         9.90        11.31 
TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 
       48.79        35.80        51.12        10.03        13.68         9.99 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC 
       44.52        36.69        25.15         4.93        22.36         6.64 
TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SH TCGA-EB-A5UN 
       19.36         7.00        13.15         0.20         0.00        13.22 
TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 
       11.57        10.55         6.31         8.12         1.12         1.35 
TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F 
       12.20         5.13         4.31        36.07         4.34         5.13 
TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D 
        9.21         1.18         7.99         9.90        37.97        11.15 
TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P 
       38.63         8.55         4.41        27.12         9.50        12.03 
TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 
        8.09         9.99         2.43         8.09        11.31        49.22 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GE 
       23.90         9.67         8.94        39.39        34.29        34.92 
TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GN 
       47.21        30.08        19.43        16.01        35.54        33.83 
TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU 
       30.84         5.42         1.15        13.02        34.98        36.33 
TCGA-EE-A2M5 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME 
        8.84         2.70         6.18        47.51         9.53        29.46 
TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2MM 
       44.25         7.96        14.56        63.42       111.78        56.02 
TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT 
       25.08        26.99        21.60        29.65        27.16        23.05 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE 
        5.56       124.31       122.73        25.84         3.68        30.15 
TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 
       13.81        15.95        12.72         3.22        22.92        21.60 
TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH 
       21.60        16.14        22.22        27.35         0.46        13.94 
TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A 
       31.40        18.61        12.95        38.40         5.72        76.41 
TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G 
       25.18         3.78         3.52        11.90        11.11       114.15 
TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P 
       34.88         4.21        13.45        28.60        42.84        34.68 
TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
        9.57        36.07        17.72        78.44        11.80         1.87 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET 
        1.51        13.08        12.62        11.74         9.04         6.58 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW 
       22.49         1.71        18.41        85.74         4.90        64.47 
TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 
        3.45        11.01        23.80        14.24        15.52         7.33 
TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG 
        7.30         3.39         8.22        19.53        11.08         7.17 
TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR 
       12.92        12.89        47.38        52.08         8.65         8.81 
TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 
       49.15        40.64         8.68         0.82         5.23        53.85 
TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC 
        7.36        28.73        14.20        10.78         5.98         6.41 
TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
        2.27         0.20         0.13         0.16         0.43         9.90 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 
        7.23        12.85        24.85        31.33        84.72        10.13 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS 
       15.42        12.16        14.70         5.79 

  PPP6C MUTATED PPP6C WILD-TYPE 
              0               0 
  PPP6C MUTATED PPP6C WILD-TYPE 
         111.91          124.31 
  PPP6C MUTATED PPP6C WILD-TYPE 
          17.77           14.22 
[1] "0.0 - 111.9 (17.8)" "0.0 - 124.3 (14.2)"
[1] "hr=" "2.2"
D13V2, survival
                 sevent
clus2               0   1
  PPP6C MUTATED    15   5
  PPP6C WILD-TYPE 117 126
  PPP6C MUTATED PPP6C WILD-TYPE 
             20             243 
  PPP6C MUTATED PPP6C WILD-TYPE 
              5             126 
$`PPP6C MUTATED`
TCGA-D3-A3C8 TCGA-D3-A3MV TCGA-D9-A6EC TCGA-DA-A1I1 TCGA-DA-A3F5 TCGA-DA-A3F8 
       46.32        21.47        66.25       194.83       215.44        15.68 
TCGA-EB-A5SG TCGA-EE-A29L TCGA-EE-A29R TCGA-EE-A29W TCGA-EE-A2GD TCGA-EE-A2GM 
       45.11         2.60        14.47       171.55       314.56        75.48 
TCGA-EE-A2M6 TCGA-EE-A2ML TCGA-EE-A3JI TCGA-FS-A1ZC TCGA-FS-A1ZH TCGA-FS-A1ZW 
      129.27       203.05       148.08       357.37        32.75        49.48 
TCGA-FW-A3R5 TCGA-GN-A267 
       22.92        64.44 

$`PPP6C WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.57        16.67       112.04       112.57        71.80       133.25 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       28.08        31.59        90.90        95.74        43.43       103.10 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
       65.49        23.77       115.53       168.00        69.90        11.87 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       48.76       113.52        42.08        12.10       171.58        56.19 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3CB 
       66.08        45.11       130.72        58.06        46.98       166.52 
TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR 
       86.93        60.23        24.53        13.87         9.34       103.59 
TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K 
       39.75       161.85        43.69        40.14       131.90        18.38 
TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR 
       10.03        51.68        15.06       135.75       137.92       166.19 
TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX 
        7.43       125.19       151.53        54.67         3.65         6.41 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-DA-A1HV TCGA-DA-A1HW 
       11.34         3.25         9.90        25.18        48.89        36.03 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 
      117.21        20.38       176.55        35.93       107.34        61.18 
TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 
       53.92        65.92        23.44        68.09        28.60        10.49 
TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X 
       13.87        10.16        35.01         3.55        52.01        29.82 
TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 
       27.22         8.65        94.98        33.73        14.70        26.89 
TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H 
       68.15         4.96       109.64       151.27        78.87       168.26 
TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E 
       13.55        63.35        80.61        47.84        13.97        39.62 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
       72.07        32.19        44.35        18.61        56.42        37.35 
TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 
       55.92        25.87        17.92        46.82       102.90        24.43 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GE TCGA-EE-A2GH 
       39.29        58.75        47.54        67.43       135.95       208.04 
TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GO 
       48.72        89.33        54.74        79.66        90.97       101.95 
TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 
       13.91        14.30        55.59        44.88        94.82        21.67 
TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG 
       28.83        19.76        61.51        47.28       103.27       103.20 
TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2MM TCGA-EE-A2MN 
       16.96       204.66        96.23       144.76       167.90        47.54 
TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU 
      248.65        43.23       103.56       136.47        41.59        53.26 
TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF 
      124.31       122.73        25.84         3.68        54.51        13.81 
TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 
       23.47       138.81       172.18       127.20        36.95        64.08 
TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A193 
       34.32        53.19        27.35        33.40       101.79        31.40 
TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B 
       35.44        13.94        50.76         9.17        77.75        98.40 
TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H 
       48.89        12.59        13.02        26.37       268.93       152.35 
TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q 
        6.44       131.51        61.05        44.05       162.08        50.89 
TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE 
       37.25       148.18        79.99        43.82        23.34        20.15 
TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV 
       16.37        31.27        32.05       247.04        80.32        46.98 
TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX 
       33.21        92.98       174.21         4.90       216.92        48.59 
TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA 
      228.59       202.65        20.91        28.08         7.79        27.72 
TCGA-FS-A1ZB TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZJ 
       48.85        53.52        40.27        15.45         9.70        47.38 
TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS 
       23.93       101.26        74.73       133.55        11.41       148.80 
TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 
       53.16        26.56        27.09        27.02        77.82        66.67 
TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD 
       28.73       174.84        12.43        26.73        49.45        77.88 
TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
        0.20        47.54         0.16         2.40         9.90         7.23 
TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A268 
       14.04       120.46       117.93        84.72        10.13        62.79 
TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS 
       32.48        39.58         6.67 

  PPP6C MUTATED PPP6C WILD-TYPE 
           2.60            0.16 
  PPP6C MUTATED PPP6C WILD-TYPE 
         357.37          268.93 
  PPP6C MUTATED PPP6C WILD-TYPE 
         65.345          47.540 
[1] "2.6 - 357.4 (65.3)" "0.2 - 268.9 (47.5)"
[1] "hr=" "4.4"
D13V3, continuous
                 vv
clus              DISTANT METASTASIS PRIMARY TUMOR
  PPP6C MUTATED                    1             1
  PPP6C WILD-TYPE                 34             3
                 vv
clus              REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  PPP6C MUTATED                                           5                  13
  PPP6C WILD-TYPE                                        53                 157
D13V4, multiclass
                                           clus
vv                                          PPP6C MUTATED PPP6C WILD-TYPE
  DISTANT METASTASIS                                    1              34
  PRIMARY TUMOR                                         1               3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE             5              53
  REGIONAL LYMPH NODE                                  13             157
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  PPP6C MUTATED             1       1       2        0        0        1
  PPP6C WILD-TYPE           9       5      20       10       24       16
                 vv
clus              STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  PPP6C MUTATED           0         1         1         1          2          3
  PPP6C WILD-TYPE        10        13         8        30         11         19
                 vv
clus              STAGE IIIC STAGE IV
  PPP6C MUTATED            5        1
  PPP6C WILD-TYPE         39       11
D13V5, multiclass
             clus
vv            PPP6C MUTATED PPP6C WILD-TYPE
  I OR II NOS             1               9
  STAGE 0                 1               5
  STAGE I                 2              20
  STAGE IA                0              10
  STAGE IB                0              24
  STAGE II                1              16
  STAGE IIA               0              10
  STAGE IIB               1              13
  STAGE IIC               1               8
  STAGE III               1              30
  STAGE IIIA              2              11
  STAGE IIIB              3              19
  STAGE IIIC              5              39
  STAGE IV                1              11
[1] 14  2
[1] 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
  PPP6C MUTATED       3  4  4  4
  PPP6C WILD-TYPE    48 54 49 51
D13V6, multiclass
       clus
vv      PPP6C MUTATED PPP6C WILD-TYPE
  T0+T1             3              48
  T2                4              54
  T3                4              49
  T4                4              51
[1] 4 2
[1] TRUE
[1] "dimension 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
  PPP6C MUTATED     7   4   4   4
  PPP6C WILD-TYPE 131  44  28  29
D13V7, multiclass
    clus
vv   PPP6C MUTATED PPP6C WILD-TYPE
  N0             7             131
  N1             4              44
  N2             4              28
  N3             4              29
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               M0  M1 M1A M1B M1C
  PPP6C MUTATED    18   0   0   0   1
  PPP6C WILD-TYPE 222   4   2   2   4
D13V8, multiclass
     clus
vv    PPP6C MUTATED PPP6C WILD-TYPE
  M0             18             222
  M1              0               4
  M1A             0               2
  M1B             0               2
  M1C             1               4
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V9, binary
                 cls
clus               0  1
  PPP6C MUTATED    7  7
  PPP6C WILD-TYPE 95 60
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PPP6C MUTATED      7    7
  PPP6C WILD-TYPE   95   60
     clus
vv    PPP6C MUTATED PPP6C WILD-TYPE
  NO              7              95
  YES             7              60
[1] 2 2
[1] FALSE
D13V10, binary
                 cls
clus                0   1
  PPP6C MUTATED     1  19
  PPP6C WILD-TYPE  32 216
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PPP6C MUTATED      1   19
  PPP6C WILD-TYPE   32  216
     clus
vv    PPP6C MUTATED PPP6C WILD-TYPE
  NO              1              32
  YES            19             216
[1] 2 2
[1] FALSE
D13V11, continuous
D13V12, binary
                 cls
clus                0   1
  PPP6C MUTATED     8  12
  PPP6C WILD-TYPE  95 153
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PPP6C MUTATED      8   12
  PPP6C WILD-TYPE   95  153
        clus
vv       PPP6C MUTATED PPP6C WILD-TYPE
  FEMALE             8              95
  MALE              12             153
[1] 2 2
[1] FALSE
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PPP6C MUTATED       0                         0    20
  PPP6C WILD-TYPE     3                         1   244
D13V13, multiclass
                           clus
vv                          PPP6C MUTATED PPP6C WILD-TYPE
  ASIAN                                 0               3
  BLACK OR AFRICAN AMERICAN             0               1
  WHITE                                20             244
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V14, binary
                 cls
clus                0   1
  PPP6C MUTATED     0  20
  PPP6C WILD-TYPE   3 241
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PPP6C MUTATED      0   20
  PPP6C WILD-TYPE    3  241
                        clus
vv                       PPP6C MUTATED PPP6C WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO            20             241
[1] 2 2
[1] FALSE

Clustering(14) Variable = IDH1 MUTATION ANALYSIS
D14V1, survival
                sevent
clus2              0   1
  IDH1 MUTATED     6   6
  IDH1 WILD-TYPE 122 124
  IDH1 MUTATED IDH1 WILD-TYPE 
            12            246 
  IDH1 MUTATED IDH1 WILD-TYPE 
             6            124 
$`IDH1 MUTATED`
TCGA-D3-A5GO TCGA-D9-A3Z1 TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29P TCGA-EE-A2GT 
       47.87         4.01         7.99         9.90        12.03        34.98 
TCGA-EE-A2GU TCGA-EE-A3J8 TCGA-EE-A3JI TCGA-ER-A3ES TCGA-FS-A1ZP TCGA-GN-A268 
       36.33        16.14        33.60         9.04        52.08        15.42 

$`IDH1 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.47         8.52       111.09        32.42        70.16       110.79 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       28.08        22.55        45.83        81.24        10.29        85.32 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
        8.38        21.14        88.50        68.22        69.90        11.41 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       30.87         7.50        36.16         6.31        92.42        56.19 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 
       64.44        45.11       114.67        15.25        46.98        46.32 
TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO 
       82.29        61.38        13.32        24.00         6.31         9.34 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H 
      103.59        26.37         5.39        80.22        42.71        15.09 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN 
       41.10        17.72         8.84        20.48        13.94        52.01 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA 
        1.55         6.97        23.11         2.89         9.90        11.31 
TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 
       13.22        48.79        35.80        51.12        10.03        39.19 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA 
       13.68         9.99        44.52        36.69        25.15         4.93 
TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 
       22.36         6.64        19.36         7.00        17.56        14.83 
TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EE-A17X 
       13.15         0.20         0.00         0.00        13.22        11.57 
TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 
       10.55         6.31         8.12         1.12         1.35        12.20 
TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H 
        5.13         4.31        36.07         4.34         5.13         9.21 
TCGA-EE-A20I TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H 
        1.18        37.97        11.15        38.63         8.55         4.41 
TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S 
        1.08        27.12         9.50         8.09         8.84         9.99 
TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 
        2.43         8.68         8.09        11.31        49.22        23.90 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE 
        9.67         8.94        39.39        34.29        17.98        34.92 
TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM 
       47.21        30.08        19.43        16.01        35.54        28.31 
TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2M5 
       33.83        30.84         5.42         1.15        13.02         8.84 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME 
       98.27         2.70         6.18        47.51         9.53        29.46 
TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML 
       44.25         7.96        14.56        63.42       111.78       111.91 
TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS 
       56.02        25.08        26.99        21.60        29.65        27.16 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD 
       23.05         5.56       124.31       122.73        25.84         3.68 
TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 
       30.15        13.81        15.95        12.72         3.22        22.92 
TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH 
       21.60        21.60        22.22        27.35         0.46        13.94 
TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A 
       31.40        18.61        12.95        38.40         5.72        76.41 
TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G 
       25.18         3.78         3.52        11.90        11.11       114.15 
TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P 
       34.88         4.21        13.45        28.60        42.84        34.68 
TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
        9.57        36.07        17.72        78.44        11.80         1.87 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ET TCGA-ER-A3EV 
        1.51        13.08        12.62        11.74         6.58        22.49 
TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX 
        1.71        18.41        85.74         4.90        64.47         3.45 
TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA 
       11.01        23.80        14.24        15.52         7.33         7.30 
TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG 
        3.39        20.38         8.22        19.53        11.08         7.17 
TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZR 
       30.87        12.92        12.89        47.38         8.65         8.81 
TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ 
       49.15        40.64         8.68        27.39         0.82         5.23 
TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB 
       53.85         7.36        28.73        14.20        10.78         5.98 
TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV 
        6.41         2.27         0.20         0.99         0.13         0.16 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 
        0.43         9.90         7.23        12.85        24.85        31.33 
TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS 
       84.72        10.13        16.24        12.16        14.70         5.79 

  IDH1 MUTATED IDH1 WILD-TYPE 
          4.01           0.00 
  IDH1 MUTATED IDH1 WILD-TYPE 
         52.08         124.31 
  IDH1 MUTATED IDH1 WILD-TYPE 
         15.78          14.63 
[1] "4.0 - 52.1 (15.8)"  "0.0 - 124.3 (14.6)"
[1] "hr=" "1"  
D14V2, survival
                sevent
clus2              0   1
  IDH1 MUTATED     7   6
  IDH1 WILD-TYPE 125 125
  IDH1 MUTATED IDH1 WILD-TYPE 
            13            250 
  IDH1 MUTATED IDH1 WILD-TYPE 
             6            125 
$`IDH1 MUTATED`
TCGA-D3-A5GO TCGA-D9-A149 TCGA-D9-A3Z1 TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29P 
      137.92        54.67        11.34        63.35        80.61        56.42 
TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A3J8 TCGA-EE-A3JI TCGA-ER-A3ES TCGA-FS-A1ZP 
       44.88        94.82        34.32       148.08       247.04        74.73 
TCGA-GN-A268 
       62.79 

$`IDH1 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.57        16.67       112.04       112.57        71.80       133.25 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       28.08        31.59        90.90        95.74        43.43       103.10 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
       65.49        23.77       115.53       168.00        69.90        11.87 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       48.76       113.52        42.08        12.10       171.58        56.19 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 
       66.08        45.11       130.72        58.06        46.98        46.32 
TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO 
      166.52        86.93        60.23        24.53        13.87         9.34 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H 
      103.59        39.75        21.47       161.85        43.69        40.14 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN 
      131.90        18.38        10.03        51.68        15.06       135.75 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A1JW TCGA-D9-A1JX 
      166.19         7.43       125.19       151.53         3.65         6.41 
TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1HW 
        3.25         9.90        25.18        66.25        48.89        36.03 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 
      117.21        20.38       194.83       176.55        35.93       107.34 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
       61.18        53.92        65.92        23.44        68.09        28.60 
TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG 
       10.49       215.44        15.68        13.87        10.16        45.11 
TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z 
       35.01         3.55        52.01        29.82        27.22         8.65 
TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 
       94.98        33.73        14.70        26.89        68.15         4.96 
TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29C 
      109.64       151.27        78.87       168.26        13.55        47.84 
TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M 
       13.97        39.62        72.07        32.19         2.60        44.35 
TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W 
       18.61        37.35        14.47        55.92        25.87       171.55 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 
       17.92        46.82       102.90        24.43        39.29        58.75 
TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI 
       47.54        67.43       314.56       135.95       208.04        48.72 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO 
       89.33        54.74        79.66        75.48        90.97       101.95 
TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 
       13.91        14.30        55.59        21.67       129.27        28.83 
TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH 
       19.76        61.51        47.28       103.27       103.20        16.96 
TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN 
      204.66        96.23       144.76       203.05       167.90        47.54 
TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU 
      248.65        43.23       103.56       136.47        41.59        53.26 
TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF 
      124.31       122.73        25.84         3.68        54.51        13.81 
TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 
       23.47       138.81       172.18       127.20        36.95        64.08 
TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A195 
       53.19        27.35        33.40       101.79        31.40        35.44 
TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C 
       13.94        50.76         9.17        77.75        98.40        48.89 
TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J 
       12.59        13.02        26.37       268.93       152.35         6.44 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S 
      131.51        61.05        44.05       162.08        50.89        37.25 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF 
      148.18        79.99        43.82        23.34        20.15        16.37 
TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN 
       31.27        32.05        80.32        46.98        33.21        92.98 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 
      174.21         4.90       216.92        48.59       228.59       202.65 
TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC 
       20.91        28.08         7.79        27.72        48.85       357.37 
TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ 
       53.52        40.27        15.45         9.70        32.75        47.38 
TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT 
       23.93       101.26       133.55        11.41       148.80        53.16 
TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 
       26.56        49.48        27.09        27.02        77.82        66.67 
TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD 
       28.73       174.84        12.43        26.73        49.45        77.88 
TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
        0.20        22.92        47.54         0.16         2.40         9.90 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 
        7.23        14.04       120.46       117.93        84.72        10.13 
TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS 
       64.44        32.48        39.58         6.67 

  IDH1 MUTATED IDH1 WILD-TYPE 
         11.34           0.16 
  IDH1 MUTATED IDH1 WILD-TYPE 
        247.04         357.37 
  IDH1 MUTATED IDH1 WILD-TYPE 
         63.35          47.54 
[1] "11.3 - 247.0 (63.4)" "0.2 - 357.4 (47.5)" 
[1] "hr=" "1.4"
D14V3, continuous
                vv
clus             DISTANT METASTASIS PRIMARY TUMOR
  IDH1 MUTATED                    4             0
  IDH1 WILD-TYPE                 31             4
                vv
clus             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  IDH1 MUTATED                                           2                   7
  IDH1 WILD-TYPE                                        56                 163
D14V4, multiclass
                                           clus
vv                                          IDH1 MUTATED IDH1 WILD-TYPE
  DISTANT METASTASIS                                   4             31
  PRIMARY TUMOR                                        0              4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE            2             56
  REGIONAL LYMPH NODE                                  7            163
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  IDH1 MUTATED             0       0       1        1        0        2
  IDH1 WILD-TYPE          10       6      21        9       24       15
                vv
clus             STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  IDH1 MUTATED           1         2         1         0          2          0
  IDH1 WILD-TYPE         9        12         8        31         11         22
                vv
clus             STAGE IIIC STAGE IV
  IDH1 MUTATED            1        0
  IDH1 WILD-TYPE         43       12
D14V5, multiclass
             clus
vv            IDH1 MUTATED IDH1 WILD-TYPE
  I OR II NOS            0             10
  STAGE 0                0              6
  STAGE I                1             21
  STAGE IA               1              9
  STAGE IB               0             24
  STAGE II               2             15
  STAGE IIA              1              9
  STAGE IIB              2             12
  STAGE IIC              1              8
  STAGE III              0             31
  STAGE IIIA             2             11
  STAGE IIIB             0             22
  STAGE IIIC             1             43
  STAGE IV               0             12
[1] 14  2
[1] 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
  IDH1 MUTATED       1  2  4  4
  IDH1 WILD-TYPE    50 56 49 51
D14V6, multiclass
       clus
vv      IDH1 MUTATED IDH1 WILD-TYPE
  T0+T1            1             50
  T2               2             56
  T3               4             49
  T4               4             51
[1] 4 2
[1] TRUE
[1] "dimension 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
  IDH1 MUTATED     8   3   0   1
  IDH1 WILD-TYPE 130  45  32  32
D14V7, multiclass
    clus
vv   IDH1 MUTATED IDH1 WILD-TYPE
  N0            8            130
  N1            3             45
  N2            0             32
  N3            1             32
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              M0  M1 M1A M1B M1C
  IDH1 MUTATED    12   0   0   0   0
  IDH1 WILD-TYPE 228   4   2   2   5
D14V8, multiclass
     clus
vv    IDH1 MUTATED IDH1 WILD-TYPE
  M0            12            228
  M1             0              4
  M1A            0              2
  M1B            0              2
  M1C            0              5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V9, binary
                cls
clus              0  1
  IDH1 MUTATED    7  2
  IDH1 WILD-TYPE 95 65
[1] "tbl2"
                cls
clus             [,1] [,2]
  IDH1 MUTATED      7    2
  IDH1 WILD-TYPE   95   65
     clus
vv    IDH1 MUTATED IDH1 WILD-TYPE
  NO             7             95
  YES            2             65
[1] 2 2
[1] FALSE
D14V10, binary
                cls
clus               0   1
  IDH1 MUTATED     0  13
  IDH1 WILD-TYPE  33 222
[1] "tbl2"
                cls
clus             [,1] [,2]
  IDH1 MUTATED      0   13
  IDH1 WILD-TYPE   33  222
     clus
vv    IDH1 MUTATED IDH1 WILD-TYPE
  NO             0             33
  YES           13            222
[1] 2 2
[1] FALSE
D14V11, continuous
D14V12, binary
                cls
clus               0   1
  IDH1 MUTATED     4   9
  IDH1 WILD-TYPE  99 156
[1] "tbl2"
                cls
clus             [,1] [,2]
  IDH1 MUTATED      4    9
  IDH1 WILD-TYPE   99  156
        clus
vv       IDH1 MUTATED IDH1 WILD-TYPE
  FEMALE            4             99
  MALE              9            156
[1] 2 2
[1] FALSE
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  IDH1 MUTATED       0                         0    13
  IDH1 WILD-TYPE     3                         1   251
D14V13, multiclass
                           clus
vv                          IDH1 MUTATED IDH1 WILD-TYPE
  ASIAN                                0              3
  BLACK OR AFRICAN AMERICAN            0              1
  WHITE                               13            251
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V14, binary
                cls
clus               0   1
  IDH1 MUTATED     0  12
  IDH1 WILD-TYPE   3 249
[1] "tbl2"
                cls
clus             [,1] [,2]
  IDH1 MUTATED      0   12
  IDH1 WILD-TYPE    3  249
                        clus
vv                       IDH1 MUTATED IDH1 WILD-TYPE
  HISPANIC OR LATINO                0              3
  NOT HISPANIC OR LATINO           12            249
[1] 2 2
[1] FALSE

Clustering(15) Variable = PDE1A MUTATION ANALYSIS
D15V1, survival
                 sevent
clus2               0   1
  PDE1A MUTATED    20  18
  PDE1A WILD-TYPE 108 112
  PDE1A MUTATED PDE1A WILD-TYPE 
             38             220 
  PDE1A MUTATED PDE1A WILD-TYPE 
             18             112 
$`PDE1A MUTATED`
TCGA-D3-A2JF TCGA-D3-A2JL TCGA-D3-A5GO TCGA-D9-A3Z1 TCGA-D9-A6EC TCGA-DA-A1IC 
       30.87        92.42        47.87         4.01        13.22         6.64 
TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A20H TCGA-EE-A29B TCGA-EE-A29D TCGA-EE-A29E 
        1.12         1.35         9.21         9.90        11.15        38.63 
TCGA-EE-A29M TCGA-EE-A29S TCGA-EE-A2A0 TCGA-EE-A2A2 TCGA-EE-A2GC TCGA-EE-A2GE 
       27.12         9.99        11.31        23.90        34.29        34.92 
TCGA-EE-A2GH TCGA-EE-A2GS TCGA-EE-A2M5 TCGA-EE-A2M8 TCGA-EE-A2MD TCGA-EE-A2MR 
       47.21        13.02         8.84         6.18         9.53        29.65 
TCGA-EE-A2MT TCGA-EE-A3AF TCGA-EE-A3JA TCGA-ER-A193 TCGA-ER-A19A TCGA-ER-A19F 
       23.05        13.81        22.22        31.40        76.41        11.11 
TCGA-ER-A19P TCGA-FR-A3YN TCGA-FS-A1Z3 TCGA-FS-A1ZQ TCGA-FS-A4F5 TCGA-FW-A3R5 
       34.68        18.41        14.24         8.65        28.73         0.99 
TCGA-FW-A3TU TCGA-GN-A265 
        0.13        84.72 

$`PDE1A WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.47         8.52       111.09        32.42        70.16       110.79 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       28.08        22.55        45.83        81.24        10.29        85.32 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
        8.38        21.14        88.50        68.22        69.90        11.41 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP 
        7.50        36.16         6.31        56.19        64.44        45.11 
TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC 
      114.67        15.25        46.98        46.32        82.29        61.38 
TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU 
       13.32        24.00         6.31         9.34       103.59        26.37 
TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K 
        5.39        80.22        42.71        15.09        41.10        17.72 
TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS 
        8.84        20.48        13.94        52.01         1.55         6.97 
TCGA-D3-A5GU TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-DA-A1HV TCGA-DA-A1HW 
       23.11         2.89         9.90        11.31        48.79        35.80 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 
       51.12        10.03        39.19        13.68         9.99        44.52 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A3F2 TCGA-DA-A3F3 
       36.69        25.15         4.93        22.36        19.36         7.00 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH 
       17.56        14.83        13.15         0.20         0.00         0.00 
TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A183 
       13.22        11.57        10.55         6.31         8.12        12.20 
TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20I 
        5.13         4.31        36.07         4.34         5.13         1.18 
TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29N 
        7.99        37.97         8.55         4.41         1.08         9.50 
TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X 
       12.03         8.09         8.84         2.43         8.68         8.09 
TCGA-EE-A2A1 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GI 
       49.22         9.67         8.94        39.39        17.98        30.08 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO 
       19.43        16.01        35.54        28.31        33.83        30.84 
TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 
        5.42         1.15        34.98        36.33        98.27         2.70 
TCGA-EE-A2MC TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ 
       47.51        29.46        44.25         7.96        14.56        63.42 
TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ 
      111.78       111.91        56.02        25.08        26.99        21.60 
TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD 
       27.16         5.56       124.31       122.73        25.84         3.68 
TCGA-EE-A3AE TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 
       30.15        15.95        12.72         3.22        22.92        21.60 
TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI 
       21.60        16.14        27.35         0.46        13.94        33.60 
TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19B TCGA-ER-A19C 
       18.61        12.95        38.40         5.72        25.18         3.78 
TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L 
        3.52        11.90       114.15        34.88         4.21        13.45 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 
       28.60        42.84         9.57        36.07        17.72        78.44 
TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH 
       11.80         1.87         1.51        13.08        12.62        11.74 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A44A TCGA-FR-A69P 
        9.04         6.58        22.49         1.71        85.74         4.90 
TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1Z7 
       64.47         3.45        11.01        23.80        15.52         7.33 
TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF 
        7.30         3.39        20.38         8.22        19.53        11.08 
TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP 
        7.17        30.87        12.92        12.89        47.38        52.08 
TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY 
        8.81        49.15        40.64         8.68        27.39         0.82 
TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB 
        5.23        53.85         7.36        14.20        10.78         5.98 
TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
        6.41         2.27         0.20         0.16         0.43         9.90 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A266 TCGA-GN-A267 
        7.23        12.85        24.85        31.33        10.13        16.24 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS 
       15.42        12.16        14.70         5.79 

  PDE1A MUTATED PDE1A WILD-TYPE 
           0.13            0.00 
  PDE1A MUTATED PDE1A WILD-TYPE 
          92.42          124.31 
  PDE1A MUTATED PDE1A WILD-TYPE 
         14.025          14.960 
[1] "0.1 - 92.4 (14.0)"  "0.0 - 124.3 (15.0)"
[1] "hr=" "1.1"
D15V2, survival
                 sevent
clus2               0   1
  PDE1A MUTATED    20  18
  PDE1A WILD-TYPE 112 113
  PDE1A MUTATED PDE1A WILD-TYPE 
             38             225 
  PDE1A MUTATED PDE1A WILD-TYPE 
             18             113 
$`PDE1A MUTATED`
TCGA-D3-A2JF TCGA-D3-A2JL TCGA-D3-A5GO TCGA-D9-A3Z1 TCGA-D9-A6EC TCGA-DA-A1IC 
       48.76       171.58       137.92        11.34        66.25        68.09 
TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A20H TCGA-EE-A29B TCGA-EE-A29D TCGA-EE-A29E 
       33.73        14.70       168.26        80.61        13.97        39.62 
TCGA-EE-A29M TCGA-EE-A29S TCGA-EE-A2A0 TCGA-EE-A2A2 TCGA-EE-A2GC TCGA-EE-A2GE 
       44.35        55.92        46.82        24.43        67.43       135.95 
TCGA-EE-A2GH TCGA-EE-A2GS TCGA-EE-A2M5 TCGA-EE-A2M8 TCGA-EE-A2MD TCGA-EE-A2MR 
      208.04        55.59        21.67        19.76        47.28       103.56 
TCGA-EE-A2MT TCGA-EE-A3AF TCGA-EE-A3JA TCGA-ER-A193 TCGA-ER-A19A TCGA-ER-A19F 
       41.59        13.81        53.19        31.40        77.75        26.37 
TCGA-ER-A19P TCGA-FR-A3YN TCGA-FS-A1Z3 TCGA-FS-A1ZQ TCGA-FS-A4F5 TCGA-FW-A3R5 
      162.08        92.98        20.91       133.55        28.73        22.92 
TCGA-FW-A3TU TCGA-GN-A265 
       47.54        84.72 

$`PDE1A WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.57        16.67       112.04       112.57        71.80       133.25 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       28.08        31.59        90.90        95.74        43.43       103.10 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
       65.49        23.77       115.53       168.00        69.90        11.87 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP 
      113.52        42.08        12.10        56.19        66.08        45.11 
TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC 
      130.72        58.06        46.98        46.32       166.52        86.93 
TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU 
       60.23        24.53        13.87         9.34       103.59        39.75 
TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K 
       21.47       161.85        43.69        40.14       131.90        18.38 
TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS 
       10.03        51.68        15.06       135.75       166.19         7.43 
TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z3 
      125.19       151.53        54.67         3.65         6.41         3.25 
TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 
        9.90        25.18        48.89        36.03       117.21        20.38 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 
      194.83       176.55        35.93       107.34        61.18        53.92 
TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 
       65.92        23.44        28.60        10.49       215.44        15.68 
TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN 
       13.87        10.16        45.11        35.01         3.55        52.01 
TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A183 TCGA-EE-A184 
       29.82        27.22         8.65        94.98        26.89        68.15 
TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29A 
        4.96       109.64       151.27        78.87        13.55        63.35 
TCGA-EE-A29C TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P 
       47.84        72.07        32.19         2.60        18.61        56.42 
TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A1 
       37.35        14.47        25.87       171.55        17.92       102.90 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GI TCGA-EE-A2GJ 
       39.29        58.75        47.54       314.56        48.72        89.33 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP 
       54.74        79.66        75.48        90.97       101.95        13.91 
TCGA-EE-A2GR TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2MC 
       14.30        44.88        94.82       129.27        28.83        61.51 
TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK 
      103.27       103.20        16.96       204.66        96.23       144.76 
TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MS 
      203.05       167.90        47.54       248.65        43.23       136.47 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE 
       53.26       124.31       122.73        25.84         3.68        54.51 
TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 
       23.47       138.81       172.18       127.20        36.95        64.08 
TCGA-EE-A3J8 TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 
       34.32        27.35        33.40       101.79       148.08        35.44 
TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D 
       13.94        50.76         9.17        98.40        48.89        12.59 
TCGA-ER-A19E TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M 
       13.02       268.93       152.35         6.44       131.51        61.05 
TCGA-ER-A19N TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
       44.05        50.89        37.25       148.18        79.99        43.82 
TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES 
       23.34        20.15        16.37        31.27        32.05       247.04 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW 
       80.32        46.98        33.21       174.21         4.90       216.92 
TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA 
       48.59       228.59       202.65        28.08         7.79        27.72 
TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG 
       48.85       357.37        53.52        40.27        15.45         9.70 
TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZR 
       32.75        47.38        23.93       101.26        74.73        11.41 
TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ 
      148.80        53.16        26.56        49.48        27.09        27.02 
TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC 
       77.82        66.67       174.84        12.43        26.73        49.45 
TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
       77.88         0.20         0.16         2.40         9.90         7.23 
TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 
       14.04       120.46       117.93        10.13        64.44        62.79 
TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS 
       32.48        39.58         6.67 

  PDE1A MUTATED PDE1A WILD-TYPE 
          11.34            0.16 
  PDE1A MUTATED PDE1A WILD-TYPE 
         208.04          357.37 
  PDE1A MUTATED PDE1A WILD-TYPE 
          48.15           48.59 
[1] "11.3 - 208.0 (48.1)" "0.2 - 357.4 (48.6)" 
[1] "hr=" "1"  
D15V3, continuous
                 vv
clus              DISTANT METASTASIS PRIMARY TUMOR
  PDE1A MUTATED                    8             1
  PDE1A WILD-TYPE                 27             3
                 vv
clus              REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  PDE1A MUTATED                                           3                  26
  PDE1A WILD-TYPE                                        55                 144
D15V4, multiclass
                                           clus
vv                                          PDE1A MUTATED PDE1A WILD-TYPE
  DISTANT METASTASIS                                    8              27
  PRIMARY TUMOR                                         1               3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE             3              55
  REGIONAL LYMPH NODE                                  26             144
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  PDE1A MUTATED             2       0       5        1        6        3
  PDE1A WILD-TYPE           8       6      17        9       18       14
                 vv
clus              STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  PDE1A MUTATED           2         3         0         2          1          2
  PDE1A WILD-TYPE         8        11         9        29         12         20
                 vv
clus              STAGE IIIC STAGE IV
  PDE1A MUTATED            5        2
  PDE1A WILD-TYPE         39       10
D15V5, multiclass
             clus
vv            PDE1A MUTATED PDE1A WILD-TYPE
  I OR II NOS             2               8
  STAGE 0                 0               6
  STAGE I                 5              17
  STAGE IA                1               9
  STAGE IB                6              18
  STAGE II                3              14
  STAGE IIA               2               8
  STAGE IIB               3              11
  STAGE IIC               0               9
  STAGE III               2              29
  STAGE IIIA              1              12
  STAGE IIIB              2              20
  STAGE IIIC              5              39
  STAGE IV                2              10
[1] 14  2
[1] 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
  PDE1A MUTATED       2 12 12  3
  PDE1A WILD-TYPE    49 46 41 52
D15V6, multiclass
       clus
vv      PDE1A MUTATED PDE1A WILD-TYPE
  T0+T1             2              49
  T2               12              46
  T3               12              41
  T4                3              52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  PDE1A MUTATED    26   6   2   2
  PDE1A WILD-TYPE 112  42  30  31
D15V7, multiclass
    clus
vv   PDE1A MUTATED PDE1A WILD-TYPE
  N0            26             112
  N1             6              42
  N2             2              30
  N3             2              31
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               M0  M1 M1A M1B M1C
  PDE1A MUTATED    34   2   0   0   0
  PDE1A WILD-TYPE 206   2   2   2   5
D15V8, multiclass
     clus
vv    PDE1A MUTATED PDE1A WILD-TYPE
  M0             34             206
  M1              2               2
  M1A             0               2
  M1B             0               2
  M1C             0               5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V9, binary
                 cls
clus               0  1
  PDE1A MUTATED   17  6
  PDE1A WILD-TYPE 85 61
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PDE1A MUTATED     17    6
  PDE1A WILD-TYPE   85   61
     clus
vv    PDE1A MUTATED PDE1A WILD-TYPE
  NO             17              85
  YES             6              61
[1] 2 2
[1] FALSE
D15V10, binary
                 cls
clus                0   1
  PDE1A MUTATED     4  34
  PDE1A WILD-TYPE  29 201
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PDE1A MUTATED      4   34
  PDE1A WILD-TYPE   29  201
     clus
vv    PDE1A MUTATED PDE1A WILD-TYPE
  NO              4              29
  YES            34             201
[1] 2 2
[1] FALSE
D15V11, continuous
D15V12, binary
                 cls
clus                0   1
  PDE1A MUTATED    13  25
  PDE1A WILD-TYPE  90 140
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PDE1A MUTATED     13   25
  PDE1A WILD-TYPE   90  140
        clus
vv       PDE1A MUTATED PDE1A WILD-TYPE
  FEMALE            13              90
  MALE              25             140
[1] 2 2
[1] FALSE
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PDE1A MUTATED       0                         0    38
  PDE1A WILD-TYPE     3                         1   226
D15V13, multiclass
                           clus
vv                          PDE1A MUTATED PDE1A WILD-TYPE
  ASIAN                                 0               3
  BLACK OR AFRICAN AMERICAN             0               1
  WHITE                                38             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"
D15V14, binary
                 cls
clus                0   1
  PDE1A MUTATED     0  38
  PDE1A WILD-TYPE   3 223
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PDE1A MUTATED      0   38
  PDE1A WILD-TYPE    3  223
                        clus
vv                       PDE1A MUTATED PDE1A WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO            38             223
[1] 2 2
[1] FALSE

Clustering(16) Variable = HMGCR MUTATION ANALYSIS
D16V1, survival
                 sevent
clus2               0   1
  HMGCR MUTATED     3   8
  HMGCR WILD-TYPE 125 122
  HMGCR MUTATED HMGCR WILD-TYPE 
             11             247 
  HMGCR MUTATED HMGCR WILD-TYPE 
              8             122 
$`HMGCR MUTATED`
TCGA-D3-A1Q3 TCGA-D3-A2JC TCGA-D3-A3CE TCGA-EE-A181 TCGA-EE-A20F TCGA-EE-A29L 
        8.52        69.90        13.32         1.12         5.13         1.08 
TCGA-EE-A29Q TCGA-ER-A19F TCGA-ER-A19P TCGA-FS-A1Z4 TCGA-FW-A3R5 
        8.09        11.11        34.68        15.52         0.99 

$`HMGCR WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       16.47       111.09        32.42        70.16       110.79        28.08 
TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 
       22.55        45.83        81.24        10.29        85.32         8.38 
TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JG 
       21.14        88.50        68.22        11.41        30.87         7.50 
TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP 
       36.16         6.31        92.42        56.19        64.44        45.11 
TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC 
      114.67        15.25        46.98        46.32        82.29        61.38 
TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV 
       24.00         6.31         9.34       103.59        26.37         5.39 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N 
       80.22        42.71        15.09        41.10        17.72         8.84 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS 
       20.48        13.94        52.01        47.87         1.55         6.97 
TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC 
       23.11         4.01         2.89         9.90        11.31        13.22 
TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 
       48.79        35.80        51.12        10.03        39.19        13.68 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB 
        9.99        44.52        36.69        25.15         4.93        22.36 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q 
        6.64        19.36         7.00        17.56        14.83        13.15 
TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y 
        0.20         0.00         0.00        13.22        11.57        10.55 
TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 
        6.31         8.12         1.35        12.20         5.13         4.31 
TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B 
       36.07         4.34         9.21         1.18         7.99         9.90 
TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M 
       37.97        11.15        38.63         8.55         4.41        27.12 
TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W 
        9.50        12.03         8.84         9.99         2.43         8.68 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 
        8.09        11.31        49.22        23.90         9.67         8.94 
TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI 
       39.39        34.29        17.98        34.92        47.21        30.08 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO 
       19.43        16.01        35.54        28.31        33.83        30.84 
TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 
        5.42         1.15        13.02        34.98        36.33         8.84 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME 
       98.27         2.70         6.18        47.51         9.53        29.46 
TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML 
       44.25         7.96        14.56        63.42       111.78       111.91 
TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS 
       56.02        25.08        26.99        21.60        29.65        27.16 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD 
       23.05         5.56       124.31       122.73        25.84         3.68 
TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 
       30.15        13.81        15.95        12.72         3.22        22.92 
TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE 
       21.60        21.60        16.14        22.22        27.35         0.46 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 
       13.94        33.60        31.40        18.61        12.95        38.40 
TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E 
        5.72        76.41        25.18         3.78         3.52        11.90 
TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N 
      114.15        34.88         4.21        13.45        28.60        42.84 
TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
        9.57        36.07        17.72        78.44        11.80         1.87 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET 
        1.51        13.08        12.62        11.74         9.04         6.58 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW 
       22.49         1.71        18.41        85.74         4.90        64.47 
TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z7 TCGA-FS-A1ZA 
        3.45        11.01        23.80        14.24         7.33         7.30 
TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG 
        3.39        20.38         8.22        19.53        11.08         7.17 
TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ 
       30.87        12.92        12.89        47.38        52.08         8.65 
TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY 
        8.81        49.15        40.64         8.68        27.39         0.82 
TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 
        5.23        53.85         7.36        28.73        14.20        10.78 
TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV 
        5.98         6.41         2.27         0.20         0.13         0.16 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 
        0.43         9.90         7.23        12.85        24.85        31.33 
TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D 
       84.72        10.13        16.24        15.42        12.16        14.70 
TCGA-QB-A6FS 
        5.79 

  HMGCR MUTATED HMGCR WILD-TYPE 
           0.99            0.00 
  HMGCR MUTATED HMGCR WILD-TYPE 
          69.90          124.31 
  HMGCR MUTATED HMGCR WILD-TYPE 
           8.52           15.25 
[1] "1.0 - 69.9 (8.5)"   "0.0 - 124.3 (15.2)"
[1] "hr=" "2.3"
D16V2, survival
                 sevent
clus2               0   1
  HMGCR MUTATED     3   8
  HMGCR WILD-TYPE 129 123
  HMGCR MUTATED HMGCR WILD-TYPE 
             11             252 
  HMGCR MUTATED HMGCR WILD-TYPE 
              8             123 
$`HMGCR MUTATED`
TCGA-D3-A1Q3 TCGA-D3-A2JC TCGA-D3-A3CE TCGA-EE-A181 TCGA-EE-A20F TCGA-EE-A29L 
       16.67        69.90        60.23        33.73        78.87         2.60 
TCGA-EE-A29Q TCGA-ER-A19F TCGA-ER-A19P TCGA-FS-A1Z4 TCGA-FW-A3R5 
       37.35        26.37       162.08        28.08        22.92 

$`HMGCR WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       16.57       112.04       112.57        71.80       133.25        28.08 
TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 
       31.59        90.90        95.74        43.43       103.10        65.49 
TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JG 
       23.77       115.53       168.00        11.87        48.76       113.52 
TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP 
       42.08        12.10       171.58        56.19        66.08        45.11 
TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC 
      130.72        58.06        46.98        46.32       166.52        86.93 
TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV 
       24.53        13.87         9.34       103.59        39.75        21.47 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N 
      161.85        43.69        40.14       131.90        18.38        10.03 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS 
       51.68        15.06       135.75       137.92       166.19         7.43 
TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 
      125.19       151.53        54.67         3.65         6.41        11.34 
TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1HW 
        3.25         9.90        25.18        66.25        48.89        36.03 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 
      117.21        20.38       194.83       176.55        35.93       107.34 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
       61.18        53.92        65.92        23.44        68.09        28.60 
TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG 
       10.49       215.44        15.68        13.87        10.16        45.11 
TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z 
       35.01         3.55        52.01        29.82        27.22         8.65 
TCGA-EE-A180 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B 
       94.98        14.70        26.89        68.15         4.96       109.64 
TCGA-EE-A20C TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C 
      151.27       168.26        13.55        63.35        80.61        47.84 
TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29N 
       13.97        39.62        72.07        32.19        44.35        18.61 
TCGA-EE-A29P TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X 
       56.42        14.47        55.92        25.87       171.55        17.92 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB 
       46.82       102.90        24.43        39.29        58.75        47.54 
TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ 
       67.43       314.56       135.95       208.04        48.72        89.33 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP 
       54.74        79.66        75.48        90.97       101.95        13.91 
TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 
       14.30        55.59        44.88        94.82        21.67       129.27 
TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG 
       28.83        19.76        61.51        47.28       103.27       103.20 
TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM 
       16.96       204.66        96.23       144.76       203.05       167.90 
TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT 
       47.54       248.65        43.23       103.56       136.47        41.59 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE 
       53.26       124.31       122.73        25.84         3.68        54.51 
TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 
       13.81        23.47       138.81       172.18       127.20        36.95 
TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH 
       64.08        34.32        53.19        27.35        33.40       101.79 
TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 
      148.08        31.40        35.44        13.94        50.76         9.17 
TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19G 
       77.75        98.40        48.89        12.59        13.02       268.93 
TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19Q 
      152.35         6.44       131.51        61.05        44.05        50.89 
TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE 
       37.25       148.18        79.99        43.82        23.34        20.15 
TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV 
       16.37        31.27        32.05       247.04        80.32        46.98 
TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX 
       33.21        92.98       174.21         4.90       216.92        48.59 
TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB 
      228.59       202.65        20.91         7.79        27.72        48.85 
TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH 
      357.37        53.52        40.27        15.45         9.70        32.75 
TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR 
       47.38        23.93       101.26        74.73       133.55        11.41 
TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ 
      148.80        53.16        26.56        49.48        27.09        27.02 
TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB 
       77.82        66.67        28.73       174.84        12.43        26.73 
TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY 
       49.45        77.88         0.20        47.54         0.16         2.40 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        9.90         7.23        14.04       120.46       117.93        84.72 
TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS 
       10.13        64.44        62.79        32.48        39.58         6.67 

  HMGCR MUTATED HMGCR WILD-TYPE 
           2.60            0.16 
  HMGCR MUTATED HMGCR WILD-TYPE 
         162.08          357.37 
  HMGCR MUTATED HMGCR WILD-TYPE 
          33.73           48.74 
[1] "2.6 - 162.1 (33.7)" "0.2 - 357.4 (48.7)"
[1] "hr=" "2"  
D16V3, continuous
                 vv
clus              DISTANT METASTASIS PRIMARY TUMOR
  HMGCR MUTATED                    0             0
  HMGCR WILD-TYPE                 35             4
                 vv
clus              REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  HMGCR MUTATED                                           1                  10
  HMGCR WILD-TYPE                                        57                 160
D16V4, multiclass
                                           clus
vv                                          HMGCR MUTATED HMGCR WILD-TYPE
  DISTANT METASTASIS                                    0              35
  PRIMARY TUMOR                                         0               4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE             1              57
  REGIONAL LYMPH NODE                                  10             160
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  HMGCR MUTATED             0       0       2        0        0        1
  HMGCR WILD-TYPE          10       6      20       10       24       16
                 vv
clus              STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  HMGCR MUTATED           0         1         1         3          0          0
  HMGCR WILD-TYPE        10        13         8        28         13         22
                 vv
clus              STAGE IIIC STAGE IV
  HMGCR MUTATED            1        0
  HMGCR WILD-TYPE         43       12
D16V5, multiclass
             clus
vv            HMGCR MUTATED HMGCR WILD-TYPE
  I OR II NOS             0              10
  STAGE 0                 0               6
  STAGE I                 2              20
  STAGE IA                0              10
  STAGE IB                0              24
  STAGE II                1              16
  STAGE IIA               0              10
  STAGE IIB               1              13
  STAGE IIC               1               8
  STAGE III               3              28
  STAGE IIIA              0              13
  STAGE IIIB              0              22
  STAGE IIIC              1              43
  STAGE IV                0              12
[1] 14  2
[1] 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
  HMGCR MUTATED       4  0  2  2
  HMGCR WILD-TYPE    47 58 51 53
D16V6, multiclass
       clus
vv      HMGCR MUTATED HMGCR WILD-TYPE
  T0+T1             4              47
  T2                0              58
  T3                2              51
  T4                2              53
[1] 4 2
[1] TRUE
[1] "dimension 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
  HMGCR MUTATED     7   1   2   1
  HMGCR WILD-TYPE 131  47  30  32
D16V7, multiclass
    clus
vv   HMGCR MUTATED HMGCR WILD-TYPE
  N0             7             131
  N1             1              47
  N2             2              30
  N3             1              32
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               M0  M1 M1A M1B M1C
  HMGCR MUTATED    11   0   0   0   0
  HMGCR WILD-TYPE 229   4   2   2   5
D16V8, multiclass
     clus
vv    HMGCR MUTATED HMGCR WILD-TYPE
  M0             11             229
  M1              0               4
  M1A             0               2
  M1B             0               2
  M1C             0               5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V9, binary
                 cls
clus                0   1
  HMGCR MUTATED     1   3
  HMGCR WILD-TYPE 101  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HMGCR MUTATED      1    3
  HMGCR WILD-TYPE  101   64
     clus
vv    HMGCR MUTATED HMGCR WILD-TYPE
  NO              1             101
  YES             3              64
[1] 2 2
[1] FALSE
D16V10, binary
                 cls
clus                0   1
  HMGCR MUTATED     2   9
  HMGCR WILD-TYPE  31 226
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HMGCR MUTATED      2    9
  HMGCR WILD-TYPE   31  226
     clus
vv    HMGCR MUTATED HMGCR WILD-TYPE
  NO              2              31
  YES             9             226
[1] 2 2
[1] FALSE
D16V11, continuous
D16V12, binary
                 cls
clus                0   1
  HMGCR MUTATED     5   6
  HMGCR WILD-TYPE  98 159
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HMGCR MUTATED      5    6
  HMGCR WILD-TYPE   98  159
        clus
vv       HMGCR MUTATED HMGCR WILD-TYPE
  FEMALE             5              98
  MALE               6             159
[1] 2 2
[1] FALSE
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  HMGCR MUTATED       0                         0    11
  HMGCR WILD-TYPE     3                         1   253
D16V13, multiclass
                           clus
vv                          HMGCR MUTATED HMGCR WILD-TYPE
  ASIAN                                 0               3
  BLACK OR AFRICAN AMERICAN             0               1
  WHITE                                11             253
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V14, binary
                 cls
clus                0   1
  HMGCR MUTATED     0  11
  HMGCR WILD-TYPE   3 250
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HMGCR MUTATED      0   11
  HMGCR WILD-TYPE    3  250
                        clus
vv                       HMGCR MUTATED HMGCR WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO            11             250
[1] 2 2
[1] FALSE

Clustering(17) Variable = PHGDH MUTATION ANALYSIS
D17V1, survival
                 sevent
clus2               0   1
  PHGDH MUTATED     5   5
  PHGDH WILD-TYPE 123 125
  PHGDH MUTATED PHGDH WILD-TYPE 
             10             248 
  PHGDH MUTATED PHGDH WILD-TYPE 
              5             125 
$`PHGDH MUTATED`
TCGA-D3-A1Q6 TCGA-D3-A2JD TCGA-D3-A5GN TCGA-EE-A29L TCGA-EE-A2GI TCGA-EE-A2MI 
       70.16        11.41        52.01         1.08        30.08        14.56 
TCGA-ER-A19F TCGA-FW-A3R5 TCGA-GN-A262 TCGA-GN-A265 
       11.11         0.99        24.85        84.72 

$`PHGDH WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       16.47         8.52       111.09        32.42       110.79        28.08 
TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 
       22.55        45.83        81.24        10.29        85.32         8.38 
TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JF TCGA-D3-A2JG 
       21.14        88.50        68.22        69.90        30.87         7.50 
TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP 
       36.16         6.31        92.42        56.19        64.44        45.11 
TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC 
      114.67        15.25        46.98        46.32        82.29        61.38 
TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU 
       13.32        24.00         6.31         9.34       103.59        26.37 
TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K 
        5.39        80.22        42.71        15.09        41.10        17.72 
TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS 
        8.84        20.48        13.94        47.87         1.55         6.97 
TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC 
       23.11         4.01         2.89         9.90        11.31        13.22 
TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 
       48.79        35.80        51.12        10.03        39.19        13.68 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB 
        9.99        44.52        36.69        25.15         4.93        22.36 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q 
        6.64        19.36         7.00        17.56        14.83        13.15 
TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y 
        0.20         0.00         0.00        13.22        11.57        10.55 
TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 
        6.31         8.12         1.12         1.35        12.20         5.13 
TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I 
        4.31        36.07         4.34         5.13         9.21         1.18 
TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G 
        7.99         9.90        37.97        11.15        38.63         8.55 
TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R 
        4.41        27.12         9.50        12.03         8.09         8.84 
TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 
        9.99         2.43         8.68         8.09        11.31        49.22 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD 
       23.90         9.67         8.94        39.39        34.29        17.98 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM 
       34.92        47.21        19.43        16.01        35.54        28.31 
TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT 
       33.83        30.84         5.42         1.15        13.02        34.98 
TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC 
       36.33         8.84        98.27         2.70         6.18        47.51 
TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MJ TCGA-EE-A2MK 
        9.53        29.46        44.25         7.96        63.42       111.78 
TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR 
      111.91        56.02        25.08        26.99        21.60        29.65 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC 
       27.16        23.05         5.56       124.31       122.73        25.84 
TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 
        3.68        30.15        13.81        15.95        12.72         3.22 
TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JD 
       22.92        21.60        21.60        16.14        22.22        27.35 
TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 
        0.46        13.94        33.60        31.40        18.61        12.95 
TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D 
       38.40         5.72        76.41        25.18         3.78         3.52 
TCGA-ER-A19E TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M 
       11.90       114.15        34.88         4.21        13.45        28.60 
TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 
       42.84        34.68         9.57        36.07        17.72        78.44 
TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH 
       11.80         1.87         1.51        13.08        12.62        11.74 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A 
        9.04         6.58        22.49         1.71        18.41        85.74 
TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
        4.90        64.47         3.45        11.01        23.80        14.24 
TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD 
       15.52         7.33         7.30         3.39        20.38         8.22 
TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK 
       19.53        11.08         7.17        30.87        12.92        12.89 
TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT 
       47.38        52.08         8.65         8.81        49.15        40.64 
TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 
        8.68        27.39         0.82         5.23        53.85         7.36 
TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD 
       28.73        14.20        10.78         5.98         6.41         2.27 
TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
        0.20         0.13         0.16         0.43         9.90         7.23 
TCGA-GF-A6C8 TCGA-GN-A264 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
       12.85        31.33        10.13        16.24        15.42        12.16 
TCGA-GN-A26D TCGA-QB-A6FS 
       14.70         5.79 

  PHGDH MUTATED PHGDH WILD-TYPE 
           0.99            0.00 
  PHGDH MUTATED PHGDH WILD-TYPE 
          84.72          124.31 
  PHGDH MUTATED PHGDH WILD-TYPE 
         19.705          14.765 
[1] "1.0 - 84.7 (19.7)"  "0.0 - 124.3 (14.8)"
[1] "hr=" "1.1"
D17V2, survival
                 sevent
clus2               0   1
  PHGDH MUTATED     5   5
  PHGDH WILD-TYPE 127 126
  PHGDH MUTATED PHGDH WILD-TYPE 
             10             253 
  PHGDH MUTATED PHGDH WILD-TYPE 
              5             126 
$`PHGDH MUTATED`
TCGA-D3-A1Q6 TCGA-D3-A2JD TCGA-D3-A5GN TCGA-EE-A29L TCGA-EE-A2GI TCGA-EE-A2MI 
       71.80        11.87       135.75         2.60        48.72       204.66 
TCGA-ER-A19F TCGA-FW-A3R5 TCGA-GN-A262 TCGA-GN-A265 
       26.37        22.92       120.46        84.72 

$`PHGDH WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       16.57        16.67       112.04       112.57       133.25        28.08 
TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 
       31.59        90.90        95.74        43.43       103.10        65.49 
TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JF TCGA-D3-A2JG 
       23.77       115.53       168.00        69.90        48.76       113.52 
TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP 
       42.08        12.10       171.58        56.19        66.08        45.11 
TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC 
      130.72        58.06        46.98        46.32       166.52        86.93 
TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU 
       60.23        24.53        13.87         9.34       103.59        39.75 
TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K 
       21.47       161.85        43.69        40.14       131.90        18.38 
TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS 
       10.03        51.68        15.06       137.92       166.19         7.43 
TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 
      125.19       151.53        54.67         3.65         6.41        11.34 
TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1HW 
        3.25         9.90        25.18        66.25        48.89        36.03 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 
      117.21        20.38       194.83       176.55        35.93       107.34 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
       61.18        53.92        65.92        23.44        68.09        28.60 
TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG 
       10.49       215.44        15.68        13.87        10.16        45.11 
TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z 
       35.01         3.55        52.01        29.82        27.22         8.65 
TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 
       94.98        33.73        14.70        26.89        68.15         4.96 
TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A 
      109.64       151.27        78.87       168.26        13.55        63.35 
TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H 
       80.61        47.84        13.97        39.62        72.07        32.19 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S 
       44.35        18.61        56.42        37.35        14.47        55.92 
TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 
       25.87       171.55        17.92        46.82       102.90        24.43 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE 
       39.29        58.75        47.54        67.43       314.56       135.95 
TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN 
      208.04        89.33        54.74        79.66        75.48        90.97 
TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU 
      101.95        13.91        14.30        55.59        44.88        94.82 
TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD 
       21.67       129.27        28.83        19.76        61.51        47.28 
TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML 
      103.27       103.20        16.96        96.23       144.76       203.05 
TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS 
      167.90        47.54       248.65        43.23       103.56       136.47 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD 
       41.59        53.26       124.31       122.73        25.84         3.68 
TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 
       54.51        13.81        23.47       138.81       172.18       127.20 
TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE 
       36.95        64.08        34.32        53.19        27.35        33.40 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 
      101.79       148.08        31.40        35.44        13.94        50.76 
TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E 
        9.17        77.75        98.40        48.89        12.59        13.02 
TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N 
      268.93       152.35         6.44       131.51        61.05        44.05 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
      162.08        50.89        37.25       148.18        79.99        43.82 
TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES 
       23.34        20.15        16.37        31.27        32.05       247.04 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
       80.32        46.98        33.21        92.98       174.21         4.90 
TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 
      216.92        48.59       228.59       202.65        20.91        28.08 
TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE 
        7.79        27.72        48.85       357.37        53.52        40.27 
TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM 
       15.45         9.70        32.75        47.38        23.93       101.26 
TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU 
       74.73       133.55        11.41       148.80        53.16        26.56 
TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 
       49.48        27.09        27.02        77.82        66.67        28.73 
TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 
      174.84        12.43        26.73        49.45        77.88         0.20 
TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 
       47.54         0.16         2.40         9.90         7.23        14.04 
TCGA-GN-A264 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D 
      117.93        10.13        64.44        62.79        32.48        39.58 
TCGA-QB-A6FS 
        6.67 

  PHGDH MUTATED PHGDH WILD-TYPE 
           2.60            0.16 
  PHGDH MUTATED PHGDH WILD-TYPE 
         204.66          357.37 
  PHGDH MUTATED PHGDH WILD-TYPE 
          60.26           47.84 
[1] "2.6 - 204.7 (60.3)" "0.2 - 357.4 (47.8)"
[1] "hr=" "1.1"
D17V3, continuous
                 vv
clus              DISTANT METASTASIS PRIMARY TUMOR
  PHGDH MUTATED                    0             0
  PHGDH WILD-TYPE                 35             4
                 vv
clus              REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  PHGDH MUTATED                                           2                   8
  PHGDH WILD-TYPE                                        56                 162
D17V4, multiclass
                                           clus
vv                                          PHGDH MUTATED PHGDH WILD-TYPE
  DISTANT METASTASIS                                    0              35
  PRIMARY TUMOR                                         0               4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE             2              56
  REGIONAL LYMPH NODE                                   8             162
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  PHGDH MUTATED             0       0       1        1        0        0
  PHGDH WILD-TYPE          10       6      21        9       24       17
                 vv
clus              STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  PHGDH MUTATED           0         1         0         2          0          0
  PHGDH WILD-TYPE        10        13         9        29         13         22
                 vv
clus              STAGE IIIC STAGE IV
  PHGDH MUTATED            2        0
  PHGDH WILD-TYPE         42       12
D17V5, multiclass
             clus
vv            PHGDH MUTATED PHGDH WILD-TYPE
  I OR II NOS             0              10
  STAGE 0                 0               6
  STAGE I                 1              21
  STAGE IA                1               9
  STAGE IB                0              24
  STAGE II                0              17
  STAGE IIA               0              10
  STAGE IIB               1              13
  STAGE IIC               0               9
  STAGE III               2              29
  STAGE IIIA              0              13
  STAGE IIIB              0              22
  STAGE IIIC              2              42
  STAGE IV                0              12
[1] 14  2
[1] 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
  PHGDH MUTATED       2  0  0  4
  PHGDH WILD-TYPE    49 58 53 51
D17V6, multiclass
       clus
vv      PHGDH MUTATED PHGDH WILD-TYPE
  T0+T1             2              49
  T2                0              58
  T3                0              53
  T4                4              51
[1] 4 2
[1] TRUE
[1] "dimension 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
  PHGDH MUTATED     4   2   1   1
  PHGDH WILD-TYPE 134  46  31  32
D17V7, multiclass
    clus
vv   PHGDH MUTATED PHGDH WILD-TYPE
  N0             4             134
  N1             2              46
  N2             1              31
  N3             1              32
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               M0  M1 M1A M1B M1C
  PHGDH MUTATED     8   0   0   0   0
  PHGDH WILD-TYPE 232   4   2   2   5
D17V8, multiclass
     clus
vv    PHGDH MUTATED PHGDH WILD-TYPE
  M0              8             232
  M1              0               4
  M1A             0               2
  M1B             0               2
  M1C             0               5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V9, binary
                 cls
clus                0   1
  PHGDH MUTATED     1   2
  PHGDH WILD-TYPE 101  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PHGDH MUTATED      1    2
  PHGDH WILD-TYPE  101   65
     clus
vv    PHGDH MUTATED PHGDH WILD-TYPE
  NO              1             101
  YES             2              65
[1] 2 2
[1] FALSE
D17V10, binary
                 cls
clus                0   1
  PHGDH MUTATED     1   9
  PHGDH WILD-TYPE  32 226
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PHGDH MUTATED      1    9
  PHGDH WILD-TYPE   32  226
     clus
vv    PHGDH MUTATED PHGDH WILD-TYPE
  NO              1              32
  YES             9             226
[1] 2 2
[1] FALSE
D17V11, continuous
D17V12, binary
                 cls
clus                0   1
  PHGDH MUTATED     2   8
  PHGDH WILD-TYPE 101 157
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PHGDH MUTATED      2    8
  PHGDH WILD-TYPE  101  157
        clus
vv       PHGDH MUTATED PHGDH WILD-TYPE
  FEMALE             2             101
  MALE               8             157
[1] 2 2
[1] FALSE
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PHGDH MUTATED       0                         0    10
  PHGDH WILD-TYPE     3                         1   254
D17V13, multiclass
                           clus
vv                          PHGDH MUTATED PHGDH WILD-TYPE
  ASIAN                                 0               3
  BLACK OR AFRICAN AMERICAN             0               1
  WHITE                                10             254
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V14, binary
                 cls
clus                0   1
  PHGDH MUTATED     0  10
  PHGDH WILD-TYPE   3 251
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PHGDH MUTATED      0   10
  PHGDH WILD-TYPE    3  251
                        clus
vv                       PHGDH MUTATED PHGDH WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO            10             251
[1] 2 2
[1] FALSE

Clustering(18) Variable = SLC38A4 MUTATION ANALYSIS
D18V1, survival
                   sevent
clus2                 0   1
  SLC38A4 MUTATED    16  15
  SLC38A4 WILD-TYPE 112 115
  SLC38A4 MUTATED SLC38A4 WILD-TYPE 
               31               227 
  SLC38A4 MUTATED SLC38A4 WILD-TYPE 
               15               115 
$`SLC38A4 MUTATED`
TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JK TCGA-D3-A51T TCGA-D3-A5GO TCGA-DA-A1I1 
       11.41        30.87         6.31        13.94        47.87        39.19 
TCGA-DA-A1IC TCGA-EB-A44Q TCGA-EE-A181 TCGA-EE-A20C TCGA-EE-A20H TCGA-EE-A29A 
        6.64        13.15         1.12         4.34         9.21         7.99 
TCGA-EE-A29G TCGA-EE-A29M TCGA-EE-A2A0 TCGA-EE-A2A2 TCGA-EE-A2GI TCGA-EE-A2MI 
        8.55        27.12        11.31        23.90        30.08        14.56 
TCGA-EE-A2MJ TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3J5 TCGA-EE-A3JA TCGA-EE-A3JD 
       63.42        27.16        23.05        21.60        22.22        27.35 
TCGA-ER-A19A TCGA-ER-A19G TCGA-FW-A3R5 TCGA-GF-A4EO TCGA-GN-A265 TCGA-GN-A266 
       76.41       114.15         0.99         7.23        84.72        10.13 
TCGA-QB-A6FS 
        5.79 

$`SLC38A4 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.47         8.52       111.09        32.42        70.16       110.79 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       28.08        22.55        45.83        81.24        10.29        85.32 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JG 
        8.38        21.14        88.50        68.22        69.90         7.50 
TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ 
       36.16        92.42        56.19        64.44        45.11       114.67 
TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE 
       15.25        46.98        46.32        82.29        61.38        13.32 
TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV 
       24.00         6.31         9.34       103.59        26.37         5.39 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N 
       80.22        42.71        15.09        41.10        17.72         8.84 
TCGA-D3-A51R TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 
       20.48        52.01         1.55         6.97        23.11         4.01 
TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1HW 
        2.89         9.90        11.31        13.22        48.79        35.80 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 
       51.12        10.03        13.68         9.99        44.52        36.69 
TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 
       25.15         4.93        22.36        19.36         7.00        17.56 
TCGA-DA-A3F8 TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EE-A17X 
       14.83         0.20         0.00         0.00        13.22        11.57 
TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 
       10.55         6.31         8.12         1.35        12.20         5.13 
TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29B TCGA-EE-A29C 
        4.31        36.07         5.13         1.18         9.90        37.97 
TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P 
       11.15        38.63         4.41         1.08         9.50        12.03 
TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X 
        8.09         8.84         9.99         2.43         8.68         8.09 
TCGA-EE-A2A1 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD 
       49.22         9.67         8.94        39.39        34.29        17.98 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM 
       34.92        47.21        19.43        16.01        35.54        28.31 
TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT 
       33.83        30.84         5.42         1.15        13.02        34.98 
TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC 
       36.33         8.84        98.27         2.70         6.18        47.51 
TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MK TCGA-EE-A2ML 
        9.53        29.46        44.25         7.96       111.78       111.91 
TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MU 
       56.02        25.08        26.99        21.60        29.65         5.56 
TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF 
      124.31       122.73        25.84         3.68        30.15        13.81 
TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 
       15.95        12.72         3.22        22.92        21.60        16.14 
TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 
        0.46        13.94        33.60        31.40        18.61        12.95 
TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E 
       38.40         5.72        25.18         3.78         3.52        11.90 
TCGA-ER-A19F TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N 
       11.11        34.88         4.21        13.45        28.60        42.84 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
       34.68         9.57        36.07        17.72        78.44        11.80 
TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES 
        1.87         1.51        13.08        12.62        11.74         9.04 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
        6.58        22.49         1.71        18.41        85.74         4.90 
TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 
       64.47         3.45        11.01        23.80        14.24        15.52 
TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE 
        7.33         7.30         3.39        20.38         8.22        19.53 
TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM 
       11.08         7.17        30.87        12.92        12.89        47.38 
TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU 
       52.08         8.65         8.81        49.15        40.64         8.68 
TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 
       27.39         0.82         5.23        53.85         7.36        28.73 
TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 
       14.20        10.78         5.98         6.41         2.27         0.20 
TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GN-A262 
        0.13         0.16         0.43         9.90        12.85        24.85 
TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D 
       31.33        16.24        15.42        12.16        14.70 

  SLC38A4 MUTATED SLC38A4 WILD-TYPE 
             0.99              0.00 
  SLC38A4 MUTATED SLC38A4 WILD-TYPE 
           114.15            124.31 
  SLC38A4 MUTATED SLC38A4 WILD-TYPE 
            14.56             14.83 
[1] "1.0 - 114.2 (14.6)" "0.0 - 124.3 (14.8)"
[1] "hr=" "1.1"
D18V2, survival
                   sevent
clus2                 0   1
  SLC38A4 MUTATED    17  15
  SLC38A4 WILD-TYPE 115 116
  SLC38A4 MUTATED SLC38A4 WILD-TYPE 
               32               231 
  SLC38A4 MUTATED SLC38A4 WILD-TYPE 
               15               116 
$`SLC38A4 MUTATED`
TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JK TCGA-D3-A51T TCGA-D3-A5GO TCGA-D9-A1JW 
       11.87        48.76        12.10        15.06       137.92         3.65 
TCGA-DA-A1I1 TCGA-DA-A1IC TCGA-EB-A44Q TCGA-EE-A181 TCGA-EE-A20C TCGA-EE-A20H 
      194.83        68.09        13.87        33.73       151.27       168.26 
TCGA-EE-A29A TCGA-EE-A29G TCGA-EE-A29M TCGA-EE-A2A0 TCGA-EE-A2A2 TCGA-EE-A2GI 
       63.35        72.07        44.35        46.82        24.43        48.72 
TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3J5 TCGA-EE-A3JA 
      204.66        96.23       136.47        41.59        36.95        53.19 
TCGA-EE-A3JD TCGA-ER-A19A TCGA-ER-A19G TCGA-FW-A3R5 TCGA-GF-A4EO TCGA-GN-A265 
       27.35        77.75       268.93        22.92         7.23        84.72 
TCGA-GN-A266 TCGA-QB-A6FS 
       10.13         6.67 

$`SLC38A4 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.57        16.67       112.04       112.57        71.80       133.25 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       28.08        31.59        90.90        95.74        43.43       103.10 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JG 
       65.49        23.77       115.53       168.00        69.90       113.52 
TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ 
       42.08       171.58        56.19        66.08        45.11       130.72 
TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE 
       58.06        46.98        46.32       166.52        86.93        60.23 
TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV 
       24.53        13.87         9.34       103.59        39.75        21.47 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N 
      161.85        43.69        40.14       131.90        18.38        10.03 
TCGA-D3-A51R TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 
       51.68       135.75       166.19         7.43       125.19       151.53 
TCGA-D9-A149 TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA 
       54.67         6.41        11.34         3.25         9.90        25.18 
TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I2 
       66.25        48.89        36.03       117.21        20.38       176.55 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB 
       35.93       107.34        61.18        53.92        65.92        23.44 
TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44R TCGA-EB-A5SG 
       28.60        10.49       215.44        15.68        10.16        45.11 
TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z 
       35.01         3.55        52.01        29.82        27.22         8.65 
TCGA-EE-A180 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B 
       94.98        14.70        26.89        68.15         4.96       109.64 
TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E 
       78.87        13.55        80.61        47.84        13.97        39.62 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R 
       32.19         2.60        18.61        56.42        37.35        14.47 
TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A1 TCGA-EE-A2A5 
       55.92        25.87       171.55        17.92       102.90        39.29 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH 
       58.75        47.54        67.43       314.56       135.95       208.04 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO 
       89.33        54.74        79.66        75.48        90.97       101.95 
TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 
       13.91        14.30        55.59        44.88        94.82        21.67 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME 
      129.27        28.83        19.76        61.51        47.28       103.27 
TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN 
      103.20        16.96       144.76       203.05       167.90        47.54 
TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB 
      248.65        43.23       103.56        53.26       124.31       122.73 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH 
       25.84         3.68        54.51        13.81        23.47       138.81 
TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JE TCGA-EE-A3JH 
      172.18       127.20        64.08        34.32        33.40       101.79 
TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 
      148.08        31.40        35.44        13.94        50.76         9.17 
TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19H 
       98.40        48.89        12.59        13.02        26.37       152.35 
TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q 
        6.44       131.51        61.05        44.05       162.08        50.89 
TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE 
       37.25       148.18        79.99        43.82        23.34        20.15 
TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV 
       16.37        31.27        32.05       247.04        80.32        46.98 
TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX 
       33.21        92.98       174.21         4.90       216.92        48.59 
TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA 
      228.59       202.65        20.91        28.08         7.79        27.72 
TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG 
       48.85       357.37        53.52        40.27        15.45         9.70 
TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ 
       32.75        47.38        23.93       101.26        74.73       133.55 
TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY 
       11.41       148.80        53.16        26.56        49.48        27.09 
TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 
       27.02        77.82        66.67        28.73       174.84        12.43 
TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV 
       26.73        49.45        77.88         0.20        47.54         0.16 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A267 
        2.40         9.90        14.04       120.46       117.93        64.44 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D 
       62.79        32.48        39.58 

  SLC38A4 MUTATED SLC38A4 WILD-TYPE 
             3.65              0.16 
  SLC38A4 MUTATED SLC38A4 WILD-TYPE 
           268.93            357.37 
  SLC38A4 MUTATED SLC38A4 WILD-TYPE 
            47.77             48.59 
[1] "3.6 - 268.9 (47.8)" "0.2 - 357.4 (48.6)"
[1] "hr=" "1.1"
D18V3, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  SLC38A4 MUTATED                    5             0
  SLC38A4 WILD-TYPE                 30             4
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  SLC38A4 MUTATED                                           6
  SLC38A4 WILD-TYPE                                        52
                   vv
clus                REGIONAL LYMPH NODE
  SLC38A4 MUTATED                    21
  SLC38A4 WILD-TYPE                 149
D18V4, multiclass
                                           clus
vv                                          SLC38A4 MUTATED SLC38A4 WILD-TYPE
  DISTANT METASTASIS                                      5                30
  PRIMARY TUMOR                                           0                 4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE               6                52
  REGIONAL LYMPH NODE                                    21               149
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  SLC38A4 MUTATED             0       1       1        2        3        3
  SLC38A4 WILD-TYPE          10       5      21        8       21       14
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  SLC38A4 MUTATED           1         1         0         4          2
  SLC38A4 WILD-TYPE         9        13         9        27         11
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  SLC38A4 MUTATED            1          7        1
  SLC38A4 WILD-TYPE         21         37       11
D18V5, multiclass
             clus
vv            SLC38A4 MUTATED SLC38A4 WILD-TYPE
  I OR II NOS               0                10
  STAGE 0                   1                 5
  STAGE I                   1                21
  STAGE IA                  2                 8
  STAGE IB                  3                21
  STAGE II                  3                14
  STAGE IIA                 1                 9
  STAGE IIB                 1                13
  STAGE IIC                 0                 9
  STAGE III                 4                27
  STAGE IIIA                2                11
  STAGE IIIB                1                21
  STAGE IIIC                7                37
  STAGE IV                  1                11
[1] 14  2
[1] 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
  SLC38A4 MUTATED       5  4  5  9
  SLC38A4 WILD-TYPE    46 54 48 46
D18V6, multiclass
       clus
vv      SLC38A4 MUTATED SLC38A4 WILD-TYPE
  T0+T1               5                46
  T2                  4                54
  T3                  5                48
  T4                  9                46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  SLC38A4 MUTATED    15   5   6   3
  SLC38A4 WILD-TYPE 123  43  26  30
D18V7, multiclass
    clus
vv   SLC38A4 MUTATED SLC38A4 WILD-TYPE
  N0              15               123
  N1               5                43
  N2               6                26
  N3               3                30
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1 M1A M1B M1C
  SLC38A4 MUTATED    28   1   0   0   0
  SLC38A4 WILD-TYPE 212   3   2   2   5
D18V8, multiclass
     clus
vv    SLC38A4 MUTATED SLC38A4 WILD-TYPE
  M0               28               212
  M1                1                 3
  M1A               0                 2
  M1B               0                 2
  M1C               0                 5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V9, binary
                   cls
clus                 0  1
  SLC38A4 MUTATED   14  5
  SLC38A4 WILD-TYPE 88 62
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC38A4 MUTATED     14    5
  SLC38A4 WILD-TYPE   88   62
     clus
vv    SLC38A4 MUTATED SLC38A4 WILD-TYPE
  NO               14                88
  YES               5                62
[1] 2 2
[1] FALSE
D18V10, binary
                   cls
clus                  0   1
  SLC38A4 MUTATED     7  25
  SLC38A4 WILD-TYPE  26 210
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC38A4 MUTATED      7   25
  SLC38A4 WILD-TYPE   26  210
     clus
vv    SLC38A4 MUTATED SLC38A4 WILD-TYPE
  NO                7                26
  YES              25               210
[1] 2 2
[1] FALSE
D18V11, continuous
D18V12, binary
                   cls
clus                  0   1
  SLC38A4 MUTATED     7  25
  SLC38A4 WILD-TYPE  96 140
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC38A4 MUTATED      7   25
  SLC38A4 WILD-TYPE   96  140
        clus
vv       SLC38A4 MUTATED SLC38A4 WILD-TYPE
  FEMALE               7                96
  MALE                25               140
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SLC38A4 MUTATED       1                         0    31
  SLC38A4 WILD-TYPE     2                         1   233
D18V13, multiclass
                           clus
vv                          SLC38A4 MUTATED SLC38A4 WILD-TYPE
  ASIAN                                   1                 2
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  31               233
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V14, binary
                   cls
clus                  0   1
  SLC38A4 MUTATED     0  31
  SLC38A4 WILD-TYPE   3 230
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC38A4 MUTATED      0   31
  SLC38A4 WILD-TYPE    3  230
                        clus
vv                       SLC38A4 MUTATED SLC38A4 WILD-TYPE
  HISPANIC OR LATINO                   0                 3
  NOT HISPANIC OR LATINO              31               230
[1] 2 2
[1] FALSE

Clustering(19) Variable = CDK4 MUTATION ANALYSIS
D19V1, survival
                sevent
clus2              0   1
  CDK4 MUTATED     1   6
  CDK4 WILD-TYPE 127 124
  CDK4 MUTATED CDK4 WILD-TYPE 
             7            251 
  CDK4 MUTATED CDK4 WILD-TYPE 
             6            124 
$`CDK4 MUTATED`
TCGA-EB-A44R TCGA-EE-A29V TCGA-EE-A2MG TCGA-EE-A3AD TCGA-ER-A19E TCGA-ER-A19W 
        0.20         2.43        44.25         3.68        11.90        17.72 
TCGA-GF-A6C8 
       12.85 

$`CDK4 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.47         8.52       111.09        32.42        70.16       110.79 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       28.08        22.55        45.83        81.24        10.29        85.32 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
        8.38        21.14        88.50        68.22        69.90        11.41 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       30.87         7.50        36.16         6.31        92.42        56.19 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 
       64.44        45.11       114.67        15.25        46.98        46.32 
TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO 
       82.29        61.38        13.32        24.00         6.31         9.34 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H 
      103.59        26.37         5.39        80.22        42.71        15.09 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN 
       41.10        17.72         8.84        20.48        13.94        52.01 
TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 
       47.87         1.55         6.97        23.11         4.01         2.89 
TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY 
        9.90        11.31        13.22        48.79        35.80        51.12 
TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 
       10.03        39.19        13.68         9.99        44.52        36.69 
TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 
       25.15         4.93        22.36         6.64        19.36         7.00 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN 
       17.56        14.83        13.15         0.00         0.00        13.22 
TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 
       11.57        10.55         6.31         8.12         1.12         1.35 
TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F 
       12.20         5.13         4.31        36.07         4.34         5.13 
TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D 
        9.21         1.18         7.99         9.90        37.97        11.15 
TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N 
       38.63         8.55         4.41         1.08        27.12         9.50 
TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29W TCGA-EE-A29X 
       12.03         8.09         8.84         9.99         8.68         8.09 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB 
       11.31        49.22        23.90         9.67         8.94        39.39 
TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ 
       34.29        17.98        34.92        47.21        30.08        19.43 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP 
       16.01        35.54        28.31        33.83        30.84         5.42 
TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 
        1.15        13.02        34.98        36.33         8.84        98.27 
TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MH 
        2.70         6.18        47.51         9.53        29.46         7.96 
TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN 
       14.56        63.42       111.78       111.91        56.02        25.08 
TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU 
       26.99        21.60        29.65        27.16        23.05         5.56 
TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG 
      124.31       122.73        25.84        30.15        13.81        15.95 
TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 
       12.72         3.22        22.92        21.60        21.60        16.14 
TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 
       22.22        27.35         0.46        13.94        33.60        31.40 
TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B 
       18.61        12.95        38.40         5.72        76.41        25.18 
TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J 
        3.78         3.52        11.11       114.15        34.88         4.21 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S 
       13.45        28.60        42.84        34.68         9.57        36.07 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG 
       78.44        11.80         1.87         1.51        13.08        12.62 
TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN 
       11.74         9.04         6.58        22.49         1.71        18.41 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 
       85.74         4.90        64.47         3.45        11.01        23.80 
TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC 
       14.24        15.52         7.33         7.30         3.39        20.38 
TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ 
        8.22        19.53        11.08         7.17        30.87        12.92 
TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS 
       12.89        47.38        52.08         8.65         8.81        49.15 
TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 
       40.64         8.68        27.39         0.82         5.23        53.85 
TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC 
        7.36        28.73        14.20        10.78         5.98         6.41 
TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY 
        2.27         0.20         0.99         0.13         0.16         0.43 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 
        9.90         7.23        24.85        31.33        84.72        10.13 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS 
       16.24        15.42        12.16        14.70         5.79 

  CDK4 MUTATED CDK4 WILD-TYPE 
           0.2            0.0 
  CDK4 MUTATED CDK4 WILD-TYPE 
         44.25         124.31 
  CDK4 MUTATED CDK4 WILD-TYPE 
         11.90          15.09 
[1] "0.2 - 44.2 (11.9)"  "0.0 - 124.3 (15.1)"
[1] "hr=" "2.8"
D19V2, survival
                sevent
clus2              0   1
  CDK4 MUTATED     1   6
  CDK4 WILD-TYPE 131 125
  CDK4 MUTATED CDK4 WILD-TYPE 
             7            256 
  CDK4 MUTATED CDK4 WILD-TYPE 
             6            125 
$`CDK4 MUTATED`
TCGA-EB-A44R TCGA-EE-A29V TCGA-EE-A2MG TCGA-EE-A3AD TCGA-ER-A19E TCGA-ER-A19W 
       10.16        25.87       103.20         3.68        13.02       148.18 
TCGA-GF-A6C8 
       14.04 

$`CDK4 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.57        16.67       112.04       112.57        71.80       133.25 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       28.08        31.59        90.90        95.74        43.43       103.10 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
       65.49        23.77       115.53       168.00        69.90        11.87 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       48.76       113.52        42.08        12.10       171.58        56.19 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 
       66.08        45.11       130.72        58.06        46.98        46.32 
TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO 
      166.52        86.93        60.23        24.53        13.87         9.34 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H 
      103.59        39.75        21.47       161.85        43.69        40.14 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN 
      131.90        18.38        10.03        51.68        15.06       135.75 
TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 
      137.92       166.19         7.43       125.19       151.53        54.67 
TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA 
        3.65         6.41        11.34         3.25         9.90        25.18 
TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 
       66.25        48.89        36.03       117.21        20.38       194.83 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA 
      176.55        35.93       107.34        61.18        53.92        65.92 
TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 
       23.44        68.09        28.60        10.49       215.44        15.68 
TCGA-EB-A44Q TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X 
       13.87        45.11        35.01         3.55        52.01        29.82 
TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 
       27.22         8.65        94.98        33.73        14.70        26.89 
TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H 
       68.15         4.96       109.64       151.27        78.87       168.26 
TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E 
       13.55        63.35        80.61        47.84        13.97        39.62 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P 
       72.07        32.19         2.60        44.35        18.61        56.42 
TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 
       37.35        14.47        55.92       171.55        17.92        46.82 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC 
      102.90        24.43        39.29        58.75        47.54        67.43 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK 
      314.56       135.95       208.04        48.72        89.33        54.74 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR 
       79.66        75.48        90.97       101.95        13.91        14.30 
TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 
       55.59        44.88        94.82        21.67       129.27        28.83 
TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MH TCGA-EE-A2MI 
       19.76        61.51        47.28       103.27        16.96       204.66 
TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP 
       96.23       144.76       203.05       167.90        47.54       248.65 
TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA 
       43.23       103.56       136.47        41.59        53.26       124.31 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH 
      122.73        25.84        54.51        13.81        23.47       138.81 
TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA 
      172.18       127.20        36.95        64.08        34.32        53.19 
TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 
       27.35        33.40       101.79       148.08        31.40        35.44 
TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C 
       13.94        50.76         9.17        77.75        98.40        48.89 
TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L 
       12.59        26.37       268.93       152.35         6.44       131.51 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A1A1 
       61.05        44.05       162.08        50.89        37.25        79.99 
TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH 
       43.82        23.34        20.15        16.37        31.27        32.05 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A 
      247.04        80.32        46.98        33.21        92.98       174.21 
TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
        4.90       216.92        48.59       228.59       202.65        20.91 
TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD 
       28.08         7.79        27.72        48.85       357.37        53.52 
TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK 
       40.27        15.45         9.70        32.75        47.38        23.93 
TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT 
      101.26        74.73       133.55        11.41       148.80        53.16 
TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 
       26.56        49.48        27.09        27.02        77.82        66.67 
TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD 
       28.73       174.84        12.43        26.73        49.45        77.88 
TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
        0.20        22.92        47.54         0.16         2.40         9.90 
TCGA-GF-A4EO TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 
        7.23       120.46       117.93        84.72        10.13        64.44 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS 
       62.79        32.48        39.58         6.67 

  CDK4 MUTATED CDK4 WILD-TYPE 
          3.68           0.16 
  CDK4 MUTATED CDK4 WILD-TYPE 
        148.18         357.37 
  CDK4 MUTATED CDK4 WILD-TYPE 
         14.04          48.74 
[1] "3.7 - 148.2 (14.0)" "0.2 - 357.4 (48.7)"
[1] "hr=" "3.1"
D19V3, continuous
                vv
clus             DISTANT METASTASIS PRIMARY TUMOR
  CDK4 MUTATED                    1             0
  CDK4 WILD-TYPE                 34             4
                vv
clus             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  CDK4 MUTATED                                           1                   5
  CDK4 WILD-TYPE                                        57                 165
D19V4, multiclass
                                           clus
vv                                          CDK4 MUTATED CDK4 WILD-TYPE
  DISTANT METASTASIS                                   1             34
  PRIMARY TUMOR                                        0              4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE            1             57
  REGIONAL LYMPH NODE                                  5            165
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  CDK4 MUTATED             0       0       1        0        1        0
  CDK4 WILD-TYPE          10       6      21       10       23       17
                vv
clus             STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  CDK4 MUTATED           0         1         0         1          0          1
  CDK4 WILD-TYPE        10        13         9        30         13         21
                vv
clus             STAGE IIIC STAGE IV
  CDK4 MUTATED            1        0
  CDK4 WILD-TYPE         43       12
D19V5, multiclass
             clus
vv            CDK4 MUTATED CDK4 WILD-TYPE
  I OR II NOS            0             10
  STAGE 0                0              6
  STAGE I                1             21
  STAGE IA               0             10
  STAGE IB               1             23
  STAGE II               0             17
  STAGE IIA              0             10
  STAGE IIB              1             13
  STAGE IIC              0              9
  STAGE III              1             30
  STAGE IIIA             0             13
  STAGE IIIB             1             21
  STAGE IIIC             1             43
  STAGE IV               0             12
[1] 14  2
[1] 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
  CDK4 MUTATED       1  2  2  0
  CDK4 WILD-TYPE    50 56 51 55
D19V6, multiclass
       clus
vv      CDK4 MUTATED CDK4 WILD-TYPE
  T0+T1            1             50
  T2               2             56
  T3               2             51
  T4               0             55
[1] 4 2
[1] TRUE
[1] "dimension 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
  CDK4 MUTATED     2   2   1   0
  CDK4 WILD-TYPE 136  46  31  33
D19V7, multiclass
    clus
vv   CDK4 MUTATED CDK4 WILD-TYPE
  N0            2            136
  N1            2             46
  N2            1             31
  N3            0             33
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              M0  M1 M1A M1B M1C
  CDK4 MUTATED     6   0   0   0   0
  CDK4 WILD-TYPE 234   4   2   2   5
D19V8, multiclass
     clus
vv    CDK4 MUTATED CDK4 WILD-TYPE
  M0             6            234
  M1             0              4
  M1A            0              2
  M1B            0              2
  M1C            0              5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V9, binary
                cls
clus               0   1
  CDK4 MUTATED     2   2
  CDK4 WILD-TYPE 100  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  CDK4 MUTATED      2    2
  CDK4 WILD-TYPE  100   65
     clus
vv    CDK4 MUTATED CDK4 WILD-TYPE
  NO             2            100
  YES            2             65
[1] 2 2
[1] FALSE
D19V10, binary
                cls
clus               0   1
  CDK4 MUTATED     1   6
  CDK4 WILD-TYPE  32 229
[1] "tbl2"
                cls
clus             [,1] [,2]
  CDK4 MUTATED      1    6
  CDK4 WILD-TYPE   32  229
     clus
vv    CDK4 MUTATED CDK4 WILD-TYPE
  NO             1             32
  YES            6            229
[1] 2 2
[1] FALSE
D19V11, continuous
D19V12, binary
                cls
clus               0   1
  CDK4 MUTATED     3   4
  CDK4 WILD-TYPE 100 161
[1] "tbl2"
                cls
clus             [,1] [,2]
  CDK4 MUTATED      3    4
  CDK4 WILD-TYPE  100  161
        clus
vv       CDK4 MUTATED CDK4 WILD-TYPE
  FEMALE            3            100
  MALE              4            161
[1] 2 2
[1] FALSE
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CDK4 MUTATED       1                         0     6
  CDK4 WILD-TYPE     2                         1   258
D19V13, multiclass
                           clus
vv                          CDK4 MUTATED CDK4 WILD-TYPE
  ASIAN                                1              2
  BLACK OR AFRICAN AMERICAN            0              1
  WHITE                                6            258
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V14, binary
                cls
clus               0   1
  CDK4 MUTATED     0   7
  CDK4 WILD-TYPE   3 254
[1] "tbl2"
                cls
clus             [,1] [,2]
  CDK4 MUTATED      0    7
  CDK4 WILD-TYPE    3  254
                        clus
vv                       CDK4 MUTATED CDK4 WILD-TYPE
  HISPANIC OR LATINO                0              3
  NOT HISPANIC OR LATINO            7            254
[1] 2 2
[1] FALSE

Clustering(20) Variable = FAM58A MUTATION ANALYSIS
D20V1, survival
                  sevent
clus2                0   1
  FAM58A MUTATED     1   4
  FAM58A WILD-TYPE 127 126
  FAM58A MUTATED FAM58A WILD-TYPE 
               5              253 
  FAM58A MUTATED FAM58A WILD-TYPE 
               4              126 
$`FAM58A MUTATED`
TCGA-DA-A1IC TCGA-EE-A29N TCGA-EE-A2MT TCGA-EE-A3J5 TCGA-EE-A3JD 
        6.64         9.50        23.05        21.60        27.35 

$`FAM58A WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.47         8.52       111.09        32.42        70.16       110.79 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       28.08        22.55        45.83        81.24        10.29        85.32 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
        8.38        21.14        88.50        68.22        69.90        11.41 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       30.87         7.50        36.16         6.31        92.42        56.19 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 
       64.44        45.11       114.67        15.25        46.98        46.32 
TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO 
       82.29        61.38        13.32        24.00         6.31         9.34 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H 
      103.59        26.37         5.39        80.22        42.71        15.09 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN 
       41.10        17.72         8.84        20.48        13.94        52.01 
TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 
       47.87         1.55         6.97        23.11         4.01         2.89 
TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY 
        9.90        11.31        13.22        48.79        35.80        51.12 
TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 
       10.03        39.19        13.68         9.99        44.52        36.69 
TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 
       25.15         4.93        22.36        19.36         7.00        17.56 
TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN 
       14.83        13.15         0.20         0.00         0.00        13.22 
TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 
       11.57        10.55         6.31         8.12         1.12         1.35 
TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F 
       12.20         5.13         4.31        36.07         4.34         5.13 
TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D 
        9.21         1.18         7.99         9.90        37.97        11.15 
TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29P 
       38.63         8.55         4.41         1.08        27.12        12.03 
TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X 
        8.09         8.84         9.99         2.43         8.68         8.09 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB 
       11.31        49.22        23.90         9.67         8.94        39.39 
TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ 
       34.29        17.98        34.92        47.21        30.08        19.43 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP 
       16.01        35.54        28.31        33.83        30.84         5.42 
TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 
        1.15        13.02        34.98        36.33         8.84        98.27 
TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG 
        2.70         6.18        47.51         9.53        29.46        44.25 
TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM 
        7.96        14.56        63.42       111.78       111.91        56.02 
TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MU 
       25.08        26.99        21.60        29.65        27.16         5.56 
TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF 
      124.31       122.73        25.84         3.68        30.15        13.81 
TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 
       15.95        12.72         3.22        22.92        21.60        16.14 
TCGA-EE-A3JA TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 
       22.22         0.46        13.94        33.60        31.40        18.61 
TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C 
       12.95        38.40         5.72        76.41        25.18         3.78 
TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J 
        3.52        11.90        11.11       114.15        34.88         4.21 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S 
       13.45        28.60        42.84        34.68         9.57        36.07 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF 
       17.72        78.44        11.80         1.87         1.51        13.08 
TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL 
       12.62        11.74         9.04         6.58        22.49         1.71 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY 
       18.41        85.74         4.90        64.47         3.45        11.01 
TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB 
       23.80        14.24        15.52         7.33         7.30         3.39 
TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH 
       20.38         8.22        19.53        11.08         7.17        30.87 
TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR 
       12.92        12.89        47.38        52.08         8.65         8.81 
TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ 
       49.15        40.64         8.68        27.39         0.82         5.23 
TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB 
       53.85         7.36        28.73        14.20        10.78         5.98 
TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV 
        6.41         2.27         0.20         0.99         0.13         0.16 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 
        0.43         9.90         7.23        12.85        24.85        31.33 
TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D 
       84.72        10.13        16.24        15.42        12.16        14.70 
TCGA-QB-A6FS 
        5.79 

  FAM58A MUTATED FAM58A WILD-TYPE 
            6.64             0.00 
  FAM58A MUTATED FAM58A WILD-TYPE 
           27.35           124.31 
  FAM58A MUTATED FAM58A WILD-TYPE 
            21.6             14.7 
[1] "6.6 - 27.4 (21.6)"  "0.0 - 124.3 (14.7)"
[1] "hr=" "1.8"
D20V2, survival
                  sevent
clus2                0   1
  FAM58A MUTATED     1   4
  FAM58A WILD-TYPE 131 127
  FAM58A MUTATED FAM58A WILD-TYPE 
               5              258 
  FAM58A MUTATED FAM58A WILD-TYPE 
               4              127 
$`FAM58A MUTATED`
TCGA-DA-A1IC TCGA-EE-A29N TCGA-EE-A2MT TCGA-EE-A3J5 TCGA-EE-A3JD 
       68.09        18.61        41.59        36.95        27.35 

$`FAM58A WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.57        16.67       112.04       112.57        71.80       133.25 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       28.08        31.59        90.90        95.74        43.43       103.10 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
       65.49        23.77       115.53       168.00        69.90        11.87 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       48.76       113.52        42.08        12.10       171.58        56.19 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 
       66.08        45.11       130.72        58.06        46.98        46.32 
TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO 
      166.52        86.93        60.23        24.53        13.87         9.34 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H 
      103.59        39.75        21.47       161.85        43.69        40.14 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN 
      131.90        18.38        10.03        51.68        15.06       135.75 
TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 
      137.92       166.19         7.43       125.19       151.53        54.67 
TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA 
        3.65         6.41        11.34         3.25         9.90        25.18 
TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 
       66.25        48.89        36.03       117.21        20.38       194.83 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA 
      176.55        35.93       107.34        61.18        53.92        65.92 
TCGA-DA-A1IB TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q 
       23.44        28.60        10.49       215.44        15.68        13.87 
TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X 
       10.16        45.11        35.01         3.55        52.01        29.82 
TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 
       27.22         8.65        94.98        33.73        14.70        26.89 
TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H 
       68.15         4.96       109.64       151.27        78.87       168.26 
TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E 
       13.55        63.35        80.61        47.84        13.97        39.62 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29Q 
       72.07        32.19         2.60        44.35        56.42        37.35 
TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 
       14.47        55.92        25.87       171.55        17.92        46.82 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC 
      102.90        24.43        39.29        58.75        47.54        67.43 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK 
      314.56       135.95       208.04        48.72        89.33        54.74 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR 
       79.66        75.48        90.97       101.95        13.91        14.30 
TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 
       55.59        44.88        94.82        21.67       129.27        28.83 
TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH 
       19.76        61.51        47.28       103.27       103.20        16.96 
TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN 
      204.66        96.23       144.76       203.05       167.90        47.54 
TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3AA 
      248.65        43.23       103.56       136.47        53.26       124.31 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG 
      122.73        25.84         3.68        54.51        13.81        23.47 
TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA 
      138.81       172.18       127.20        64.08        34.32        53.19 
TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 
       33.40       101.79       148.08        31.40        35.44        13.94 
TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D 
       50.76         9.17        77.75        98.40        48.89        12.59 
TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L 
       13.02        26.37       268.93       152.35         6.44       131.51 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W 
       61.05        44.05       162.08        50.89        37.25       148.18 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG 
       79.99        43.82        23.34        20.15        16.37        31.27 
TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN 
       32.05       247.04        80.32        46.98        33.21        92.98 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 
      174.21         4.90       216.92        48.59       228.59       202.65 
TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC 
       20.91        28.08         7.79        27.72        48.85       357.37 
TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ 
       53.52        40.27        15.45         9.70        32.75        47.38 
TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS 
       23.93       101.26        74.73       133.55        11.41       148.80 
TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 
       53.16        26.56        49.48        27.09        27.02        77.82 
TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC 
       66.67        28.73       174.84        12.43        26.73        49.45 
TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY 
       77.88         0.20        22.92        47.54         0.16         2.40 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        9.90         7.23        14.04       120.46       117.93        84.72 
TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS 
       10.13        64.44        62.79        32.48        39.58         6.67 

  FAM58A MUTATED FAM58A WILD-TYPE 
           18.61             0.16 
  FAM58A MUTATED FAM58A WILD-TYPE 
           68.09           357.37 
  FAM58A MUTATED FAM58A WILD-TYPE 
           36.95            48.74 
[1] "18.6 - 68.1 (37.0)" "0.2 - 357.4 (48.7)"
[1] "hr=" "2.5"
D20V3, continuous
                  vv
clus               DISTANT METASTASIS PRIMARY TUMOR
  FAM58A MUTATED                    0             0
  FAM58A WILD-TYPE                 35             4
                  vv
clus               REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  FAM58A MUTATED                                           2
  FAM58A WILD-TYPE                                        56
                  vv
clus               REGIONAL LYMPH NODE
  FAM58A MUTATED                     3
  FAM58A WILD-TYPE                 167
D20V4, multiclass
                                           clus
vv                                          FAM58A MUTATED FAM58A WILD-TYPE
  DISTANT METASTASIS                                     0               35
  PRIMARY TUMOR                                          0                4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE              2               56
  REGIONAL LYMPH NODE                                    3              167
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  FAM58A MUTATED             1       0       0        0        1        0
  FAM58A WILD-TYPE           9       6      22       10       23       17
                  vv
clus               STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  FAM58A MUTATED           0         0         0         2          0
  FAM58A WILD-TYPE        10        14         9        29         13
                  vv
clus               STAGE IIIB STAGE IIIC STAGE IV
  FAM58A MUTATED            1          0        0
  FAM58A WILD-TYPE         21         44       12
D20V5, multiclass
             clus
vv            FAM58A MUTATED FAM58A WILD-TYPE
  I OR II NOS              1                9
  STAGE 0                  0                6
  STAGE I                  0               22
  STAGE IA                 0               10
  STAGE IB                 1               23
  STAGE II                 0               17
  STAGE IIA                0               10
  STAGE IIB                0               14
  STAGE IIC                0                9
  STAGE III                2               29
  STAGE IIIA               0               13
  STAGE IIIB               1               21
  STAGE IIIC               0               44
  STAGE IV                 0               12
[1] 14  2
[1] 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
  FAM58A MUTATED       0  1  1  1
  FAM58A WILD-TYPE    51 57 52 54
D20V6, multiclass
       clus
vv      FAM58A MUTATED FAM58A WILD-TYPE
  T0+T1              0               51
  T2                 1               57
  T3                 1               52
  T4                 1               54
[1] 4 2
[1] TRUE
[1] "dimension 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
  FAM58A MUTATED     2   1   2   0
  FAM58A WILD-TYPE 136  47  30  33
D20V7, multiclass
    clus
vv   FAM58A MUTATED FAM58A WILD-TYPE
  N0              2              136
  N1              1               47
  N2              2               30
  N3              0               33
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                M0  M1 M1A M1B M1C
  FAM58A MUTATED     5   0   0   0   0
  FAM58A WILD-TYPE 235   4   2   2   5
D20V8, multiclass
     clus
vv    FAM58A MUTATED FAM58A WILD-TYPE
  M0               5              235
  M1               0                4
  M1A              0                2
  M1B              0                2
  M1C              0                5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V9, binary
                  cls
clus                0  1
  FAM58A MUTATED    3  0
  FAM58A WILD-TYPE 99 67
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM58A MUTATED      3    0
  FAM58A WILD-TYPE   99   67
     clus
vv    FAM58A MUTATED FAM58A WILD-TYPE
  NO               3               99
  YES              0               67
[1] 2 2
[1] FALSE
D20V10, binary
                  cls
clus                 0   1
  FAM58A MUTATED     1   4
  FAM58A WILD-TYPE  32 231
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM58A MUTATED      1    4
  FAM58A WILD-TYPE   32  231
     clus
vv    FAM58A MUTATED FAM58A WILD-TYPE
  NO               1               32
  YES              4              231
[1] 2 2
[1] FALSE
D20V11, continuous
D20V12, binary
                  cls
clus                 0   1
  FAM58A MUTATED     0   5
  FAM58A WILD-TYPE 103 160
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM58A MUTATED      0    5
  FAM58A WILD-TYPE  103  160
        clus
vv       FAM58A MUTATED FAM58A WILD-TYPE
  FEMALE              0              103
  MALE                5              160
[1] 2 2
[1] FALSE
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  FAM58A MUTATED       0                         0     5
  FAM58A WILD-TYPE     3                         1   259
D20V13, multiclass
                           clus
vv                          FAM58A MUTATED FAM58A WILD-TYPE
  ASIAN                                  0                3
  BLACK OR AFRICAN AMERICAN              0                1
  WHITE                                  5              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"
D20V14, binary
                  cls
clus                 0   1
  FAM58A MUTATED     0   5
  FAM58A WILD-TYPE   3 256
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM58A MUTATED      0    5
  FAM58A WILD-TYPE    3  256
                        clus
vv                       FAM58A MUTATED FAM58A WILD-TYPE
  HISPANIC OR LATINO                  0                3
  NOT HISPANIC OR LATINO              5              256
[1] 2 2
[1] FALSE

Clustering(21) Variable = EMG1 MUTATION ANALYSIS
D21V1, survival
                sevent
clus2              0   1
  EMG1 MUTATED     3   5
  EMG1 WILD-TYPE 125 125
  EMG1 MUTATED EMG1 WILD-TYPE 
             8            250 
  EMG1 MUTATED EMG1 WILD-TYPE 
             5            125 
$`EMG1 MUTATED`
TCGA-D3-A3CB TCGA-D9-A6EC TCGA-EE-A20C TCGA-EE-A29V TCGA-EE-A3J8 TCGA-ER-A19D 
       82.29        13.22         4.34         2.43        16.14         3.52 
TCGA-FS-A1ZF TCGA-FS-A4FD 
       11.08         2.27 

$`EMG1 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.47         8.52       111.09        32.42        70.16       110.79 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       28.08        22.55        45.83        81.24        10.29        85.32 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
        8.38        21.14        88.50        68.22        69.90        11.41 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       30.87         7.50        36.16         6.31        92.42        56.19 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 
       64.44        45.11       114.67        15.25        46.98        46.32 
TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR 
       61.38        13.32        24.00         6.31         9.34       103.59 
TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J 
       26.37         5.39        80.22        42.71        15.09        41.10 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO 
       17.72         8.84        20.48        13.94        52.01        47.87 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 
        1.55         6.97        23.11         4.01         2.89         9.90 
TCGA-D9-A6EA TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 
       11.31        48.79        35.80        51.12        10.03        39.19 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA 
       13.68         9.99        44.52        36.69        25.15         4.93 
TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 
       22.36         6.64        19.36         7.00        17.56        14.83 
TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EE-A17X 
       13.15         0.20         0.00         0.00        13.22        11.57 
TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 
       10.55         6.31         8.12         1.12         1.35        12.20 
TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I 
        5.13         4.31        36.07         5.13         9.21         1.18 
TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G 
        7.99         9.90        37.97        11.15        38.63         8.55 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
        4.41         1.08        27.12         9.50        12.03         8.09 
TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 
        8.84         9.99         8.68         8.09        11.31        49.22 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD 
       23.90         9.67         8.94        39.39        34.29        17.98 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
       34.92        47.21        30.08        19.43        16.01        35.54 
TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS 
       28.31        33.83        30.84         5.42         1.15        13.02 
TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 
       34.98        36.33         8.84        98.27         2.70         6.18 
TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI 
       47.51         9.53        29.46        44.25         7.96        14.56 
TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP 
       63.42       111.78       111.91        56.02        25.08        26.99 
TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA 
       21.60        29.65        27.16        23.05         5.56       124.31 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG 
      122.73        25.84         3.68        30.15        13.81        15.95 
TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3JA 
       12.72         3.22        22.92        21.60        21.60        22.22 
TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 
       27.35         0.46        13.94        33.60        31.40        18.61 
TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C 
       12.95        38.40         5.72        76.41        25.18         3.78 
TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L 
       11.90        11.11       114.15        34.88         4.21        13.45 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W 
       28.60        42.84        34.68         9.57        36.07        17.72 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG 
       78.44        11.80         1.87         1.51        13.08        12.62 
TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN 
       11.74         9.04         6.58        22.49         1.71        18.41 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 
       85.74         4.90        64.47         3.45        11.01        23.80 
TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC 
       14.24        15.52         7.33         7.30         3.39        20.38 
TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK 
        8.22        19.53         7.17        30.87        12.92        12.89 
TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT 
       47.38        52.08         8.65         8.81        49.15        40.64 
TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 
        8.68        27.39         0.82         5.23        53.85         7.36 
TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FW-A3I3 
       28.73        14.20        10.78         5.98         6.41         0.20 
TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
        0.99         0.13         0.16         0.43         9.90         7.23 
TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 
       12.85        24.85        31.33        84.72        10.13        16.24 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS 
       15.42        12.16        14.70         5.79 

  EMG1 MUTATED EMG1 WILD-TYPE 
          2.27           0.00 
  EMG1 MUTATED EMG1 WILD-TYPE 
         82.29         124.31 
  EMG1 MUTATED EMG1 WILD-TYPE 
          7.71          15.17 
[1] "2.3 - 82.3 (7.7)"   "0.0 - 124.3 (15.2)"
[1] "hr=" "2"  
D21V2, survival
                sevent
clus2              0   1
  EMG1 MUTATED     3   5
  EMG1 WILD-TYPE 129 126
  EMG1 MUTATED EMG1 WILD-TYPE 
             8            255 
  EMG1 MUTATED EMG1 WILD-TYPE 
             5            126 
$`EMG1 MUTATED`
TCGA-D3-A3CB TCGA-D9-A6EC TCGA-EE-A20C TCGA-EE-A29V TCGA-EE-A3J8 TCGA-ER-A19D 
      166.52        66.25       151.27        25.87        34.32        12.59 
TCGA-FS-A1ZF TCGA-FS-A4FD 
       15.45        77.88 

$`EMG1 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.57        16.67       112.04       112.57        71.80       133.25 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       28.08        31.59        90.90        95.74        43.43       103.10 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
       65.49        23.77       115.53       168.00        69.90        11.87 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       48.76       113.52        42.08        12.10       171.58        56.19 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 
       66.08        45.11       130.72        58.06        46.98        46.32 
TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR 
       86.93        60.23        24.53        13.87         9.34       103.59 
TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J 
       39.75        21.47       161.85        43.69        40.14       131.90 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO 
       18.38        10.03        51.68        15.06       135.75       137.92 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW 
      166.19         7.43       125.19       151.53        54.67         3.65 
TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-DA-A1HV 
        6.41        11.34         3.25         9.90        25.18        48.89 
TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 
       36.03       117.21        20.38       194.83       176.55        35.93 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC 
      107.34        61.18        53.92        65.92        23.44        68.09 
TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R 
       28.60        10.49       215.44        15.68        13.87        10.16 
TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y 
       45.11        35.01         3.55        52.01        29.82        27.22 
TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 
        8.65        94.98        33.73        14.70        26.89        68.15 
TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A 
        4.96       109.64        78.87       168.26        13.55        63.35 
TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H 
       80.61        47.84        13.97        39.62        72.07        32.19 
TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R 
        2.60        44.35        18.61        56.42        37.35        14.47 
TCGA-EE-A29S TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 
       55.92       171.55        17.92        46.82       102.90        24.43 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE 
       39.29        58.75        47.54        67.43       314.56       135.95 
TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM 
      208.04        48.72        89.33        54.74        79.66        75.48 
TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT 
       90.97       101.95        13.91        14.30        55.59        44.88 
TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC 
       94.82        21.67       129.27        28.83        19.76        61.51 
TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ 
       47.28       103.27       103.20        16.96       204.66        96.23 
TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ 
      144.76       203.05       167.90        47.54       248.65        43.23 
TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB 
      103.56       136.47        41.59        53.26       124.31       122.73 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH 
       25.84         3.68        54.51        13.81        23.47       138.81 
TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3JA TCGA-EE-A3JD 
      172.18       127.20        36.95        64.08        53.19        27.35 
TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 
       33.40       101.79       148.08        31.40        35.44        13.94 
TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19E 
       50.76         9.17        77.75        98.40        48.89        13.02 
TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M 
       26.37       268.93       152.35         6.44       131.51        61.05 
TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 
       44.05       162.08        50.89        37.25       148.18        79.99 
TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH 
       43.82        23.34        20.15        16.37        31.27        32.05 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A 
      247.04        80.32        46.98        33.21        92.98       174.21 
TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
        4.90       216.92        48.59       228.59       202.65        20.91 
TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD 
       28.08         7.79        27.72        48.85       357.37        53.52 
TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM 
       40.27         9.70        32.75        47.38        23.93       101.26 
TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU 
       74.73       133.55        11.41       148.80        53.16        26.56 
TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 
       49.48        27.09        27.02        77.82        66.67        28.73 
TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FW-A3I3 TCGA-FW-A3R5 
      174.84        12.43        26.73        49.45         0.20        22.92 
TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 
       47.54         0.16         2.40         9.90         7.23        14.04 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 
      120.46       117.93        84.72        10.13        64.44        62.79 
TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS 
       32.48        39.58         6.67 

  EMG1 MUTATED EMG1 WILD-TYPE 
         12.59           0.16 
  EMG1 MUTATED EMG1 WILD-TYPE 
        166.52         357.37 
  EMG1 MUTATED EMG1 WILD-TYPE 
        50.285         48.590 
[1] "12.6 - 166.5 (50.3)" "0.2 - 357.4 (48.6)" 
[1] "hr=" "1.3"
D21V3, continuous
                vv
clus             DISTANT METASTASIS PRIMARY TUMOR
  EMG1 MUTATED                    3             1
  EMG1 WILD-TYPE                 32             3
                vv
clus             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  EMG1 MUTATED                                           2                   2
  EMG1 WILD-TYPE                                        56                 168
D21V4, multiclass
                                           clus
vv                                          EMG1 MUTATED EMG1 WILD-TYPE
  DISTANT METASTASIS                                   3             32
  PRIMARY TUMOR                                        1              3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE            2             56
  REGIONAL LYMPH NODE                                  2            168
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  EMG1 MUTATED             1       1       0        0        1        0
  EMG1 WILD-TYPE           9       5      22       10       23       17
                vv
clus             STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  EMG1 MUTATED           0         0         1         0          2          0
  EMG1 WILD-TYPE        10        14         8        31         11         22
                vv
clus             STAGE IIIC STAGE IV
  EMG1 MUTATED            2        0
  EMG1 WILD-TYPE         42       12
D21V5, multiclass
             clus
vv            EMG1 MUTATED EMG1 WILD-TYPE
  I OR II NOS            1              9
  STAGE 0                1              5
  STAGE I                0             22
  STAGE IA               0             10
  STAGE IB               1             23
  STAGE II               0             17
  STAGE IIA              0             10
  STAGE IIB              0             14
  STAGE IIC              1              8
  STAGE III              0             31
  STAGE IIIA             2             11
  STAGE IIIB             0             22
  STAGE IIIC             2             42
  STAGE IV               0             12
[1] 14  2
[1] 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
  EMG1 MUTATED       0  3  2  2
  EMG1 WILD-TYPE    51 55 51 53
D21V6, multiclass
       clus
vv      EMG1 MUTATED EMG1 WILD-TYPE
  T0+T1            0             51
  T2               3             55
  T3               2             51
  T4               2             53
[1] 4 2
[1] TRUE
[1] "dimension 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
  EMG1 MUTATED     4   3   0   1
  EMG1 WILD-TYPE 134  45  32  32
D21V7, multiclass
    clus
vv   EMG1 MUTATED EMG1 WILD-TYPE
  N0            4            134
  N1            3             45
  N2            0             32
  N3            1             32
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              M0  M1 M1A M1B M1C
  EMG1 MUTATED     8   0   0   0   0
  EMG1 WILD-TYPE 232   4   2   2   5
D21V8, multiclass
     clus
vv    EMG1 MUTATED EMG1 WILD-TYPE
  M0             8            232
  M1             0              4
  M1A            0              2
  M1B            0              2
  M1C            0              5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V9, binary
                cls
clus              0  1
  EMG1 MUTATED    3  2
  EMG1 WILD-TYPE 99 65
[1] "tbl2"
                cls
clus             [,1] [,2]
  EMG1 MUTATED      3    2
  EMG1 WILD-TYPE   99   65
     clus
vv    EMG1 MUTATED EMG1 WILD-TYPE
  NO             3             99
  YES            2             65
[1] 2 2
[1] FALSE
D21V10, binary
                cls
clus               0   1
  EMG1 MUTATED     0   8
  EMG1 WILD-TYPE  33 227
[1] "tbl2"
                cls
clus             [,1] [,2]
  EMG1 MUTATED      0    8
  EMG1 WILD-TYPE   33  227
     clus
vv    EMG1 MUTATED EMG1 WILD-TYPE
  NO             0             33
  YES            8            227
[1] 2 2
[1] FALSE
D21V11, continuous
D21V12, binary
                cls
clus               0   1
  EMG1 MUTATED     3   5
  EMG1 WILD-TYPE 100 160
[1] "tbl2"
                cls
clus             [,1] [,2]
  EMG1 MUTATED      3    5
  EMG1 WILD-TYPE  100  160
        clus
vv       EMG1 MUTATED EMG1 WILD-TYPE
  FEMALE            3            100
  MALE              5            160
[1] 2 2
[1] FALSE
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  EMG1 MUTATED       0                         0     8
  EMG1 WILD-TYPE     3                         1   256
D21V13, multiclass
                           clus
vv                          EMG1 MUTATED EMG1 WILD-TYPE
  ASIAN                                0              3
  BLACK OR AFRICAN AMERICAN            0              1
  WHITE                                8            256
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V14, binary
                cls
clus               0   1
  EMG1 MUTATED     0   8
  EMG1 WILD-TYPE   3 253
[1] "tbl2"
                cls
clus             [,1] [,2]
  EMG1 MUTATED      0    8
  EMG1 WILD-TYPE    3  253
                        clus
vv                       EMG1 MUTATED EMG1 WILD-TYPE
  HISPANIC OR LATINO                0              3
  NOT HISPANIC OR LATINO            8            253
[1] 2 2
[1] FALSE

Clustering(22) Variable = RQCD1 MUTATION ANALYSIS
D22V1, survival
                 sevent
clus2               0   1
  RQCD1 MUTATED     5   2
  RQCD1 WILD-TYPE 123 128
  RQCD1 MUTATED RQCD1 WILD-TYPE 
              7             251 
  RQCD1 MUTATED RQCD1 WILD-TYPE 
              2             128 
$`RQCD1 MUTATED`
TCGA-D9-A6EC TCGA-EE-A29P TCGA-EE-A2GM TCGA-EE-A2GS TCGA-ER-A19P TCGA-FR-A3YN 
       13.22        12.03        28.31        13.02        34.68        18.41 
TCGA-FS-A1ZU 
        8.68 

$`RQCD1 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.47         8.52       111.09        32.42        70.16       110.79 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       28.08        22.55        45.83        81.24        10.29        85.32 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
        8.38        21.14        88.50        68.22        69.90        11.41 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       30.87         7.50        36.16         6.31        92.42        56.19 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 
       64.44        45.11       114.67        15.25        46.98        46.32 
TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO 
       82.29        61.38        13.32        24.00         6.31         9.34 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H 
      103.59        26.37         5.39        80.22        42.71        15.09 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN 
       41.10        17.72         8.84        20.48        13.94        52.01 
TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 
       47.87         1.55         6.97        23.11         4.01         2.89 
TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 
        9.90        11.31        48.79        35.80        51.12        10.03 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 
       39.19        13.68         9.99        44.52        36.69        25.15 
TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 
        4.93        22.36         6.64        19.36         7.00        17.56 
TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN 
       14.83        13.15         0.20         0.00         0.00        13.22 
TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 
       11.57        10.55         6.31         8.12         1.12         1.35 
TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F 
       12.20         5.13         4.31        36.07         4.34         5.13 
TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D 
        9.21         1.18         7.99         9.90        37.97        11.15 
TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N 
       38.63         8.55         4.41         1.08        27.12         9.50 
TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X 
        8.09         8.84         9.99         2.43         8.68         8.09 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB 
       11.31        49.22        23.90         9.67         8.94        39.39 
TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ 
       34.29        17.98        34.92        47.21        30.08        19.43 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR 
       16.01        35.54        33.83        30.84         5.42         1.15 
TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 
       34.98        36.33         8.84        98.27         2.70         6.18 
TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI 
       47.51         9.53        29.46        44.25         7.96        14.56 
TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP 
       63.42       111.78       111.91        56.02        25.08        26.99 
TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA 
       21.60        29.65        27.16        23.05         5.56       124.31 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG 
      122.73        25.84         3.68        30.15        13.81        15.95 
TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 
       12.72         3.22        22.92        21.60        21.60        16.14 
TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 
       22.22        27.35         0.46        13.94        33.60        31.40 
TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B 
       18.61        12.95        38.40         5.72        76.41        25.18 
TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H 
        3.78         3.52        11.90        11.11       114.15        34.88 
TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19Q TCGA-ER-A19S 
        4.21        13.45        28.60        42.84         9.57        36.07 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF 
       17.72        78.44        11.80         1.87         1.51        13.08 
TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL 
       12.62        11.74         9.04         6.58        22.49         1.71 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 
       85.74         4.90        64.47         3.45        11.01        23.80 
TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC 
       14.24        15.52         7.33         7.30         3.39        20.38 
TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ 
        8.22        19.53        11.08         7.17        30.87        12.92 
TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS 
       12.89        47.38        52.08         8.65         8.81        49.15 
TCGA-FS-A1ZT TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 
       40.64        27.39         0.82         5.23        53.85         7.36 
TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD 
       28.73        14.20        10.78         5.98         6.41         2.27 
TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
        0.20         0.99         0.13         0.16         0.43         9.90 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 
        7.23        12.85        24.85        31.33        84.72        10.13 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS 
       16.24        15.42        12.16        14.70         5.79 

  RQCD1 MUTATED RQCD1 WILD-TYPE 
           8.68            0.00 
  RQCD1 MUTATED RQCD1 WILD-TYPE 
          34.68          124.31 
  RQCD1 MUTATED RQCD1 WILD-TYPE 
          13.22           14.83 
[1] "8.7 - 34.7 (13.2)"  "0.0 - 124.3 (14.8)"
[1] "hr=" "1.7"
D22V2, survival
                 sevent
clus2               0   1
  RQCD1 MUTATED     5   2
  RQCD1 WILD-TYPE 127 129
  RQCD1 MUTATED RQCD1 WILD-TYPE 
              7             256 
  RQCD1 MUTATED RQCD1 WILD-TYPE 
              2             129 
$`RQCD1 MUTATED`
TCGA-D9-A6EC TCGA-EE-A29P TCGA-EE-A2GM TCGA-EE-A2GS TCGA-ER-A19P TCGA-FR-A3YN 
       66.25        56.42        75.48        55.59       162.08        92.98 
TCGA-FS-A1ZU 
       26.56 

$`RQCD1 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.57        16.67       112.04       112.57        71.80       133.25 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       28.08        31.59        90.90        95.74        43.43       103.10 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
       65.49        23.77       115.53       168.00        69.90        11.87 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       48.76       113.52        42.08        12.10       171.58        56.19 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 
       66.08        45.11       130.72        58.06        46.98        46.32 
TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO 
      166.52        86.93        60.23        24.53        13.87         9.34 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H 
      103.59        39.75        21.47       161.85        43.69        40.14 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN 
      131.90        18.38        10.03        51.68        15.06       135.75 
TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 
      137.92       166.19         7.43       125.19       151.53        54.67 
TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA 
        3.65         6.41        11.34         3.25         9.90        25.18 
TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 
       48.89        36.03       117.21        20.38       194.83       176.55 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB 
       35.93       107.34        61.18        53.92        65.92        23.44 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q 
       68.09        28.60        10.49       215.44        15.68        13.87 
TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X 
       10.16        45.11        35.01         3.55        52.01        29.82 
TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 
       27.22         8.65        94.98        33.73        14.70        26.89 
TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H 
       68.15         4.96       109.64       151.27        78.87       168.26 
TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E 
       13.55        63.35        80.61        47.84        13.97        39.62 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29Q 
       72.07        32.19         2.60        44.35        18.61        37.35 
TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 
       14.47        55.92        25.87       171.55        17.92        46.82 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC 
      102.90        24.43        39.29        58.75        47.54        67.43 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK 
      314.56       135.95       208.04        48.72        89.33        54.74 
TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GT 
       79.66        90.97       101.95        13.91        14.30        44.88 
TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC 
       94.82        21.67       129.27        28.83        19.76        61.51 
TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ 
       47.28       103.27       103.20        16.96       204.66        96.23 
TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ 
      144.76       203.05       167.90        47.54       248.65        43.23 
TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB 
      103.56       136.47        41.59        53.26       124.31       122.73 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH 
       25.84         3.68        54.51        13.81        23.47       138.81 
TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA 
      172.18       127.20        36.95        64.08        34.32        53.19 
TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 
       27.35        33.40       101.79       148.08        31.40        35.44 
TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C 
       13.94        50.76         9.17        77.75        98.40        48.89 
TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J 
       12.59        13.02        26.37       268.93       152.35         6.44 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W 
      131.51        61.05        44.05        50.89        37.25       148.18 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG 
       79.99        43.82        23.34        20.15        16.37        31.27 
TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A44A 
       32.05       247.04        80.32        46.98        33.21       174.21 
TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
        4.90       216.92        48.59       228.59       202.65        20.91 
TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD 
       28.08         7.79        27.72        48.85       357.37        53.52 
TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK 
       40.27        15.45         9.70        32.75        47.38        23.93 
TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT 
      101.26        74.73       133.55        11.41       148.80        53.16 
TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 
       49.48        27.09        27.02        77.82        66.67        28.73 
TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 
      174.84        12.43        26.73        49.45        77.88         0.20 
TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
       22.92        47.54         0.16         2.40         9.90         7.23 
TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 
       14.04       120.46       117.93        84.72        10.13        64.44 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS 
       62.79        32.48        39.58         6.67 

  RQCD1 MUTATED RQCD1 WILD-TYPE 
          26.56            0.16 
  RQCD1 MUTATED RQCD1 WILD-TYPE 
         162.08          357.37 
  RQCD1 MUTATED RQCD1 WILD-TYPE 
          66.25           47.54 
[1] "26.6 - 162.1 (66.2)" "0.2 - 357.4 (47.5)" 
[1] "hr=" "2"  
D22V3, continuous
                 vv
clus              DISTANT METASTASIS PRIMARY TUMOR
  RQCD1 MUTATED                    1             1
  RQCD1 WILD-TYPE                 34             3
                 vv
clus              REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  RQCD1 MUTATED                                           2                   4
  RQCD1 WILD-TYPE                                        56                 166
D22V4, multiclass
                                           clus
vv                                          RQCD1 MUTATED RQCD1 WILD-TYPE
  DISTANT METASTASIS                                    1              34
  PRIMARY TUMOR                                         1               3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE             2              56
  REGIONAL LYMPH NODE                                   4             166
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  RQCD1 MUTATED             0       1       0        0        2        0
  RQCD1 WILD-TYPE          10       5      22       10       22       17
                 vv
clus              STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  RQCD1 MUTATED           0         0         3         0          1          0
  RQCD1 WILD-TYPE        10        14         6        31         12         22
                 vv
clus              STAGE IIIC STAGE IV
  RQCD1 MUTATED            0        0
  RQCD1 WILD-TYPE         44       12
D22V5, multiclass
             clus
vv            RQCD1 MUTATED RQCD1 WILD-TYPE
  I OR II NOS             0              10
  STAGE 0                 1               5
  STAGE I                 0              22
  STAGE IA                0              10
  STAGE IB                2              22
  STAGE II                0              17
  STAGE IIA               0              10
  STAGE IIB               0              14
  STAGE IIC               3               6
  STAGE III               0              31
  STAGE IIIA              1              12
  STAGE IIIB              0              22
  STAGE IIIC              0              44
  STAGE IV                0              12
[1] 14  2
[1] 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
  RQCD1 MUTATED       0  2  1  3
  RQCD1 WILD-TYPE    51 56 52 52
D22V6, multiclass
       clus
vv      RQCD1 MUTATED RQCD1 WILD-TYPE
  T0+T1             0              51
  T2                2              56
  T3                1              52
  T4                3              52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  RQCD1 MUTATED     7   1   0   0
  RQCD1 WILD-TYPE 131  47  32  33
D22V7, multiclass
    clus
vv   RQCD1 MUTATED RQCD1 WILD-TYPE
  N0             7             131
  N1             1              47
  N2             0              32
  N3             0              33
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               M0  M1 M1A M1B M1C
  RQCD1 MUTATED     8   0   0   0   0
  RQCD1 WILD-TYPE 232   4   2   2   5
D22V8, multiclass
     clus
vv    RQCD1 MUTATED RQCD1 WILD-TYPE
  M0              8             232
  M1              0               4
  M1A             0               2
  M1B             0               2
  M1C             0               5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V9, binary
                 cls
clus               0  1
  RQCD1 MUTATED    3  3
  RQCD1 WILD-TYPE 99 64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RQCD1 MUTATED      3    3
  RQCD1 WILD-TYPE   99   64
     clus
vv    RQCD1 MUTATED RQCD1 WILD-TYPE
  NO              3              99
  YES             3              64
[1] 2 2
[1] FALSE
D22V10, binary
                 cls
clus                0   1
  RQCD1 MUTATED     0   8
  RQCD1 WILD-TYPE  33 227
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RQCD1 MUTATED      0    8
  RQCD1 WILD-TYPE   33  227
     clus
vv    RQCD1 MUTATED RQCD1 WILD-TYPE
  NO              0              33
  YES             8             227
[1] 2 2
[1] FALSE
D22V11, continuous
D22V12, binary
                 cls
clus                0   1
  RQCD1 MUTATED     6   2
  RQCD1 WILD-TYPE  97 163
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RQCD1 MUTATED      6    2
  RQCD1 WILD-TYPE   97  163
        clus
vv       RQCD1 MUTATED RQCD1 WILD-TYPE
  FEMALE             6              97
  MALE               2             163
[1] 2 2
[1] FALSE
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RQCD1 MUTATED       0                         0     8
  RQCD1 WILD-TYPE     3                         1   256
D22V13, multiclass
                           clus
vv                          RQCD1 MUTATED RQCD1 WILD-TYPE
  ASIAN                                 0               3
  BLACK OR AFRICAN AMERICAN             0               1
  WHITE                                 8             256
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V14, binary
                 cls
clus                0   1
  RQCD1 MUTATED     0   8
  RQCD1 WILD-TYPE   3 253
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RQCD1 MUTATED      0    8
  RQCD1 WILD-TYPE    3  253
                        clus
vv                       RQCD1 MUTATED RQCD1 WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO             8             253
[1] 2 2
[1] FALSE

Clustering(23) Variable = HSD11B1 MUTATION ANALYSIS
D23V1, survival
                   sevent
clus2                 0   1
  HSD11B1 MUTATED    10   4
  HSD11B1 WILD-TYPE 118 126
  HSD11B1 MUTATED HSD11B1 WILD-TYPE 
               14               244 
  HSD11B1 MUTATED HSD11B1 WILD-TYPE 
                4               126 
$`HSD11B1 MUTATED`
TCGA-D3-A1Q6 TCGA-D3-A2JF TCGA-D3-A2JH TCGA-D3-A51T TCGA-EB-A5SG TCGA-EE-A29M 
       70.16        30.87        36.16        13.94         0.00        27.12 
TCGA-EE-A29R TCGA-EE-A2A0 TCGA-EE-A2GM TCGA-EE-A2MD TCGA-EE-A2MQ TCGA-EE-A2MR 
        8.84        11.31        28.31         9.53        21.60        29.65 
TCGA-FW-A3R5 TCGA-QB-A6FS 
        0.99         5.79 

$`HSD11B1 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       16.47         8.52       111.09        32.42       110.79        28.08 
TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 
       22.55        45.83        81.24        10.29        85.32         8.38 
TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JG 
       21.14        88.50        68.22        69.90        11.41         7.50 
TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ 
        6.31        92.42        56.19        64.44        45.11       114.67 
TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE 
       15.25        46.98        46.32        82.29        61.38        13.32 
TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV 
       24.00         6.31         9.34       103.59        26.37         5.39 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N 
       80.22        42.71        15.09        41.10        17.72         8.84 
TCGA-D3-A51R TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU 
       20.48        52.01        47.87         1.55         6.97        23.11 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1HV 
        4.01         2.89         9.90        11.31        13.22        48.79 
TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 
       35.80        51.12        10.03        39.19        13.68         9.99 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC 
       44.52        36.69        25.15         4.93        22.36         6.64 
TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R 
       19.36         7.00        17.56        14.83        13.15         0.20 
TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 
        0.00        13.22        11.57        10.55         6.31         8.12 
TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B 
        1.12         1.35        12.20         5.13         4.31        36.07 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B 
        4.34         5.13         9.21         1.18         7.99         9.90 
TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L 
       37.97        11.15        38.63         8.55         4.41         1.08 
TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W 
        9.50        12.03         8.09         9.99         2.43         8.68 
TCGA-EE-A29X TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB 
        8.09        49.22        23.90         9.67         8.94        39.39 
TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ 
       34.29        17.98        34.92        47.21        30.08        19.43 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR 
       16.01        35.54        33.83        30.84         5.42         1.15 
TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 
       13.02        34.98        36.33         8.84        98.27         2.70 
TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI 
        6.18        47.51        29.46        44.25         7.96        14.56 
TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP 
       63.42       111.78       111.91        56.02        25.08        26.99 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC 
       27.16        23.05         5.56       124.31       122.73        25.84 
TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 
        3.68        30.15        13.81        15.95        12.72         3.22 
TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JD 
       22.92        21.60        21.60        16.14        22.22        27.35 
TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 
        0.46        13.94        33.60        31.40        18.61        12.95 
TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D 
       38.40         5.72        76.41        25.18         3.78         3.52 
TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L 
       11.90        11.11       114.15        34.88         4.21        13.45 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W 
       28.60        42.84        34.68         9.57        36.07        17.72 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG 
       78.44        11.80         1.87         1.51        13.08        12.62 
TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN 
       11.74         9.04         6.58        22.49         1.71        18.41 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 
       85.74         4.90        64.47         3.45        11.01        23.80 
TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC 
       14.24        15.52         7.33         7.30         3.39        20.38 
TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ 
        8.22        19.53        11.08         7.17        30.87        12.92 
TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS 
       12.89        47.38        52.08         8.65         8.81        49.15 
TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 
       40.64         8.68        27.39         0.82         5.23        53.85 
TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC 
        7.36        28.73        14.20        10.78         5.98         6.41 
TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
        2.27         0.20         0.13         0.16         0.43         9.90 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 
        7.23        12.85        24.85        31.33        84.72        10.13 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D 
       16.24        15.42        12.16        14.70 

  HSD11B1 MUTATED HSD11B1 WILD-TYPE 
                0                 0 
  HSD11B1 MUTATED HSD11B1 WILD-TYPE 
            70.16            124.31 
  HSD11B1 MUTATED HSD11B1 WILD-TYPE 
           17.770            14.765 
[1] "0.0 - 70.2 (17.8)"  "0.0 - 124.3 (14.8)"
[1] "hr=" "1.7"
D23V2, survival
                   sevent
clus2                 0   1
  HSD11B1 MUTATED    10   4
  HSD11B1 WILD-TYPE 122 127
  HSD11B1 MUTATED HSD11B1 WILD-TYPE 
               14               249 
  HSD11B1 MUTATED HSD11B1 WILD-TYPE 
                4               127 
$`HSD11B1 MUTATED`
TCGA-D3-A1Q6 TCGA-D3-A2JF TCGA-D3-A2JH TCGA-D3-A51T TCGA-EB-A5SG TCGA-EE-A29M 
       71.80        48.76        42.08        15.06        45.11        44.35 
TCGA-EE-A29R TCGA-EE-A2A0 TCGA-EE-A2GM TCGA-EE-A2MD TCGA-EE-A2MQ TCGA-EE-A2MR 
       14.47        46.82        75.48        47.28        43.23       103.56 
TCGA-FW-A3R5 TCGA-QB-A6FS 
       22.92         6.67 

$`HSD11B1 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       16.57        16.67       112.04       112.57       133.25        28.08 
TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 
       31.59        90.90        95.74        43.43       103.10        65.49 
TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JG 
       23.77       115.53       168.00        69.90        11.87       113.52 
TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ 
       12.10       171.58        56.19        66.08        45.11       130.72 
TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE 
       58.06        46.98        46.32       166.52        86.93        60.23 
TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV 
       24.53        13.87         9.34       103.59        39.75        21.47 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N 
      161.85        43.69        40.14       131.90        18.38        10.03 
TCGA-D3-A51R TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU 
       51.68       135.75       137.92       166.19         7.43       125.19 
TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 
      151.53        54.67         3.65         6.41        11.34         3.25 
TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY 
        9.90        25.18        66.25        48.89        36.03       117.21 
TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 
       20.38       194.83       176.55        35.93       107.34        61.18 
TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 
       53.92        65.92        23.44        68.09        28.60        10.49 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SH TCGA-EB-A5UL 
      215.44        15.68        13.87        10.16        35.01         3.55 
TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 
       52.01        29.82        27.22         8.65        94.98        33.73 
TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C 
       14.70        26.89        68.15         4.96       109.64       151.27 
TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C 
       78.87       168.26        13.55        63.35        80.61        47.84 
TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29N 
       13.97        39.62        72.07        32.19         2.60        18.61 
TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X 
       56.42        37.35        55.92        25.87       171.55        17.92 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC 
      102.90        24.43        39.29        58.75        47.54        67.43 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK 
      314.56       135.95       208.04        48.72        89.33        54.74 
TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS 
       79.66        90.97       101.95        13.91        14.30        55.59 
TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 
       44.88        94.82        21.67       129.27        28.83        19.76 
TCGA-EE-A2MC TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ 
       61.51       103.27       103.20        16.96       204.66        96.23 
TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MS 
      144.76       203.05       167.90        47.54       248.65       136.47 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD 
       41.59        53.26       124.31       122.73        25.84         3.68 
TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 
       54.51        13.81        23.47       138.81       172.18       127.20 
TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE 
       36.95        64.08        34.32        53.19        27.35        33.40 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 
      101.79       148.08        31.40        35.44        13.94        50.76 
TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E 
        9.17        77.75        98.40        48.89        12.59        13.02 
TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M 
       26.37       268.93       152.35         6.44       131.51        61.05 
TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 
       44.05       162.08        50.89        37.25       148.18        79.99 
TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH 
       43.82        23.34        20.15        16.37        31.27        32.05 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A 
      247.04        80.32        46.98        33.21        92.98       174.21 
TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
        4.90       216.92        48.59       228.59       202.65        20.91 
TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD 
       28.08         7.79        27.72        48.85       357.37        53.52 
TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK 
       40.27        15.45         9.70        32.75        47.38        23.93 
TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT 
      101.26        74.73       133.55        11.41       148.80        53.16 
TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 
       26.56        49.48        27.09        27.02        77.82        66.67 
TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD 
       28.73       174.84        12.43        26.73        49.45        77.88 
TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
        0.20        47.54         0.16         2.40         9.90         7.23 
TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 
       14.04       120.46       117.93        84.72        10.13        64.44 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D 
       62.79        32.48        39.58 

  HSD11B1 MUTATED HSD11B1 WILD-TYPE 
             6.67              0.16 
  HSD11B1 MUTATED HSD11B1 WILD-TYPE 
           103.56            357.37 
  HSD11B1 MUTATED HSD11B1 WILD-TYPE 
            44.73             48.89 
[1] "6.7 - 103.6 (44.7)" "0.2 - 357.4 (48.9)"
[1] "hr=" "1.2"
D23V3, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  HSD11B1 MUTATED                    1             0
  HSD11B1 WILD-TYPE                 34             4
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  HSD11B1 MUTATED                                           3
  HSD11B1 WILD-TYPE                                        55
                   vv
clus                REGIONAL LYMPH NODE
  HSD11B1 MUTATED                    10
  HSD11B1 WILD-TYPE                 160
D23V4, multiclass
                                           clus
vv                                          HSD11B1 MUTATED HSD11B1 WILD-TYPE
  DISTANT METASTASIS                                      1                34
  PRIMARY TUMOR                                           0                 4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE               3                55
  REGIONAL LYMPH NODE                                    10               160
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  HSD11B1 MUTATED             0       0       1        1        2        1
  HSD11B1 WILD-TYPE          10       6      21        9       22       16
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  HSD11B1 MUTATED           1         0         1         2          1
  HSD11B1 WILD-TYPE         9        14         8        29         12
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  HSD11B1 MUTATED            0          3        0
  HSD11B1 WILD-TYPE         22         41       12
D23V5, multiclass
             clus
vv            HSD11B1 MUTATED HSD11B1 WILD-TYPE
  I OR II NOS               0                10
  STAGE 0                   0                 6
  STAGE I                   1                21
  STAGE IA                  1                 9
  STAGE IB                  2                22
  STAGE II                  1                16
  STAGE IIA                 1                 9
  STAGE IIB                 0                14
  STAGE IIC                 1                 8
  STAGE III                 2                29
  STAGE IIIA                1                12
  STAGE IIIB                0                22
  STAGE IIIC                3                41
  STAGE IV                  0                12
[1] 14  2
[1] 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
  HSD11B1 MUTATED       3  2  4  3
  HSD11B1 WILD-TYPE    48 56 49 52
D23V6, multiclass
       clus
vv      HSD11B1 MUTATED HSD11B1 WILD-TYPE
  T0+T1               3                48
  T2                  2                56
  T3                  4                49
  T4                  3                52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  HSD11B1 MUTATED     7   3   2   1
  HSD11B1 WILD-TYPE 131  45  30  32
D23V7, multiclass
    clus
vv   HSD11B1 MUTATED HSD11B1 WILD-TYPE
  N0               7               131
  N1               3                45
  N2               2                30
  N3               1                32
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1 M1A M1B M1C
  HSD11B1 MUTATED    13   0   0   0   0
  HSD11B1 WILD-TYPE 227   4   2   2   5
D23V8, multiclass
     clus
vv    HSD11B1 MUTATED HSD11B1 WILD-TYPE
  M0               13               227
  M1                0                 4
  M1A               0                 2
  M1B               0                 2
  M1C               0                 5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V9, binary
                   cls
clus                 0  1
  HSD11B1 MUTATED    7  4
  HSD11B1 WILD-TYPE 95 63
[1] "tbl2"
                   cls
clus                [,1] [,2]
  HSD11B1 MUTATED      7    4
  HSD11B1 WILD-TYPE   95   63
     clus
vv    HSD11B1 MUTATED HSD11B1 WILD-TYPE
  NO                7                95
  YES               4                63
[1] 2 2
[1] FALSE
D23V10, binary
                   cls
clus                  0   1
  HSD11B1 MUTATED     1  13
  HSD11B1 WILD-TYPE  32 222
[1] "tbl2"
                   cls
clus                [,1] [,2]
  HSD11B1 MUTATED      1   13
  HSD11B1 WILD-TYPE   32  222
     clus
vv    HSD11B1 MUTATED HSD11B1 WILD-TYPE
  NO                1                32
  YES              13               222
[1] 2 2
[1] FALSE
D23V11, continuous
D23V12, binary
                   cls
clus                  0   1
  HSD11B1 MUTATED     7   7
  HSD11B1 WILD-TYPE  96 158
[1] "tbl2"
                   cls
clus                [,1] [,2]
  HSD11B1 MUTATED      7    7
  HSD11B1 WILD-TYPE   96  158
        clus
vv       HSD11B1 MUTATED HSD11B1 WILD-TYPE
  FEMALE               7                96
  MALE                 7               158
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  HSD11B1 MUTATED       0                         0    14
  HSD11B1 WILD-TYPE     3                         1   250
D23V13, multiclass
                           clus
vv                          HSD11B1 MUTATED HSD11B1 WILD-TYPE
  ASIAN                                   0                 3
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  14               250
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V14, binary
                   cls
clus                  0   1
  HSD11B1 MUTATED     0  14
  HSD11B1 WILD-TYPE   3 247
[1] "tbl2"
                   cls
clus                [,1] [,2]
  HSD11B1 MUTATED      0   14
  HSD11B1 WILD-TYPE    3  247
                        clus
vv                       HSD11B1 MUTATED HSD11B1 WILD-TYPE
  HISPANIC OR LATINO                   0                 3
  NOT HISPANIC OR LATINO              14               247
[1] 2 2
[1] FALSE

Clustering(24) Variable = DMC1 MUTATION ANALYSIS
D24V1, survival
                sevent
clus2              0   1
  DMC1 MUTATED     8   4
  DMC1 WILD-TYPE 120 126
  DMC1 MUTATED DMC1 WILD-TYPE 
            12            246 
  DMC1 MUTATED DMC1 WILD-TYPE 
             4            126 
$`DMC1 MUTATED`
TCGA-D3-A1Q3 TCGA-D3-A3MV TCGA-DA-A1I7 TCGA-EB-A5SG TCGA-EE-A29A TCGA-EE-A29G 
        8.52         5.39        36.69         0.00         7.99         8.55 
TCGA-EE-A29S TCGA-EE-A2MR TCGA-EE-A3J7 TCGA-ER-A19A TCGA-ER-A19M TCGA-GF-A3OT 
        9.99        29.65        21.60        76.41        28.60         9.90 

$`DMC1 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       16.47       111.09        32.42        70.16       110.79        28.08 
TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 
       22.55        45.83        81.24        10.29        85.32         8.38 
TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF 
       21.14        88.50        68.22        69.90        11.41        30.87 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO 
        7.50        36.16         6.31        92.42        56.19        64.44 
TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB 
       45.11       114.67        15.25        46.98        46.32        82.29 
TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR 
       61.38        13.32        24.00         6.31         9.34       103.59 
TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K 
       26.37        80.22        42.71        15.09        41.10        17.72 
TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR 
        8.84        20.48        13.94        52.01        47.87         1.55 
TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA 
        6.97        23.11         4.01         2.89         9.90        11.31 
TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 
       13.22        48.79        35.80        51.12        10.03        39.19 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB 
       13.68         9.99        44.52        25.15         4.93        22.36 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q 
        6.64        19.36         7.00        17.56        14.83        13.15 
TCGA-EB-A44R TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z 
        0.20         0.00        13.22        11.57        10.55         6.31 
TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 
        8.12         1.12         1.35        12.20         5.13         4.31 
TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29B 
       36.07         4.34         5.13         9.21         1.18         9.90 
TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M 
       37.97        11.15        38.63         4.41         1.08        27.12 
TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29V TCGA-EE-A29W 
        9.50        12.03         8.09         8.84         2.43         8.68 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 
        8.09        11.31        49.22        23.90         9.67         8.94 
TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI 
       39.39        34.29        17.98        34.92        47.21        30.08 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO 
       19.43        16.01        35.54        28.31        33.83        30.84 
TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 
        5.42         1.15        13.02        34.98        36.33         8.84 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME 
       98.27         2.70         6.18        47.51         9.53        29.46 
TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML 
       44.25         7.96        14.56        63.42       111.78       111.91 
TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MS TCGA-EE-A2MT 
       56.02        25.08        26.99        21.60        27.16        23.05 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE 
        5.56       124.31       122.73        25.84         3.68        30.15 
TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 
       13.81        15.95        12.72         3.22        22.92        21.60 
TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI 
       16.14        22.22        27.35         0.46        13.94        33.60 
TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19B 
       31.40        18.61        12.95        38.40         5.72        25.18 
TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H 
        3.78         3.52        11.90        11.11       114.15        34.88 
TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S 
        4.21        13.45        42.84        34.68         9.57        36.07 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF 
       17.72        78.44        11.80         1.87         1.51        13.08 
TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL 
       12.62        11.74         9.04         6.58        22.49         1.71 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY 
       18.41        85.74         4.90        64.47         3.45        11.01 
TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB 
       23.80        14.24        15.52         7.33         7.30         3.39 
TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH 
       20.38         8.22        19.53        11.08         7.17        30.87 
TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR 
       12.92        12.89        47.38        52.08         8.65         8.81 
TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ 
       49.15        40.64         8.68        27.39         0.82         5.23 
TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB 
       53.85         7.36        28.73        14.20        10.78         5.98 
TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV 
        6.41         2.27         0.20         0.99         0.13         0.16 
TCGA-FW-A5DY TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        0.43         7.23        12.85        24.85        31.33        84.72 
TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS 
       10.13        16.24        15.42        12.16        14.70         5.79 

  DMC1 MUTATED DMC1 WILD-TYPE 
             0              0 
  DMC1 MUTATED DMC1 WILD-TYPE 
         76.41         124.31 
  DMC1 MUTATED DMC1 WILD-TYPE 
         9.945         14.960 
[1] "0.0 - 76.4 (9.9)"   "0.0 - 124.3 (15.0)"
[1] "hr=" "1.3"
D24V2, survival
                sevent
clus2              0   1
  DMC1 MUTATED     8   4
  DMC1 WILD-TYPE 124 127
  DMC1 MUTATED DMC1 WILD-TYPE 
            12            251 
  DMC1 MUTATED DMC1 WILD-TYPE 
             4            127 
$`DMC1 MUTATED`
TCGA-D3-A1Q3 TCGA-D3-A3MV TCGA-DA-A1I7 TCGA-EB-A5SG TCGA-EE-A29A TCGA-EE-A29G 
       16.67        21.47        61.18        45.11        63.35        72.07 
TCGA-EE-A29S TCGA-EE-A2MR TCGA-EE-A3J7 TCGA-ER-A19A TCGA-ER-A19M TCGA-GF-A3OT 
       55.92       103.56        64.08        77.75        61.05         9.90 

$`DMC1 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       16.57       112.04       112.57        71.80       133.25        28.08 
TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 
       31.59        90.90        95.74        43.43       103.10        65.49 
TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF 
       23.77       115.53       168.00        69.90        11.87        48.76 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO 
      113.52        42.08        12.10       171.58        56.19        66.08 
TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB 
       45.11       130.72        58.06        46.98        46.32       166.52 
TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR 
       86.93        60.23        24.53        13.87         9.34       103.59 
TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K 
       39.75       161.85        43.69        40.14       131.90        18.38 
TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR 
       10.03        51.68        15.06       135.75       137.92       166.19 
TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX 
        7.43       125.19       151.53        54.67         3.65         6.41 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1HV 
       11.34         3.25         9.90        25.18        66.25        48.89 
TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 
       36.03       117.21        20.38       194.83       176.55        35.93 
TCGA-DA-A1I5 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
      107.34        53.92        65.92        23.44        68.09        28.60 
TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SH 
       10.49       215.44        15.68        13.87        10.16        35.01 
TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 
        3.55        52.01        29.82        27.22         8.65        94.98 
TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B 
       33.73        14.70        26.89        68.15         4.96       109.64 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29B TCGA-EE-A29C 
      151.27        78.87       168.26        13.55        80.61        47.84 
TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N 
       13.97        39.62        32.19         2.60        44.35        18.61 
TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X 
       56.42        37.35        14.47        25.87       171.55        17.92 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB 
       46.82       102.90        24.43        39.29        58.75        47.54 
TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ 
       67.43       314.56       135.95       208.04        48.72        89.33 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP 
       54.74        79.66        75.48        90.97       101.95        13.91 
TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 
       14.30        55.59        44.88        94.82        21.67       129.27 
TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG 
       28.83        19.76        61.51        47.28       103.27       103.20 
TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM 
       16.96       204.66        96.23       144.76       203.05       167.90 
TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU 
       47.54       248.65        43.23       136.47        41.59        53.26 
TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF 
      124.31       122.73        25.84         3.68        54.51        13.81 
TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J8 
       23.47       138.81       172.18       127.20        36.95        34.32 
TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 
       53.19        27.35        33.40       101.79       148.08        31.40 
TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19B TCGA-ER-A19C 
       35.44        13.94        50.76         9.17        98.40        48.89 
TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J 
       12.59        13.02        26.37       268.93       152.35         6.44 
TCGA-ER-A19L TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W 
      131.51        44.05       162.08        50.89        37.25       148.18 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG 
       79.99        43.82        23.34        20.15        16.37        31.27 
TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN 
       32.05       247.04        80.32        46.98        33.21        92.98 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 
      174.21         4.90       216.92        48.59       228.59       202.65 
TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC 
       20.91        28.08         7.79        27.72        48.85       357.37 
TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ 
       53.52        40.27        15.45         9.70        32.75        47.38 
TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS 
       23.93       101.26        74.73       133.55        11.41       148.80 
TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 
       53.16        26.56        49.48        27.09        27.02        77.82 
TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC 
       66.67        28.73       174.84        12.43        26.73        49.45 
TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY 
       77.88         0.20        22.92        47.54         0.16         2.40 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 
        7.23        14.04       120.46       117.93        84.72        10.13 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS 
       64.44        62.79        32.48        39.58         6.67 

  DMC1 MUTATED DMC1 WILD-TYPE 
          9.90           0.16 
  DMC1 MUTATED DMC1 WILD-TYPE 
        103.56         357.37 
  DMC1 MUTATED DMC1 WILD-TYPE 
        61.115         47.540 
[1] "9.9 - 103.6 (61.1)" "0.2 - 357.4 (47.5)"
[1] "hr=" "1.3"
D24V3, continuous
                vv
clus             DISTANT METASTASIS PRIMARY TUMOR
  DMC1 MUTATED                    1             0
  DMC1 WILD-TYPE                 34             4
                vv
clus             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  DMC1 MUTATED                                           5                   6
  DMC1 WILD-TYPE                                        53                 164
D24V4, multiclass
                                           clus
vv                                          DMC1 MUTATED DMC1 WILD-TYPE
  DISTANT METASTASIS                                   1             34
  PRIMARY TUMOR                                        0              4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE            5             53
  REGIONAL LYMPH NODE                                  6            164
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  DMC1 MUTATED             0       0       2        0        1        0
  DMC1 WILD-TYPE          10       6      20       10       23       17
                vv
clus             STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DMC1 MUTATED           1         0         1         0          2          2
  DMC1 WILD-TYPE         9        14         8        31         11         20
                vv
clus             STAGE IIIC STAGE IV
  DMC1 MUTATED            1        1
  DMC1 WILD-TYPE         43       11
D24V5, multiclass
             clus
vv            DMC1 MUTATED DMC1 WILD-TYPE
  I OR II NOS            0             10
  STAGE 0                0              6
  STAGE I                2             20
  STAGE IA               0             10
  STAGE IB               1             23
  STAGE II               0             17
  STAGE IIA              1              9
  STAGE IIB              0             14
  STAGE IIC              1              8
  STAGE III              0             31
  STAGE IIIA             2             11
  STAGE IIIB             2             20
  STAGE IIIC             1             43
  STAGE IV               1             11
[1] 14  2
[1] 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
  DMC1 MUTATED       1  4  3  2
  DMC1 WILD-TYPE    50 54 50 53
D24V6, multiclass
       clus
vv      DMC1 MUTATED DMC1 WILD-TYPE
  T0+T1            1             50
  T2               4             54
  T3               3             50
  T4               2             53
[1] 4 2
[1] TRUE
[1] "dimension 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
  DMC1 MUTATED     6   1   3   1
  DMC1 WILD-TYPE 132  47  29  32
D24V7, multiclass
    clus
vv   DMC1 MUTATED DMC1 WILD-TYPE
  N0            6            132
  N1            1             47
  N2            3             29
  N3            1             32
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              M0  M1 M1A M1B M1C
  DMC1 MUTATED    10   1   0   0   0
  DMC1 WILD-TYPE 230   3   2   2   5
D24V8, multiclass
     clus
vv    DMC1 MUTATED DMC1 WILD-TYPE
  M0            10            230
  M1             1              3
  M1A            0              2
  M1B            0              2
  M1C            0              5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V9, binary
                cls
clus              0  1
  DMC1 MUTATED    6  3
  DMC1 WILD-TYPE 96 64
[1] "tbl2"
                cls
clus             [,1] [,2]
  DMC1 MUTATED      6    3
  DMC1 WILD-TYPE   96   64
     clus
vv    DMC1 MUTATED DMC1 WILD-TYPE
  NO             6             96
  YES            3             64
[1] 2 2
[1] FALSE
D24V10, binary
                cls
clus               0   1
  DMC1 MUTATED     2  10
  DMC1 WILD-TYPE  31 225
[1] "tbl2"
                cls
clus             [,1] [,2]
  DMC1 MUTATED      2   10
  DMC1 WILD-TYPE   31  225
     clus
vv    DMC1 MUTATED DMC1 WILD-TYPE
  NO             2             31
  YES           10            225
[1] 2 2
[1] FALSE
D24V11, continuous
D24V12, binary
                cls
clus               0   1
  DMC1 MUTATED     3   9
  DMC1 WILD-TYPE 100 156
[1] "tbl2"
                cls
clus             [,1] [,2]
  DMC1 MUTATED      3    9
  DMC1 WILD-TYPE  100  156
        clus
vv       DMC1 MUTATED DMC1 WILD-TYPE
  FEMALE            3            100
  MALE              9            156
[1] 2 2
[1] FALSE
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DMC1 MUTATED       0                         0    12
  DMC1 WILD-TYPE     3                         1   252
D24V13, multiclass
                           clus
vv                          DMC1 MUTATED DMC1 WILD-TYPE
  ASIAN                                0              3
  BLACK OR AFRICAN AMERICAN            0              1
  WHITE                               12            252
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V14, binary
                cls
clus               0   1
  DMC1 MUTATED     0  11
  DMC1 WILD-TYPE   3 250
[1] "tbl2"
                cls
clus             [,1] [,2]
  DMC1 MUTATED      0   11
  DMC1 WILD-TYPE    3  250
                        clus
vv                       DMC1 MUTATED DMC1 WILD-TYPE
  HISPANIC OR LATINO                0              3
  NOT HISPANIC OR LATINO           11            250
[1] 2 2
[1] FALSE

Clustering(25) Variable = NRK MUTATION ANALYSIS
D25V1, survival
               sevent
clus2             0   1
  NRK MUTATED    23  16
  NRK WILD-TYPE 105 114
  NRK MUTATED NRK WILD-TYPE 
           39           219 
  NRK MUTATED NRK WILD-TYPE 
           16           114 
$`NRK MUTATED`
TCGA-D3-A2J8 TCGA-D3-A2JF TCGA-D3-A2JO TCGA-D3-A3C7 TCGA-D3-A3MR TCGA-D3-A3MU 
        8.38        30.87        64.44        46.98       103.59        26.37 
TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D9-A6EC TCGA-DA-A1I7 TCGA-DA-A1IC 
       52.01        47.87         1.55        13.22        36.69         6.64 
TCGA-EB-A5UN TCGA-EE-A17Z TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20F TCGA-EE-A29Q 
       13.22         6.31        12.20         4.31         5.13         8.09 
TCGA-EE-A2A1 TCGA-EE-A2A5 TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2MD TCGA-EE-A2MQ 
       49.22         9.67         1.15        13.02         9.53        21.60 
TCGA-EE-A3AF TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3JD TCGA-ER-A19S TCGA-ER-A1A1 
       13.81        22.92        21.60        27.35        36.07        78.44 
TCGA-FS-A1YY TCGA-FS-A1ZC TCGA-FS-A1ZK TCGA-FS-A4F0 TCGA-FS-A4FC TCGA-FW-A3R5 
       11.01        20.38        12.89        53.85         6.41         0.99 
TCGA-FW-A3TU TCGA-FW-A5DY TCGA-GF-A3OT 
        0.13         0.43         9.90 

$`NRK WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.47         8.52       111.09        32.42        70.16       110.79 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       28.08        22.55        45.83        81.24        10.29        85.32 
TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JG 
       21.14        88.50        68.22        69.90        11.41         7.50 
TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3BZ 
       36.16         6.31        92.42        56.19        45.11       114.67 
TCGA-D3-A3C6 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF 
       15.25        46.32        82.29        61.38        13.32        24.00 
TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H 
        6.31         9.34         5.39        80.22        42.71        15.09 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GS 
       41.10        17.72         8.84        20.48        13.94         6.97 
TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-DA-A1HV 
       23.11         4.01         2.89         9.90        11.31        48.79 
TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 
       35.80        51.12        10.03        39.19        13.68         9.99 
TCGA-DA-A1I5 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A3F2 TCGA-DA-A3F3 
       44.52        25.15         4.93        22.36        19.36         7.00 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH 
       17.56        14.83        13.15         0.20         0.00         0.00 
TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A184 
       11.57        10.55         8.12         1.12         1.35         5.13 
TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B 
       36.07         4.34         9.21         1.18         7.99         9.90 
TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L 
       37.97        11.15        38.63         8.55         4.41         1.08 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V 
       27.12         9.50        12.03         8.84         9.99         2.43 
TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB 
        8.68         8.09        11.31        23.90         8.94        39.39 
TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ 
       34.29        17.98        34.92        47.21        30.08        19.43 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP 
       16.01        35.54        28.31        33.83        30.84         5.42 
TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 
       34.98        36.33         8.84        98.27         2.70         6.18 
TCGA-EE-A2MC TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ 
       47.51        29.46        44.25         7.96        14.56        63.42 
TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MR 
      111.78       111.91        56.02        25.08        26.99        29.65 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC 
       27.16        23.05         5.56       124.31       122.73        25.84 
TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J7 
        3.68        30.15        15.95        12.72         3.22        21.60 
TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 
       16.14        22.22         0.46        13.94        33.60        31.40 
TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B 
       18.61        12.95        38.40         5.72        76.41        25.18 
TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H 
        3.78         3.52        11.90        11.11       114.15        34.88 
TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q 
        4.21        13.45        28.60        42.84        34.68         9.57 
TCGA-ER-A19W TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG 
       17.72        11.80         1.87         1.51        13.08        12.62 
TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN 
       11.74         9.04         6.58        22.49         1.71        18.41 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1Z0 TCGA-FS-A1Z3 
       85.74         4.90        64.47         3.45        23.80        14.24 
TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZD TCGA-FS-A1ZE 
       15.52         7.33         7.30         3.39         8.22        19.53 
TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZP 
       11.08         7.17        30.87        12.92        47.38        52.08 
TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW 
        8.65         8.81        49.15        40.64         8.68        27.39 
TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 
        0.82         5.23         7.36        28.73        14.20        10.78 
TCGA-FS-A4FB TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TV TCGA-GF-A4EO TCGA-GF-A6C8 
        5.98         2.27         0.20         0.16         7.23        12.85 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 
       24.85        31.33        84.72        10.13        16.24        15.42 
TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS 
       12.16        14.70         5.79 

  NRK MUTATED NRK WILD-TYPE 
         0.13          0.00 
  NRK MUTATED NRK WILD-TYPE 
       103.59        124.31 
  NRK MUTATED NRK WILD-TYPE 
        13.22         15.25 
[1] "0.1 - 103.6 (13.2)" "0.0 - 124.3 (15.2)"
[1] "hr=" "1.2"
D25V2, survival
               sevent
clus2             0   1
  NRK MUTATED    24  16
  NRK WILD-TYPE 108 115
  NRK MUTATED NRK WILD-TYPE 
           40           223 
  NRK MUTATED NRK WILD-TYPE 
           16           115 
$`NRK MUTATED`
TCGA-D3-A2J8 TCGA-D3-A2JF TCGA-D3-A2JO TCGA-D3-A3C7 TCGA-D3-A3MR TCGA-D3-A3MU 
       65.49        48.76        66.08        46.98       103.59        39.75 
TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D9-A6EC TCGA-DA-A1I7 TCGA-DA-A1IC 
      135.75       137.92       166.19        66.25        61.18        68.09 
TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17Z TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20F 
        3.55        52.01         8.65        26.89         4.96        78.87 
TCGA-EE-A29Q TCGA-EE-A2A1 TCGA-EE-A2A5 TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2MD 
       37.35       102.90        39.29        14.30        55.59        47.28 
TCGA-EE-A2MQ TCGA-EE-A3AF TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3JD TCGA-ER-A19S 
       43.23        13.81       127.20        36.95        27.35        37.25 
TCGA-ER-A1A1 TCGA-FS-A1YY TCGA-FS-A1ZC TCGA-FS-A1ZK TCGA-FS-A4F0 TCGA-FS-A4FC 
       79.99       228.59       357.37        23.93        77.82        49.45 
TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A5DY TCGA-GF-A3OT 
       22.92        47.54         2.40         9.90 

$`NRK WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.57        16.67       112.04       112.57        71.80       133.25 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       28.08        31.59        90.90        95.74        43.43       103.10 
TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JG 
       23.77       115.53       168.00        69.90        11.87       113.52 
TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3BZ 
       42.08        12.10       171.58        56.19        45.11       130.72 
TCGA-D3-A3C6 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF 
       58.06        46.32       166.52        86.93        60.23        24.53 
TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H 
       13.87         9.34        21.47       161.85        43.69        40.14 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GS 
      131.90        18.38        10.03        51.68        15.06         7.43 
TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 
      125.19       151.53        54.67         3.65         6.41        11.34 
TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY 
        3.25         9.90        25.18        48.89        36.03       117.21 
TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I8 
       20.38       194.83       176.55        35.93       107.34        53.92 
TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 
       65.92        23.44        28.60        10.49       215.44        15.68 
TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EE-A17X TCGA-EE-A17Y 
       13.87        10.16        45.11        35.01        29.82        27.22 
TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A184 TCGA-EE-A20B TCGA-EE-A20C 
       94.98        33.73        14.70        68.15       109.64       151.27 
TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D 
      168.26        13.55        63.35        80.61        47.84        13.97 
TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N 
       39.62        72.07        32.19         2.60        44.35        18.61 
TCGA-EE-A29P TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X 
       56.42        14.47        55.92        25.87       171.55        17.92 
TCGA-EE-A2A0 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD 
       46.82        24.43        58.75        47.54        67.43       314.56 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
      135.95       208.04        48.72        89.33        54.74        79.66 
TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GT TCGA-EE-A2GU 
       75.48        90.97       101.95        13.91        44.88        94.82 
TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2ME 
       21.67       129.27        28.83        19.76        61.51       103.27 
TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML 
      103.20        16.96       204.66        96.23       144.76       203.05 
TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT 
      167.90        47.54       248.65       103.56       136.47        41.59 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE 
       53.26       124.31       122.73        25.84         3.68        54.51 
TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA 
       23.47       138.81       172.18        64.08        34.32        53.19 
TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 
       33.40       101.79       148.08        31.40        35.44        13.94 
TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D 
       50.76         9.17        77.75        98.40        48.89        12.59 
TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L 
       13.02        26.37       268.93       152.35         6.44       131.51 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19W TCGA-ER-A2NC 
       61.05        44.05       162.08        50.89       148.18        43.82 
TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES 
       23.34        20.15        16.37        31.27        32.05       247.04 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
       80.32        46.98        33.21        92.98       174.21         4.90 
TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 
      216.92        48.59       202.65        20.91        28.08         7.79 
TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG 
       27.72        48.85        53.52        40.27        15.45         9.70 
TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR 
       32.75        47.38       101.26        74.73       133.55        11.41 
TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ 
      148.80        53.16        26.56        49.48        27.09        27.02 
TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FD 
       66.67        28.73       174.84        12.43        26.73        77.88 
TCGA-FW-A3I3 TCGA-FW-A3TV TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 
        0.20         0.16         7.23        14.04       120.46       117.93 
TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D 
       84.72        10.13        64.44        62.79        32.48        39.58 
TCGA-QB-A6FS 
        6.67 

  NRK MUTATED NRK WILD-TYPE 
         2.40          0.16 
  NRK MUTATED NRK WILD-TYPE 
       357.37        314.56 
  NRK MUTATED NRK WILD-TYPE 
        48.15         48.59 
[1] "2.4 - 357.4 (48.1)" "0.2 - 314.6 (48.6)"
[1] "hr=" "1.4"
D25V3, continuous
               vv
clus            DISTANT METASTASIS PRIMARY TUMOR
  NRK MUTATED                    8             1
  NRK WILD-TYPE                 27             3
               vv
clus            REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  NRK MUTATED                                          11                  21
  NRK WILD-TYPE                                        47                 149
D25V4, multiclass
                                           clus
vv                                          NRK MUTATED NRK WILD-TYPE
  DISTANT METASTASIS                                  8            27
  PRIMARY TUMOR                                       1             3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE          11            47
  REGIONAL LYMPH NODE                                21           149
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  NRK MUTATED             2       1       2        1        4        5
  NRK WILD-TYPE           8       5      20        9       20       12
               vv
clus            STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  NRK MUTATED           2         3         1         8          3          2
  NRK WILD-TYPE         8        11         8        23         10         20
               vv
clus            STAGE IIIC STAGE IV
  NRK MUTATED            5        0
  NRK WILD-TYPE         39       12
D25V5, multiclass
             clus
vv            NRK MUTATED NRK WILD-TYPE
  I OR II NOS           2             8
  STAGE 0               1             5
  STAGE I               2            20
  STAGE IA              1             9
  STAGE IB              4            20
  STAGE II              5            12
  STAGE IIA             2             8
  STAGE IIB             3            11
  STAGE IIC             1             8
  STAGE III             8            23
  STAGE IIIA            3            10
  STAGE IIIB            2            20
  STAGE IIIC            5            39
  STAGE IV              0            12
[1] 14  2
[1] 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
  NRK MUTATED       8  5 11  8
  NRK WILD-TYPE    43 53 42 47
D25V6, multiclass
       clus
vv      NRK MUTATED NRK WILD-TYPE
  T0+T1           8            43
  T2              5            53
  T3             11            42
  T4              8            47
[1] 4 2
[1] TRUE
[1] "dimension 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
  NRK MUTATED    20   7   6   5
  NRK WILD-TYPE 118  41  26  28
D25V7, multiclass
    clus
vv   NRK MUTATED NRK WILD-TYPE
  N0          20           118
  N1           7            41
  N2           6            26
  N3           5            28
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             M0  M1 M1A M1B M1C
  NRK MUTATED    38   0   0   0   0
  NRK WILD-TYPE 202   4   2   2   5
D25V8, multiclass
     clus
vv    NRK MUTATED NRK WILD-TYPE
  M0           38           202
  M1            0             4
  M1A           0             2
  M1B           0             2
  M1C           0             5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V9, binary
               cls
clus             0  1
  NRK MUTATED   14  6
  NRK WILD-TYPE 88 61
[1] "tbl2"
               cls
clus            [,1] [,2]
  NRK MUTATED     14    6
  NRK WILD-TYPE   88   61
     clus
vv    NRK MUTATED NRK WILD-TYPE
  NO           14            88
  YES           6            61
[1] 2 2
[1] FALSE
D25V10, binary
               cls
clus              0   1
  NRK MUTATED     7  34
  NRK WILD-TYPE  26 201
[1] "tbl2"
               cls
clus            [,1] [,2]
  NRK MUTATED      7   34
  NRK WILD-TYPE   26  201
     clus
vv    NRK MUTATED NRK WILD-TYPE
  NO            7            26
  YES          34           201
[1] 2 2
[1] FALSE
D25V11, continuous
D25V12, binary
               cls
clus              0   1
  NRK MUTATED    18  23
  NRK WILD-TYPE  85 142
[1] "tbl2"
               cls
clus            [,1] [,2]
  NRK MUTATED     18   23
  NRK WILD-TYPE   85  142
        clus
vv       NRK MUTATED NRK WILD-TYPE
  FEMALE          18            85
  MALE            23           142
[1] 2 2
[1] FALSE
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  NRK MUTATED       0                         0    41
  NRK WILD-TYPE     3                         1   223
D25V13, multiclass
                           clus
vv                          NRK MUTATED NRK WILD-TYPE
  ASIAN                               0             3
  BLACK OR AFRICAN AMERICAN           0             1
  WHITE                              41           223
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V14, binary
               cls
clus              0   1
  NRK MUTATED     0  41
  NRK WILD-TYPE   3 220
[1] "tbl2"
               cls
clus            [,1] [,2]
  NRK MUTATED      0   41
  NRK WILD-TYPE    3  220
                        clus
vv                       NRK MUTATED NRK WILD-TYPE
  HISPANIC OR LATINO               0             3
  NOT HISPANIC OR LATINO          41           220
[1] 2 2
[1] FALSE

Clustering(26) Variable = TAF1A MUTATION ANALYSIS
D26V1, survival
                 sevent
clus2               0   1
  TAF1A MUTATED     4   9
  TAF1A WILD-TYPE 124 121
  TAF1A MUTATED TAF1A WILD-TYPE 
             13             245 
  TAF1A MUTATED TAF1A WILD-TYPE 
              9             121 
$`TAF1A MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1QA TCGA-D3-A2JK TCGA-D3-A2JO TCGA-D3-A3C6 
       16.47         8.52        45.83         6.31        64.44        15.25 
TCGA-D3-A3CE TCGA-EE-A181 TCGA-EE-A2MT TCGA-EE-A3AA TCGA-ER-A19Q TCGA-FS-A1ZJ 
       13.32         1.12        23.05       124.31         9.57        12.92 
TCGA-GN-A26A 
       12.16 

$`TAF1A WILD-TYPE`
TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 
      111.09        32.42        70.16       110.79        28.08        22.55 
TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA 
       81.24        10.29        85.32         8.38        21.14        88.50 
TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH 
       68.22        69.90        11.41        30.87         7.50        36.16 
TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C7 TCGA-D3-A3C8 
       92.42        56.19        45.11       114.67        46.98        46.32 
TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR 
       82.29        61.38        24.00         6.31         9.34       103.59 
TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J 
       26.37         5.39        80.22        42.71        15.09        41.10 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO 
       17.72         8.84        20.48        13.94        52.01        47.87 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 
        1.55         6.97        23.11         4.01         2.89         9.90 
TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 
       11.31        13.22        48.79        35.80        51.12        10.03 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 
       39.19        13.68         9.99        44.52        36.69        25.15 
TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 
        4.93        22.36         6.64        19.36         7.00        17.56 
TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN 
       14.83        13.15         0.20         0.00         0.00        13.22 
TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A182 TCGA-EE-A183 
       11.57        10.55         6.31         8.12         1.35        12.20 
TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H 
        5.13         4.31        36.07         4.34         5.13         9.21 
TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E 
        1.18         7.99         9.90        37.97        11.15        38.63 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P 
        8.55         4.41         1.08        27.12         9.50        12.03 
TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X 
        8.09         8.84         9.99         2.43         8.68         8.09 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB 
       11.31        49.22        23.90         9.67         8.94        39.39 
TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ 
       34.29        17.98        34.92        47.21        30.08        19.43 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP 
       16.01        35.54        28.31        33.83        30.84         5.42 
TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 
        1.15        13.02        34.98        36.33         8.84        98.27 
TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG 
        2.70         6.18        47.51         9.53        29.46        44.25 
TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM 
        7.96        14.56        63.42       111.78       111.91        56.02 
TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MU 
       25.08        26.99        21.60        29.65        27.16         5.56 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG 
      122.73        25.84         3.68        30.15        13.81        15.95 
TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 
       12.72         3.22        22.92        21.60        21.60        16.14 
TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 
       22.22        27.35         0.46        13.94        33.60        31.40 
TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B 
       18.61        12.95        38.40         5.72        76.41        25.18 
TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H 
        3.78         3.52        11.90        11.11       114.15        34.88 
TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19S 
        4.21        13.45        28.60        42.84        34.68        36.07 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF 
       17.72        78.44        11.80         1.87         1.51        13.08 
TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL 
       12.62        11.74         9.04         6.58        22.49         1.71 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY 
       18.41        85.74         4.90        64.47         3.45        11.01 
TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB 
       23.80        14.24        15.52         7.33         7.30         3.39 
TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH 
       20.38         8.22        19.53        11.08         7.17        30.87 
TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS 
       12.89        47.38        52.08         8.65         8.81        49.15 
TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 
       40.64         8.68        27.39         0.82         5.23        53.85 
TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC 
        7.36        28.73        14.20        10.78         5.98         6.41 
TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY 
        2.27         0.20         0.99         0.13         0.16         0.43 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        9.90         7.23        12.85        24.85        31.33        84.72 
TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26D TCGA-QB-A6FS 
       10.13        16.24        15.42        14.70         5.79 

  TAF1A MUTATED TAF1A WILD-TYPE 
           1.12            0.00 
  TAF1A MUTATED TAF1A WILD-TYPE 
         124.31          122.73 
  TAF1A MUTATED TAF1A WILD-TYPE 
          13.32           14.83 
[1] "1.1 - 124.3 (13.3)" "0.0 - 122.7 (14.8)"
[1] "hr=" "1.4"
D26V2, survival
                 sevent
clus2               0   1
  TAF1A MUTATED     4   9
  TAF1A WILD-TYPE 128 122
  TAF1A MUTATED TAF1A WILD-TYPE 
             13             250 
  TAF1A MUTATED TAF1A WILD-TYPE 
              9             122 
$`TAF1A MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1QA TCGA-D3-A2JK TCGA-D3-A2JO TCGA-D3-A3C6 
       16.57        16.67        90.90        12.10        66.08        58.06 
TCGA-D3-A3CE TCGA-EE-A181 TCGA-EE-A2MT TCGA-EE-A3AA TCGA-ER-A19Q TCGA-FS-A1ZJ 
       60.23        33.73        41.59       124.31        50.89        47.38 
TCGA-GN-A26A 
       32.48 

$`TAF1A WILD-TYPE`
TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 
      112.04       112.57        71.80       133.25        28.08        31.59 
TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA 
       95.74        43.43       103.10        65.49        23.77       115.53 
TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH 
      168.00        69.90        11.87        48.76       113.52        42.08 
TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C7 TCGA-D3-A3C8 
      171.58        56.19        45.11       130.72        46.98        46.32 
TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR 
      166.52        86.93        24.53        13.87         9.34       103.59 
TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J 
       39.75        21.47       161.85        43.69        40.14       131.90 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO 
       18.38        10.03        51.68        15.06       135.75       137.92 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW 
      166.19         7.43       125.19       151.53        54.67         3.65 
TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC 
        6.41        11.34         3.25         9.90        25.18        66.25 
TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 
       48.89        36.03       117.21        20.38       194.83       176.55 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB 
       35.93       107.34        61.18        53.92        65.92        23.44 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q 
       68.09        28.60        10.49       215.44        15.68        13.87 
TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X 
       10.16        45.11        35.01         3.55        52.01        29.82 
TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 
       27.22         8.65        94.98        14.70        26.89        68.15 
TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I 
        4.96       109.64       151.27        78.87       168.26        13.55 
TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G 
       63.35        80.61        47.84        13.97        39.62        72.07 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
       32.19         2.60        44.35        18.61        56.42        37.35 
TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 
       14.47        55.92        25.87       171.55        17.92        46.82 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC 
      102.90        24.43        39.29        58.75        47.54        67.43 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK 
      314.56       135.95       208.04        48.72        89.33        54.74 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR 
       79.66        75.48        90.97       101.95        13.91        14.30 
TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 
       55.59        44.88        94.82        21.67       129.27        28.83 
TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH 
       19.76        61.51        47.28       103.27       103.20        16.96 
TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN 
      204.66        96.23       144.76       203.05       167.90        47.54 
TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3AB 
      248.65        43.23       103.56       136.47        53.26       122.73 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH 
       25.84         3.68        54.51        13.81        23.47       138.81 
TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA 
      172.18       127.20        36.95        64.08        34.32        53.19 
TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 
       27.35        33.40       101.79       148.08        31.40        35.44 
TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C 
       13.94        50.76         9.17        77.75        98.40        48.89 
TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J 
       12.59        13.02        26.37       268.93       152.35         6.44 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19S TCGA-ER-A19W 
      131.51        61.05        44.05       162.08        37.25       148.18 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG 
       79.99        43.82        23.34        20.15        16.37        31.27 
TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN 
       32.05       247.04        80.32        46.98        33.21        92.98 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 
      174.21         4.90       216.92        48.59       228.59       202.65 
TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC 
       20.91        28.08         7.79        27.72        48.85       357.37 
TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZK 
       53.52        40.27        15.45         9.70        32.75        23.93 
TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT 
      101.26        74.73       133.55        11.41       148.80        53.16 
TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 
       26.56        49.48        27.09        27.02        77.82        66.67 
TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD 
       28.73       174.84        12.43        26.73        49.45        77.88 
TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
        0.20        22.92        47.54         0.16         2.40         9.90 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 
        7.23        14.04       120.46       117.93        84.72        10.13 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26D TCGA-QB-A6FS 
       64.44        62.79        39.58         6.67 

  TAF1A MUTATED TAF1A WILD-TYPE 
          12.10            0.16 
  TAF1A MUTATED TAF1A WILD-TYPE 
         124.31          357.37 
  TAF1A MUTATED TAF1A WILD-TYPE 
         47.380          48.655 
[1] "12.1 - 124.3 (47.4)" "0.2 - 357.4 (48.7)" 
[1] "hr=" "1.9"
D26V3, continuous
                 vv
clus              DISTANT METASTASIS PRIMARY TUMOR
  TAF1A MUTATED                    0             0
  TAF1A WILD-TYPE                 35             4
                 vv
clus              REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  TAF1A MUTATED                                           2                  11
  TAF1A WILD-TYPE                                        56                 159
D26V4, multiclass
                                           clus
vv                                          TAF1A MUTATED TAF1A WILD-TYPE
  DISTANT METASTASIS                                    0              35
  PRIMARY TUMOR                                         0               4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE             2              56
  REGIONAL LYMPH NODE                                  11             159
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  TAF1A MUTATED             0       0       1        0        3        1
  TAF1A WILD-TYPE          10       6      21       10       21       16
                 vv
clus              STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  TAF1A MUTATED           0         0         1         2          1          0
  TAF1A WILD-TYPE        10        14         8        29         12         22
                 vv
clus              STAGE IIIC STAGE IV
  TAF1A MUTATED            3        0
  TAF1A WILD-TYPE         41       12
D26V5, multiclass
             clus
vv            TAF1A MUTATED TAF1A WILD-TYPE
  I OR II NOS             0              10
  STAGE 0                 0               6
  STAGE I                 1              21
  STAGE IA                0              10
  STAGE IB                3              21
  STAGE II                1              16
  STAGE IIA               0              10
  STAGE IIB               0              14
  STAGE IIC               1               8
  STAGE III               2              29
  STAGE IIIA              1              12
  STAGE IIIB              0              22
  STAGE IIIC              3              41
  STAGE IV                0              12
[1] 14  2
[1] 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
  TAF1A MUTATED       3  4  2  2
  TAF1A WILD-TYPE    48 54 51 53
D26V6, multiclass
       clus
vv      TAF1A MUTATED TAF1A WILD-TYPE
  T0+T1             3              48
  T2                4              54
  T3                2              51
  T4                2              53
[1] 4 2
[1] TRUE
[1] "dimension 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
  TAF1A MUTATED     7   3   1   2
  TAF1A WILD-TYPE 131  45  31  31
D26V7, multiclass
    clus
vv   TAF1A MUTATED TAF1A WILD-TYPE
  N0             7             131
  N1             3              45
  N2             1              31
  N3             2              31
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               M0  M1 M1A M1B M1C
  TAF1A MUTATED    13   0   0   0   0
  TAF1A WILD-TYPE 227   4   2   2   5
D26V8, multiclass
     clus
vv    TAF1A MUTATED TAF1A WILD-TYPE
  M0             13             227
  M1              0               4
  M1A             0               2
  M1B             0               2
  M1C             0               5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V9, binary
                 cls
clus               0  1
  TAF1A MUTATED    7  3
  TAF1A WILD-TYPE 95 64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TAF1A MUTATED      7    3
  TAF1A WILD-TYPE   95   64
     clus
vv    TAF1A MUTATED TAF1A WILD-TYPE
  NO              7              95
  YES             3              64
[1] 2 2
[1] FALSE
D26V10, binary
                 cls
clus                0   1
  TAF1A MUTATED     2  11
  TAF1A WILD-TYPE  31 224
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TAF1A MUTATED      2   11
  TAF1A WILD-TYPE   31  224
     clus
vv    TAF1A MUTATED TAF1A WILD-TYPE
  NO              2              31
  YES            11             224
[1] 2 2
[1] FALSE
D26V11, continuous
D26V12, binary
                 cls
clus                0   1
  TAF1A MUTATED     8   5
  TAF1A WILD-TYPE  95 160
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TAF1A MUTATED      8    5
  TAF1A WILD-TYPE   95  160
        clus
vv       TAF1A MUTATED TAF1A WILD-TYPE
  FEMALE             8              95
  MALE               5             160
[1] 2 2
[1] FALSE
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TAF1A MUTATED       0                         0    13
  TAF1A WILD-TYPE     3                         1   251
D26V13, multiclass
                           clus
vv                          TAF1A MUTATED TAF1A WILD-TYPE
  ASIAN                                 0               3
  BLACK OR AFRICAN AMERICAN             0               1
  WHITE                                13             251
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V14, binary
                 cls
clus                0   1
  TAF1A MUTATED     0  13
  TAF1A WILD-TYPE   3 248
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TAF1A MUTATED      0   13
  TAF1A WILD-TYPE    3  248
                        clus
vv                       TAF1A MUTATED TAF1A WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO            13             248
[1] 2 2
[1] FALSE

Clustering(27) Variable = OXA1L MUTATION ANALYSIS
D27V1, survival
                 sevent
clus2               0   1
  OXA1L MUTATED     4   4
  OXA1L WILD-TYPE 124 126
  OXA1L MUTATED OXA1L WILD-TYPE 
              8             250 
  OXA1L MUTATED OXA1L WILD-TYPE 
              4             126 
$`OXA1L MUTATED`
TCGA-D3-A51T TCGA-DA-A1IA TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A2GB TCGA-EE-A2MS 
       13.94         4.93         8.12         1.12        39.39        27.16 
TCGA-EE-A3JD TCGA-FW-A3R5 
       27.35         0.99 

$`OXA1L WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.47         8.52       111.09        32.42        70.16       110.79 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       28.08        22.55        45.83        81.24        10.29        85.32 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
        8.38        21.14        88.50        68.22        69.90        11.41 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       30.87         7.50        36.16         6.31        92.42        56.19 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 
       64.44        45.11       114.67        15.25        46.98        46.32 
TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO 
       82.29        61.38        13.32        24.00         6.31         9.34 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H 
      103.59        26.37         5.39        80.22        42.71        15.09 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A5GN TCGA-D3-A5GO 
       41.10        17.72         8.84        20.48        52.01        47.87 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 
        1.55         6.97        23.11         4.01         2.89         9.90 
TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 
       11.31        13.22        48.79        35.80        51.12        10.03 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 
       39.19        13.68         9.99        44.52        36.69        25.15 
TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 
       22.36         6.64        19.36         7.00        17.56        14.83 
TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EE-A17X 
       13.15         0.20         0.00         0.00        13.22        11.57 
TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 
       10.55         6.31         1.35        12.20         5.13         4.31 
TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A 
       36.07         4.34         5.13         9.21         1.18         7.99 
TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H 
        9.90        37.97        11.15        38.63         8.55         4.41 
TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R 
        1.08        27.12         9.50        12.03         8.09         8.84 
TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 
        9.99         2.43         8.68         8.09        11.31        49.22 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE 
       23.90         9.67         8.94        34.29        17.98        34.92 
TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM 
       47.21        30.08        19.43        16.01        35.54        28.31 
TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT 
       33.83        30.84         5.42         1.15        13.02        34.98 
TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC 
       36.33         8.84        98.27         2.70         6.18        47.51 
TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ 
        9.53        29.46        44.25         7.96        14.56        63.42 
TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ 
      111.78       111.91        56.02        25.08        26.99        21.60 
TCGA-EE-A2MR TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC 
       29.65        23.05         5.56       124.31       122.73        25.84 
TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 
        3.68        30.15        13.81        15.95        12.72         3.22 
TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JE 
       22.92        21.60        21.60        16.14        22.22         0.46 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 
       13.94        33.60        31.40        18.61        12.95        38.40 
TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E 
        5.72        76.41        25.18         3.78         3.52        11.90 
TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M 
       11.11       114.15        34.88         4.21        13.45        28.60 
TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 
       42.84        34.68         9.57        36.07        17.72        78.44 
TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH 
       11.80         1.87         1.51        13.08        12.62        11.74 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A 
        9.04         6.58        22.49         1.71        18.41        85.74 
TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
        4.90        64.47         3.45        11.01        23.80        14.24 
TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD 
       15.52         7.33         7.30         3.39        20.38         8.22 
TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK 
       19.53        11.08         7.17        30.87        12.92        12.89 
TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT 
       47.38        52.08         8.65         8.81        49.15        40.64 
TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 
        8.68        27.39         0.82         5.23        53.85         7.36 
TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD 
       28.73        14.20        10.78         5.98         6.41         2.27 
TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
        0.20         0.13         0.16         0.43         9.90         7.23 
TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 
       12.85        24.85        31.33        84.72        10.13        16.24 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS 
       15.42        12.16        14.70         5.79 

  OXA1L MUTATED OXA1L WILD-TYPE 
           0.99            0.00 
  OXA1L MUTATED OXA1L WILD-TYPE 
          39.39          124.31 
  OXA1L MUTATED OXA1L WILD-TYPE 
          11.03           14.96 
[1] "1.0 - 39.4 (11.0)"  "0.0 - 124.3 (15.0)"
[1] "hr=" "1.4"
D27V2, survival
                 sevent
clus2               0   1
  OXA1L MUTATED     4   4
  OXA1L WILD-TYPE 128 127
  OXA1L MUTATED OXA1L WILD-TYPE 
              8             255 
  OXA1L MUTATED OXA1L WILD-TYPE 
              4             127 
$`OXA1L MUTATED`
TCGA-D3-A51T TCGA-DA-A1IA TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A2GB TCGA-EE-A2MS 
       15.06        65.92        94.98        33.73        47.54       136.47 
TCGA-EE-A3JD TCGA-FW-A3R5 
       27.35        22.92 

$`OXA1L WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.57        16.67       112.04       112.57        71.80       133.25 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       28.08        31.59        90.90        95.74        43.43       103.10 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
       65.49        23.77       115.53       168.00        69.90        11.87 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       48.76       113.52        42.08        12.10       171.58        56.19 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 
       66.08        45.11       130.72        58.06        46.98        46.32 
TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO 
      166.52        86.93        60.23        24.53        13.87         9.34 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H 
      103.59        39.75        21.47       161.85        43.69        40.14 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A5GN TCGA-D3-A5GO 
      131.90        18.38        10.03        51.68       135.75       137.92 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW 
      166.19         7.43       125.19       151.53        54.67         3.65 
TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC 
        6.41        11.34         3.25         9.90        25.18        66.25 
TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 
       48.89        36.03       117.21        20.38       194.83       176.55 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IB TCGA-DA-A1IC 
       35.93       107.34        61.18        53.92        23.44        68.09 
TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R 
       28.60        10.49       215.44        15.68        13.87        10.16 
TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y 
       45.11        35.01         3.55        52.01        29.82        27.22 
TCGA-EE-A17Z TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B 
        8.65        14.70        26.89        68.15         4.96       109.64 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B 
      151.27        78.87       168.26        13.55        63.35        80.61 
TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L 
       47.84        13.97        39.62        72.07        32.19         2.60 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S 
       44.35        18.61        56.42        37.35        14.47        55.92 
TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 
       25.87       171.55        17.92        46.82       102.90        24.43 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH 
       39.29        58.75        67.43       314.56       135.95       208.04 
TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN 
       48.72        89.33        54.74        79.66        75.48        90.97 
TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU 
      101.95        13.91        14.30        55.59        44.88        94.82 
TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD 
       21.67       129.27        28.83        19.76        61.51        47.28 
TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK 
      103.27       103.20        16.96       204.66        96.23       144.76 
TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR 
      203.05       167.90        47.54       248.65        43.23       103.56 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD 
       41.59        53.26       124.31       122.73        25.84         3.68 
TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 
       54.51        13.81        23.47       138.81       172.18       127.20 
TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JE TCGA-EE-A3JH 
       36.95        64.08        34.32        53.19        33.40       101.79 
TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 
      148.08        31.40        35.44        13.94        50.76         9.17 
TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F 
       77.75        98.40        48.89        12.59        13.02        26.37 
TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N 
      268.93       152.35         6.44       131.51        61.05        44.05 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
      162.08        50.89        37.25       148.18        79.99        43.82 
TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES 
       23.34        20.15        16.37        31.27        32.05       247.04 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
       80.32        46.98        33.21        92.98       174.21         4.90 
TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 
      216.92        48.59       228.59       202.65        20.91        28.08 
TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE 
        7.79        27.72        48.85       357.37        53.52        40.27 
TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM 
       15.45         9.70        32.75        47.38        23.93       101.26 
TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU 
       74.73       133.55        11.41       148.80        53.16        26.56 
TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 
       49.48        27.09        27.02        77.82        66.67        28.73 
TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 
      174.84        12.43        26.73        49.45        77.88         0.20 
TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 
       47.54         0.16         2.40         9.90         7.23        14.04 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 
      120.46       117.93        84.72        10.13        64.44        62.79 
TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS 
       32.48        39.58         6.67 

  OXA1L MUTATED OXA1L WILD-TYPE 
          15.06            0.16 
  OXA1L MUTATED OXA1L WILD-TYPE 
         136.47          357.37 
  OXA1L MUTATED OXA1L WILD-TYPE 
         40.635          48.720 
[1] "15.1 - 136.5 (40.6)" "0.2 - 357.4 (48.7)" 
[1] "hr=" "1.2"
D27V3, continuous
                 vv
clus              DISTANT METASTASIS PRIMARY TUMOR
  OXA1L MUTATED                    2             0
  OXA1L WILD-TYPE                 33             4
                 vv
clus              REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  OXA1L MUTATED                                           0                   6
  OXA1L WILD-TYPE                                        58                 164
D27V4, multiclass
                                           clus
vv                                          OXA1L MUTATED OXA1L WILD-TYPE
  DISTANT METASTASIS                                    2              33
  PRIMARY TUMOR                                         0               4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE             0              58
  REGIONAL LYMPH NODE                                   6             164
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  OXA1L MUTATED             0       0       0        0        0        2
  OXA1L WILD-TYPE          10       6      22       10       24       15
                 vv
clus              STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  OXA1L MUTATED           0         0         0         3          0          2
  OXA1L WILD-TYPE        10        14         9        28         13         20
                 vv
clus              STAGE IIIC STAGE IV
  OXA1L MUTATED            1        0
  OXA1L WILD-TYPE         43       12
D27V5, multiclass
             clus
vv            OXA1L MUTATED OXA1L WILD-TYPE
  I OR II NOS             0              10
  STAGE 0                 0               6
  STAGE I                 0              22
  STAGE IA                0              10
  STAGE IB                0              24
  STAGE II                2              15
  STAGE IIA               0              10
  STAGE IIB               0              14
  STAGE IIC               0               9
  STAGE III               3              28
  STAGE IIIA              0              13
  STAGE IIIB              2              20
  STAGE IIIC              1              43
  STAGE IV                0              12
[1] 14  2
[1] 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
  OXA1L MUTATED       0  2  2  2
  OXA1L WILD-TYPE    51 56 51 53
D27V6, multiclass
       clus
vv      OXA1L MUTATED OXA1L WILD-TYPE
  T0+T1             0              51
  T2                2              56
  T3                2              51
  T4                2              53
[1] 4 2
[1] TRUE
[1] "dimension 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
  OXA1L MUTATED     3   3   2   0
  OXA1L WILD-TYPE 135  45  30  33
D27V7, multiclass
    clus
vv   OXA1L MUTATED OXA1L WILD-TYPE
  N0             3             135
  N1             3              45
  N2             2              30
  N3             0              33
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               M0  M1 M1A M1B M1C
  OXA1L MUTATED     8   0   0   0   0
  OXA1L WILD-TYPE 232   4   2   2   5
D27V8, multiclass
     clus
vv    OXA1L MUTATED OXA1L WILD-TYPE
  M0              8             232
  M1              0               4
  M1A             0               2
  M1B             0               2
  M1C             0               5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V9, binary
                 cls
clus               0  1
  OXA1L MUTATED    3  2
  OXA1L WILD-TYPE 99 65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OXA1L MUTATED      3    2
  OXA1L WILD-TYPE   99   65
     clus
vv    OXA1L MUTATED OXA1L WILD-TYPE
  NO              3              99
  YES             2              65
[1] 2 2
[1] FALSE
D27V10, binary
                 cls
clus                0   1
  OXA1L MUTATED     1   7
  OXA1L WILD-TYPE  32 228
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OXA1L MUTATED      1    7
  OXA1L WILD-TYPE   32  228
     clus
vv    OXA1L MUTATED OXA1L WILD-TYPE
  NO              1              32
  YES             7             228
[1] 2 2
[1] FALSE
D27V11, continuous
D27V12, binary
                 cls
clus                0   1
  OXA1L MUTATED     3   5
  OXA1L WILD-TYPE 100 160
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OXA1L MUTATED      3    5
  OXA1L WILD-TYPE  100  160
        clus
vv       OXA1L MUTATED OXA1L WILD-TYPE
  FEMALE             3             100
  MALE               5             160
[1] 2 2
[1] FALSE
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  OXA1L MUTATED       0                         0     8
  OXA1L WILD-TYPE     3                         1   256
D27V13, multiclass
                           clus
vv                          OXA1L MUTATED OXA1L WILD-TYPE
  ASIAN                                 0               3
  BLACK OR AFRICAN AMERICAN             0               1
  WHITE                                 8             256
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V14, binary
                 cls
clus                0   1
  OXA1L MUTATED     0   8
  OXA1L WILD-TYPE   3 253
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OXA1L MUTATED      0    8
  OXA1L WILD-TYPE    3  253
                        clus
vv                       OXA1L MUTATED OXA1L WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO             8             253
[1] 2 2
[1] FALSE

Clustering(28) Variable = COL3A1 MUTATION ANALYSIS
D28V1, survival
                  sevent
clus2                0   1
  COL3A1 MUTATED    23  28
  COL3A1 WILD-TYPE 105 102
  COL3A1 MUTATED COL3A1 WILD-TYPE 
              51              207 
  COL3A1 MUTATED COL3A1 WILD-TYPE 
              28              102 
$`COL3A1 MUTATED`
TCGA-D3-A1Q6 TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JK TCGA-D3-A2JO TCGA-D3-A3C7 
       70.16        69.90        11.41         6.31        64.44        46.98 
TCGA-D3-A3ML TCGA-D3-A3MV TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GS TCGA-D9-A6EC 
        6.31         5.39        52.01        47.87         6.97        13.22 
TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A3F5 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A181 
       51.12        39.19        17.56        11.57        10.55         1.12 
TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29L TCGA-EE-A2A5 TCGA-EE-A2GC TCGA-EE-A2GI 
       11.15        38.63         1.08         9.67        34.29        30.08 
TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2M5 TCGA-EE-A2MC TCGA-EE-A2MJ TCGA-EE-A2MR 
       30.84         5.42         8.84        47.51        63.42        29.65 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AC TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J5 
       27.16        23.05        25.84        15.95        12.72        21.60 
TCGA-EE-A3JD TCGA-EE-A3JE TCGA-ER-A193 TCGA-ER-A19C TCGA-ER-A19F TCGA-ER-A19H 
       27.35         0.46        31.40         3.78        11.11        34.88 
TCGA-ER-A19J TCGA-ER-A2NC TCGA-FS-A1Z3 TCGA-FS-A1ZK TCGA-FS-A4F5 TCGA-FS-A4F9 
        4.21        11.80        14.24        12.89        28.73        10.78 
TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-GN-A266 
        0.99         0.13        10.13 

$`COL3A1 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       16.47         8.52       111.09        32.42       110.79        28.08 
TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 
       22.55        45.83        81.24        10.29        85.32         8.38 
TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH 
       21.14        88.50        68.22        30.87         7.50        36.16 
TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C8 
       92.42        56.19        45.11       114.67        15.25        46.32 
TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MR 
       82.29        61.38        13.32        24.00         9.34       103.59 
TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K 
       26.37        80.22        42.71        15.09        41.10        17.72 
TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GR TCGA-D3-A5GU TCGA-D9-A3Z1 
        8.84        20.48        13.94         1.55        23.11         4.01 
TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1I0 
        2.89         9.90        11.31        48.79        35.80        10.03 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA 
       13.68         9.99        44.52        36.69        25.15         4.93 
TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-EB-A44Q 
       22.36         6.64        19.36         7.00        14.83        13.15 
TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EE-A17Z TCGA-EE-A180 
        0.20         0.00         0.00        13.22         6.31         8.12 
TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C 
        1.35        12.20         5.13         4.31        36.07         4.34 
TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C 
        5.13         9.21         1.18         7.99         9.90        37.97 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
        8.55         4.41        27.12         9.50        12.03         8.09 
TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 
        8.84         9.99         2.43         8.68         8.09        11.31 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE 
       49.22        23.90         8.94        39.39        17.98        34.92 
TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN 
       47.21        19.43        16.01        35.54        28.31        33.83 
TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 
        1.15        13.02        34.98        36.33        98.27         2.70 
TCGA-EE-A2M8 TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI 
        6.18         9.53        29.46        44.25         7.96        14.56 
TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ 
      111.78       111.91        56.02        25.08        26.99        21.60 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF 
        5.56       124.31       122.73         3.68        30.15        13.81 
TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JH 
        3.22        22.92        21.60        16.14        22.22        13.94 
TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A 
       33.60        18.61        12.95        38.40         5.72        76.41 
TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19G TCGA-ER-A19L TCGA-ER-A19M 
       25.18         3.52        11.90       114.15        13.45        28.60 
TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 
       42.84        34.68         9.57        36.07        17.72        78.44 
TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES 
        1.87         1.51        13.08        12.62        11.74         9.04 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
        6.58        22.49         1.71        18.41        85.74         4.90 
TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1Z7 
       64.47         3.45        11.01        23.80        15.52         7.33 
TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF 
        7.30         3.39        20.38         8.22        19.53        11.08 
TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ 
        7.17        30.87        12.92        47.38        52.08         8.65 
TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY 
        8.81        49.15        40.64         8.68        27.39         0.82 
TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4FB TCGA-FS-A4FC 
        5.23        53.85         7.36        14.20         5.98         6.41 
TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
        2.27         0.20         0.16         0.43         9.90         7.23 
TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 
       12.85        24.85        31.33        84.72        16.24        15.42 
TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS 
       12.16        14.70         5.79 

  COL3A1 MUTATED COL3A1 WILD-TYPE 
            0.13             0.00 
  COL3A1 MUTATED COL3A1 WILD-TYPE 
           70.16           124.31 
  COL3A1 MUTATED COL3A1 WILD-TYPE 
           14.24            14.83 
[1] "0.1 - 70.2 (14.2)"  "0.0 - 124.3 (14.8)"
[1] "hr=" "1.1"
D28V2, survival
                  sevent
clus2                0   1
  COL3A1 MUTATED    24  28
  COL3A1 WILD-TYPE 108 103
  COL3A1 MUTATED COL3A1 WILD-TYPE 
              52              211 
  COL3A1 MUTATED COL3A1 WILD-TYPE 
              28              103 
$`COL3A1 MUTATED`
TCGA-D3-A1Q6 TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JK TCGA-D3-A2JO TCGA-D3-A3C7 
       71.80        69.90        11.87        12.10        66.08        46.98 
TCGA-D3-A3ML TCGA-D3-A3MV TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GS TCGA-D9-A1JW 
       13.87        21.47       135.75       137.92         7.43         3.65 
TCGA-D9-A6EC TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A3F5 TCGA-EE-A17X TCGA-EE-A17Y 
       66.25       117.21       194.83       215.44        29.82        27.22 
TCGA-EE-A181 TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29L TCGA-EE-A2A5 TCGA-EE-A2GC 
       33.73        13.97        39.62         2.60        39.29        67.43 
TCGA-EE-A2GI TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2M5 TCGA-EE-A2MC TCGA-EE-A2MJ 
       48.72       101.95        13.91        21.67        61.51        96.23 
TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AC TCGA-EE-A3AG TCGA-EE-A3AH 
      103.56       136.47        41.59        25.84        23.47       138.81 
TCGA-EE-A3J5 TCGA-EE-A3JD TCGA-EE-A3JE TCGA-ER-A193 TCGA-ER-A19C TCGA-ER-A19F 
       36.95        27.35        33.40        31.40        48.89        26.37 
TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A2NC TCGA-FS-A1Z3 TCGA-FS-A1ZK TCGA-FS-A4F5 
      152.35         6.44        43.82        20.91        23.93        28.73 
TCGA-FS-A4F9 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-GN-A266 
       12.43        22.92        47.54        10.13 

$`COL3A1 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       16.57        16.67       112.04       112.57       133.25        28.08 
TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 
       31.59        90.90        95.74        43.43       103.10        65.49 
TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH 
       23.77       115.53       168.00        48.76       113.52        42.08 
TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C8 
      171.58        56.19        45.11       130.72        58.06        46.32 
TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MR 
      166.52        86.93        60.23        24.53         9.34       103.59 
TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K 
       39.75       161.85        43.69        40.14       131.90        18.38 
TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GR TCGA-D3-A5GU TCGA-D9-A148 
       10.03        51.68        15.06       166.19       125.19       151.53 
TCGA-D9-A149 TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA 
       54.67         6.41        11.34         3.25         9.90        25.18 
TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 
       48.89        36.03        20.38       176.55        35.93       107.34 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
       61.18        53.92        65.92        23.44        68.09        28.60 
TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH 
       10.49        15.68        13.87        10.16        45.11        35.01 
TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A182 TCGA-EE-A183 
        3.55        52.01         8.65        94.98        14.70        26.89 
TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H 
       68.15         4.96       109.64       151.27        78.87       168.26 
TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29G TCGA-EE-A29H 
       13.55        63.35        80.61        47.84        72.07        32.19 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S 
       44.35        18.61        56.42        37.35        14.47        55.92 
TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 
       25.87       171.55        17.92        46.82       102.90        24.43 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ 
       58.75        47.54       314.56       135.95       208.04        89.33 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GR TCGA-EE-A2GS 
       54.74        79.66        75.48        90.97        14.30        55.59 
TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MD 
       44.88        94.82       129.27        28.83        19.76        47.28 
TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2ML 
      103.27       103.20        16.96       204.66       144.76       203.05 
TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MU TCGA-EE-A3AA 
      167.90        47.54       248.65        43.23        53.26       124.31 
TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-EE-A3J4 
      122.73         3.68        54.51        13.81       172.18       127.20 
TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 
       64.08        34.32        53.19       101.79       148.08        35.44 
TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19D 
       13.94        50.76         9.17        77.75        98.40        12.59 
TCGA-ER-A19E TCGA-ER-A19G TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P 
       13.02       268.93       131.51        61.05        44.05       162.08 
TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2ND TCGA-ER-A2NE 
       50.89        37.25       148.18        79.99        23.34        20.15 
TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV 
       16.37        31.27        32.05       247.04        80.32        46.98 
TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX 
       33.21        92.98       174.21         4.90       216.92        48.59 
TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB 
      228.59       202.65        28.08         7.79        27.72        48.85 
TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH 
      357.37        53.52        40.27        15.45         9.70        32.75 
TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS 
       47.38       101.26        74.73       133.55        11.41       148.80 
TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 
       53.16        26.56        49.48        27.09        27.02        77.82 
TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 
       66.67       174.84        26.73        49.45        77.88         0.20 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 
        0.16         2.40         9.90         7.23        14.04       120.46 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D 
      117.93        84.72        64.44        62.79        32.48        39.58 
TCGA-QB-A6FS 
        6.67 

  COL3A1 MUTATED COL3A1 WILD-TYPE 
            2.60             0.16 
  COL3A1 MUTATED COL3A1 WILD-TYPE 
          215.44           357.37 
  COL3A1 MUTATED COL3A1 WILD-TYPE 
           35.34            50.89 
[1] "2.6 - 215.4 (35.3)" "0.2 - 357.4 (50.9)"
[1] "hr=" "1.5"
D28V3, continuous
                  vv
clus               DISTANT METASTASIS PRIMARY TUMOR
  COL3A1 MUTATED                    5             1
  COL3A1 WILD-TYPE                 30             3
                  vv
clus               REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  COL3A1 MUTATED                                          14
  COL3A1 WILD-TYPE                                        44
                  vv
clus               REGIONAL LYMPH NODE
  COL3A1 MUTATED                    33
  COL3A1 WILD-TYPE                 137
D28V4, multiclass
                                           clus
vv                                          COL3A1 MUTATED COL3A1 WILD-TYPE
  DISTANT METASTASIS                                     5               30
  PRIMARY TUMOR                                          1                3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE             14               44
  REGIONAL LYMPH NODE                                   33              137
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  COL3A1 MUTATED             0       0       5        2        4        6
  COL3A1 WILD-TYPE          10       6      17        8       20       11
                  vv
clus               STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  COL3A1 MUTATED           0         2         0         9          2
  COL3A1 WILD-TYPE        10        12         9        22         11
                  vv
clus               STAGE IIIB STAGE IIIC STAGE IV
  COL3A1 MUTATED            6          9        3
  COL3A1 WILD-TYPE         16         35        9
D28V5, multiclass
             clus
vv            COL3A1 MUTATED COL3A1 WILD-TYPE
  I OR II NOS              0               10
  STAGE 0                  0                6
  STAGE I                  5               17
  STAGE IA                 2                8
  STAGE IB                 4               20
  STAGE II                 6               11
  STAGE IIA                0               10
  STAGE IIB                2               12
  STAGE IIC                0                9
  STAGE III                9               22
  STAGE IIIA               2               11
  STAGE IIIB               6               16
  STAGE IIIC               9               35
  STAGE IV                 3                9
[1] 14  2
[1] 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
  COL3A1 MUTATED      11 10 13 10
  COL3A1 WILD-TYPE    40 48 40 45
D28V6, multiclass
       clus
vv      COL3A1 MUTATED COL3A1 WILD-TYPE
  T0+T1             11               40
  T2                10               48
  T3                13               40
  T4                10               45
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  COL3A1 MUTATED    22  12   9   7
  COL3A1 WILD-TYPE 116  36  23  26
D28V7, multiclass
    clus
vv   COL3A1 MUTATED COL3A1 WILD-TYPE
  N0             22              116
  N1             12               36
  N2              9               23
  N3              7               26
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                M0  M1 M1A M1B M1C
  COL3A1 MUTATED    48   2   0   0   1
  COL3A1 WILD-TYPE 192   2   2   2   4
D28V8, multiclass
     clus
vv    COL3A1 MUTATED COL3A1 WILD-TYPE
  M0              48              192
  M1               2                2
  M1A              0                2
  M1B              0                2
  M1C              1                4
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V9, binary
                  cls
clus                0  1
  COL3A1 MUTATED   21 12
  COL3A1 WILD-TYPE 81 55
[1] "tbl2"
                  cls
clus               [,1] [,2]
  COL3A1 MUTATED     21   12
  COL3A1 WILD-TYPE   81   55
     clus
vv    COL3A1 MUTATED COL3A1 WILD-TYPE
  NO              21               81
  YES             12               55
[1] 2 2
[1] FALSE
D28V10, binary
                  cls
clus                 0   1
  COL3A1 MUTATED     9  44
  COL3A1 WILD-TYPE  24 191
[1] "tbl2"
                  cls
clus               [,1] [,2]
  COL3A1 MUTATED      9   44
  COL3A1 WILD-TYPE   24  191
     clus
vv    COL3A1 MUTATED COL3A1 WILD-TYPE
  NO               9               24
  YES             44              191
[1] 2 2
[1] FALSE
D28V11, continuous
D28V12, binary
                  cls
clus                 0   1
  COL3A1 MUTATED    11  42
  COL3A1 WILD-TYPE  92 123
[1] "tbl2"
                  cls
clus               [,1] [,2]
  COL3A1 MUTATED     11   42
  COL3A1 WILD-TYPE   92  123
        clus
vv       COL3A1 MUTATED COL3A1 WILD-TYPE
  FEMALE             11               92
  MALE               42              123
[1] 2 2
[1] FALSE
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  COL3A1 MUTATED       1                         0    52
  COL3A1 WILD-TYPE     2                         1   212
D28V13, multiclass
                           clus
vv                          COL3A1 MUTATED COL3A1 WILD-TYPE
  ASIAN                                  1                2
  BLACK OR AFRICAN AMERICAN              0                1
  WHITE                                 52              212
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V14, binary
                  cls
clus                 0   1
  COL3A1 MUTATED     0  51
  COL3A1 WILD-TYPE   3 210
[1] "tbl2"
                  cls
clus               [,1] [,2]
  COL3A1 MUTATED      0   51
  COL3A1 WILD-TYPE    3  210
                        clus
vv                       COL3A1 MUTATED COL3A1 WILD-TYPE
  HISPANIC OR LATINO                  0                3
  NOT HISPANIC OR LATINO             51              210
[1] 2 2
[1] FALSE

Clustering(29) Variable = TCHHL1 MUTATION ANALYSIS
D29V1, survival
                  sevent
clus2                0   1
  TCHHL1 MUTATED    25  11
  TCHHL1 WILD-TYPE 103 119
  TCHHL1 MUTATED TCHHL1 WILD-TYPE 
              36              222 
  TCHHL1 MUTATED TCHHL1 WILD-TYPE 
              11              119 
$`TCHHL1 MUTATED`
TCGA-D3-A2JF TCGA-D3-A2JL TCGA-D3-A3C7 TCGA-D3-A3MV TCGA-D3-A51R TCGA-D3-A51T 
       30.87        92.42        46.98         5.39        20.48        13.94 
TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1I0 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 
       13.22        48.79        10.03         1.12         1.35        12.20 
TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29M TCGA-EE-A29S TCGA-EE-A2GI TCGA-EE-A2GJ 
       38.63         8.55        27.12         9.99        30.08        19.43 
TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2MC TCGA-EE-A2MR TCGA-EE-A2MU 
       34.98        36.33        98.27        47.51        29.65         5.56 
TCGA-EE-A3AA TCGA-EE-A3J5 TCGA-ER-A19A TCGA-ER-A19D TCGA-ER-A19G TCGA-ER-A19N 
      124.31        21.60        76.41         3.52       114.15        42.84 
TCGA-FR-A3YN TCGA-FS-A4FB TCGA-FS-A4FD TCGA-FW-A3R5 TCGA-GN-A266 TCGA-GN-A26A 
       18.41         5.98         2.27         0.99        10.13        12.16 

$`TCHHL1 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.47         8.52       111.09        32.42        70.16       110.79 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       28.08        22.55        45.83        81.24        10.29        85.32 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
        8.38        21.14        88.50        68.22        69.90        11.41 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP 
        7.50        36.16         6.31        56.19        64.44        45.11 
TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE 
      114.67        15.25        46.32        82.29        61.38        13.32 
TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E 
       24.00         6.31         9.34       103.59        26.37        80.22 
TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A5GN 
       42.71        15.09        41.10        17.72         8.84        52.01 
TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 
       47.87         1.55         6.97        23.11         4.01         2.89 
TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 
        9.90        11.31        35.80        51.12        39.19        13.68 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB 
        9.99        44.52        36.69        25.15         4.93        22.36 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q 
        6.64        19.36         7.00        17.56        14.83        13.15 
TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y 
        0.20         0.00         0.00        13.22        11.57        10.55 
TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C 
        6.31         8.12         5.13         4.31        36.07         4.34 
TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C 
        5.13         9.21         1.18         7.99         9.90        37.97 
TCGA-EE-A29D TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
       11.15         4.41         1.08         9.50        12.03         8.09 
TCGA-EE-A29R TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 
        8.84         2.43         8.68         8.09        11.31        49.22 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD 
       23.90         9.67         8.94        39.39        34.29        17.98 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN 
       34.92        47.21        16.01        35.54        28.31        33.83 
TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2M5 TCGA-EE-A2M7 
       30.84         5.42         1.15        13.02         8.84         2.70 
TCGA-EE-A2M8 TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI 
        6.18         9.53        29.46        44.25         7.96        14.56 
TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP 
       63.42       111.78       111.91        56.02        25.08        26.99 
TCGA-EE-A2MQ TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD 
       21.60        27.16        23.05       122.73        25.84         3.68 
TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 
       30.15        13.81        15.95        12.72         3.22        22.92 
TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH 
       21.60        16.14        22.22        27.35         0.46        13.94 
TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 
       33.60        31.40        18.61        12.95        38.40         5.72 
TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19H TCGA-ER-A19J 
       25.18         3.78        11.90        11.11        34.88         4.21 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W 
       13.45        28.60        34.68         9.57        36.07        17.72 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG 
       78.44        11.80         1.87         1.51        13.08        12.62 
TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A44A 
       11.74         9.04         6.58        22.49         1.71        85.74 
TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
        4.90        64.47         3.45        11.01        23.80        14.24 
TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD 
       15.52         7.33         7.30         3.39        20.38         8.22 
TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK 
       19.53        11.08         7.17        30.87        12.92        12.89 
TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT 
       47.38        52.08         8.65         8.81        49.15        40.64 
TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 
        8.68        27.39         0.82         5.23        53.85         7.36 
TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FW-A3I3 TCGA-FW-A3TU 
       28.73        14.20        10.78         6.41         0.20         0.13 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 
        0.16         0.43         9.90         7.23        12.85        24.85 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26D TCGA-QB-A6FS 
       31.33        84.72        16.24        15.42        14.70         5.79 

  TCHHL1 MUTATED TCHHL1 WILD-TYPE 
            0.99             0.00 
  TCHHL1 MUTATED TCHHL1 WILD-TYPE 
          124.31           122.73 
  TCHHL1 MUTATED TCHHL1 WILD-TYPE 
          19.955           14.400 
[1] "1.0 - 124.3 (20.0)" "0.0 - 122.7 (14.4)"
[1] "hr=" "2"  
D29V2, survival
                  sevent
clus2                0   1
  TCHHL1 MUTATED    26  11
  TCHHL1 WILD-TYPE 106 120
  TCHHL1 MUTATED TCHHL1 WILD-TYPE 
              37              226 
  TCHHL1 MUTATED TCHHL1 WILD-TYPE 
              11              120 
$`TCHHL1 MUTATED`
TCGA-D3-A2JF TCGA-D3-A2JL TCGA-D3-A3C7 TCGA-D3-A3MV TCGA-D3-A51R TCGA-D3-A51T 
       48.76       171.58        46.98        21.47        51.68        15.06 
TCGA-D9-A1JW TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1I0 TCGA-EE-A181 TCGA-EE-A182 
        3.65        66.25        48.89        20.38        33.73        14.70 
TCGA-EE-A183 TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29M TCGA-EE-A29S TCGA-EE-A2GI 
       26.89        39.62        72.07        44.35        55.92        48.72 
TCGA-EE-A2GJ TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2MC TCGA-EE-A2MR 
       89.33        44.88        94.82       129.27        61.51       103.56 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3J5 TCGA-ER-A19A TCGA-ER-A19D TCGA-ER-A19G 
       53.26       124.31        36.95        77.75        12.59       268.93 
TCGA-ER-A19N TCGA-FR-A3YN TCGA-FS-A4FB TCGA-FS-A4FD TCGA-FW-A3R5 TCGA-GN-A266 
       44.05        92.98        26.73        77.88        22.92        10.13 
TCGA-GN-A26A 
       32.48 

$`TCHHL1 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.57        16.67       112.04       112.57        71.80       133.25 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       28.08        31.59        90.90        95.74        43.43       103.10 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
       65.49        23.77       115.53       168.00        69.90        11.87 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP 
      113.52        42.08        12.10        56.19        66.08        45.11 
TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE 
      130.72        58.06        46.32       166.52        86.93        60.23 
TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E 
       24.53        13.87         9.34       103.59        39.75       161.85 
TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A5GN 
       43.69        40.14       131.90        18.38        10.03       135.75 
TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 
      137.92       166.19         7.43       125.19       151.53        54.67 
TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-DA-A1HW 
        6.41        11.34         3.25         9.90        25.18        36.03 
TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 
      117.21       194.83       176.55        35.93       107.34        61.18 
TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 
       53.92        65.92        23.44        68.09        28.60        10.49 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH 
      215.44        15.68        13.87        10.16        45.11        35.01 
TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 
        3.55        52.01        29.82        27.22         8.65        94.98 
TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H 
       68.15         4.96       109.64       151.27        78.87       168.26 
TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29H 
       13.55        63.35        80.61        47.84        13.97        32.19 
TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29V 
        2.60        18.61        56.42        37.35        14.47        25.87 
TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 
      171.55        17.92        46.82       102.90        24.43        39.29 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH 
       58.75        47.54        67.43       314.56       135.95       208.04 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP 
       54.74        79.66        75.48        90.97       101.95        13.91 
TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2M5 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MD 
       14.30        55.59        21.67        28.83        19.76        47.28 
TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK 
      103.27       103.20        16.96       204.66        96.23       144.76 
TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MS 
      203.05       167.90        47.54       248.65        43.23       136.47 
TCGA-EE-A2MT TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF 
       41.59       122.73        25.84         3.68        54.51        13.81 
TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 
       23.47       138.81       172.18       127.20        64.08        34.32 
TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 
       53.19        27.35        33.40       101.79       148.08        31.40 
TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19B TCGA-ER-A19C 
       35.44        13.94        50.76         9.17        98.40        48.89 
TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M 
       13.02        26.37       152.35         6.44       131.51        61.05 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
      162.08        50.89        37.25       148.18        79.99        43.82 
TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES 
       23.34        20.15        16.37        31.27        32.05       247.04 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW 
       80.32        46.98        33.21       174.21         4.90       216.92 
TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 
       48.59       228.59       202.65        20.91        28.08         7.79 
TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF 
       27.72        48.85       357.37        53.52        40.27        15.45 
TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP 
        9.70        32.75        47.38        23.93       101.26        74.73 
TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW 
      133.55        11.41       148.80        53.16        26.56        49.48 
TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 
       27.09        27.02        77.82        66.67        28.73       174.84 
TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY 
       12.43        49.45         0.20        47.54         0.16         2.40 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        9.90         7.23        14.04       120.46       117.93        84.72 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26D TCGA-QB-A6FS 
       64.44        62.79        39.58         6.67 

  TCHHL1 MUTATED TCHHL1 WILD-TYPE 
            3.65             0.16 
  TCHHL1 MUTATED TCHHL1 WILD-TYPE 
          268.93           357.37 
  TCHHL1 MUTATED TCHHL1 WILD-TYPE 
          48.720           48.215 
[1] "3.6 - 268.9 (48.7)" "0.2 - 357.4 (48.2)"
[1] "hr=" "1.6"
D29V3, continuous
                  vv
clus               DISTANT METASTASIS PRIMARY TUMOR
  TCHHL1 MUTATED                    2             1
  TCHHL1 WILD-TYPE                 33             3
                  vv
clus               REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  TCHHL1 MUTATED                                          10
  TCHHL1 WILD-TYPE                                        48
                  vv
clus               REGIONAL LYMPH NODE
  TCHHL1 MUTATED                    25
  TCHHL1 WILD-TYPE                 145
D29V4, multiclass
                                           clus
vv                                          TCHHL1 MUTATED TCHHL1 WILD-TYPE
  DISTANT METASTASIS                                     2               33
  PRIMARY TUMOR                                          1                3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE             10               48
  REGIONAL LYMPH NODE                                   25              145
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  TCHHL1 MUTATED             1       2       3        5        3        1
  TCHHL1 WILD-TYPE           9       4      19        5       21       16
                  vv
clus               STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  TCHHL1 MUTATED           3         0         0         5          3
  TCHHL1 WILD-TYPE         7        14         9        26         10
                  vv
clus               STAGE IIIB STAGE IIIC STAGE IV
  TCHHL1 MUTATED            3          3        2
  TCHHL1 WILD-TYPE         19         41       10
D29V5, multiclass
             clus
vv            TCHHL1 MUTATED TCHHL1 WILD-TYPE
  I OR II NOS              1                9
  STAGE 0                  2                4
  STAGE I                  3               19
  STAGE IA                 5                5
  STAGE IB                 3               21
  STAGE II                 1               16
  STAGE IIA                3                7
  STAGE IIB                0               14
  STAGE IIC                0                9
  STAGE III                5               26
  STAGE IIIA               3               10
  STAGE IIIB               3               19
  STAGE IIIC               3               41
  STAGE IV                 2               10
[1] 14  2
[1] 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
  TCHHL1 MUTATED      10  8  7  5
  TCHHL1 WILD-TYPE    41 50 46 50
D29V6, multiclass
       clus
vv      TCHHL1 MUTATED TCHHL1 WILD-TYPE
  T0+T1             10               41
  T2                 8               50
  T3                 7               46
  T4                 5               50
[1] 4 2
[1] TRUE
[1] "dimension 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
  TCHHL1 MUTATED    20   9   5   2
  TCHHL1 WILD-TYPE 118  39  27  31
D29V7, multiclass
    clus
vv   TCHHL1 MUTATED TCHHL1 WILD-TYPE
  N0             20              118
  N1              9               39
  N2              5               27
  N3              2               31
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                M0  M1 M1A M1B M1C
  TCHHL1 MUTATED    34   1   1   0   0
  TCHHL1 WILD-TYPE 206   3   1   2   5
D29V8, multiclass
     clus
vv    TCHHL1 MUTATED TCHHL1 WILD-TYPE
  M0              34              206
  M1               1                3
  M1A              1                1
  M1B              0                2
  M1C              0                5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V9, binary
                  cls
clus                0  1
  TCHHL1 MUTATED   21  4
  TCHHL1 WILD-TYPE 81 63
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TCHHL1 MUTATED     21    4
  TCHHL1 WILD-TYPE   81   63
     clus
vv    TCHHL1 MUTATED TCHHL1 WILD-TYPE
  NO              21               81
  YES              4               63
[1] 2 2
[1] FALSE
D29V10, binary
                  cls
clus                 0   1
  TCHHL1 MUTATED     6  32
  TCHHL1 WILD-TYPE  27 203
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TCHHL1 MUTATED      6   32
  TCHHL1 WILD-TYPE   27  203
     clus
vv    TCHHL1 MUTATED TCHHL1 WILD-TYPE
  NO               6               27
  YES             32              203
[1] 2 2
[1] FALSE
D29V11, continuous
D29V12, binary
                  cls
clus                 0   1
  TCHHL1 MUTATED    14  24
  TCHHL1 WILD-TYPE  89 141
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TCHHL1 MUTATED     14   24
  TCHHL1 WILD-TYPE   89  141
        clus
vv       TCHHL1 MUTATED TCHHL1 WILD-TYPE
  FEMALE             14               89
  MALE               24              141
[1] 2 2
[1] FALSE
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TCHHL1 MUTATED       0                         0    38
  TCHHL1 WILD-TYPE     3                         1   226
D29V13, multiclass
                           clus
vv                          TCHHL1 MUTATED TCHHL1 WILD-TYPE
  ASIAN                                  0                3
  BLACK OR AFRICAN AMERICAN              0                1
  WHITE                                 38              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"
D29V14, binary
                  cls
clus                 0   1
  TCHHL1 MUTATED     0  38
  TCHHL1 WILD-TYPE   3 223
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TCHHL1 MUTATED      0   38
  TCHHL1 WILD-TYPE    3  223
                        clus
vv                       TCHHL1 MUTATED TCHHL1 WILD-TYPE
  HISPANIC OR LATINO                  0                3
  NOT HISPANIC OR LATINO             38              223
[1] 2 2
[1] FALSE

Clustering(30) Variable = IL5RA MUTATION ANALYSIS
D30V1, survival
                 sevent
clus2               0   1
  IL5RA MUTATED     8   9
  IL5RA WILD-TYPE 120 121
  IL5RA MUTATED IL5RA WILD-TYPE 
             17             241 
  IL5RA MUTATED IL5RA WILD-TYPE 
              9             121 
$`IL5RA MUTATED`
TCGA-D3-A51T TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A29E TCGA-EE-A29L TCGA-EE-A2MJ 
       13.94        11.57        10.55        38.63         1.08        63.42 
TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A3AE TCGA-EE-A3J5 TCGA-EE-A3JD TCGA-ER-A193 
       29.65        27.16        30.15        21.60        27.35        31.40 
TCGA-ER-A19C TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3R5 TCGA-GN-A266 
        3.78         6.41         2.27         0.99        10.13 

$`IL5RA WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.47         8.52       111.09        32.42        70.16       110.79 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       28.08        22.55        45.83        81.24        10.29        85.32 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
        8.38        21.14        88.50        68.22        69.90        11.41 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       30.87         7.50        36.16         6.31        92.42        56.19 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 
       64.44        45.11       114.67        15.25        46.98        46.32 
TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO 
       82.29        61.38        13.32        24.00         6.31         9.34 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H 
      103.59        26.37         5.39        80.22        42.71        15.09 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A5GN TCGA-D3-A5GO 
       41.10        17.72         8.84        20.48        52.01        47.87 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 
        1.55         6.97        23.11         4.01         2.89         9.90 
TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 
       11.31        13.22        48.79        35.80        51.12        10.03 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 
       39.19        13.68         9.99        44.52        36.69        25.15 
TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 
        4.93        22.36         6.64        19.36         7.00        17.56 
TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN 
       14.83        13.15         0.20         0.00         0.00        13.22 
TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 
        6.31         8.12         1.12         1.35        12.20         5.13 
TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I 
        4.31        36.07         4.34         5.13         9.21         1.18 
TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29H 
        7.99         9.90        37.97        11.15         8.55         4.41 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S 
       27.12         9.50        12.03         8.09         8.84         9.99 
TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 
        2.43         8.68         8.09        11.31        49.22        23.90 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE 
        9.67         8.94        39.39        34.29        17.98        34.92 
TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM 
       47.21        30.08        19.43        16.01        35.54        28.31 
TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT 
       33.83        30.84         5.42         1.15        13.02        34.98 
TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC 
       36.33         8.84        98.27         2.70         6.18        47.51 
TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MK 
        9.53        29.46        44.25         7.96        14.56       111.78 
TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MT 
      111.91        56.02        25.08        26.99        21.60        23.05 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AF 
        5.56       124.31       122.73        25.84         3.68        13.81 
TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 
       15.95        12.72         3.22        22.92        21.60        16.14 
TCGA-EE-A3JA TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 
       22.22         0.46        13.94        33.60        18.61        12.95 
TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19E 
       38.40         5.72        76.41        25.18         3.52        11.90 
TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M 
       11.11       114.15        34.88         4.21        13.45        28.60 
TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 
       42.84        34.68         9.57        36.07        17.72        78.44 
TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH 
       11.80         1.87         1.51        13.08        12.62        11.74 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A 
        9.04         6.58        22.49         1.71        18.41        85.74 
TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
        4.90        64.47         3.45        11.01        23.80        14.24 
TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD 
       15.52         7.33         7.30         3.39        20.38         8.22 
TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK 
       19.53        11.08         7.17        30.87        12.92        12.89 
TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT 
       47.38        52.08         8.65         8.81        49.15        40.64 
TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 
        8.68        27.39         0.82         5.23        53.85         7.36 
TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FW-A3I3 TCGA-FW-A3TU 
       28.73        14.20        10.78         5.98         0.20         0.13 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 
        0.16         0.43         9.90         7.23        12.85        24.85 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D 
       31.33        84.72        16.24        15.42        12.16        14.70 
TCGA-QB-A6FS 
        5.79 

  IL5RA MUTATED IL5RA WILD-TYPE 
           0.99            0.00 
  IL5RA MUTATED IL5RA WILD-TYPE 
          63.42          124.31 
  IL5RA MUTATED IL5RA WILD-TYPE 
          13.94           14.83 
[1] "1.0 - 63.4 (13.9)"  "0.0 - 124.3 (14.8)"
[1] "hr=" "1.2"
D30V2, survival
                 sevent
clus2               0   1
  IL5RA MUTATED     8   9
  IL5RA WILD-TYPE 124 122
  IL5RA MUTATED IL5RA WILD-TYPE 
             17             246 
  IL5RA MUTATED IL5RA WILD-TYPE 
              9             122 
$`IL5RA MUTATED`
TCGA-D3-A51T TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A29E TCGA-EE-A29L TCGA-EE-A2MJ 
       15.06        29.82        27.22        39.62         2.60        96.23 
TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A3AE TCGA-EE-A3J5 TCGA-EE-A3JD TCGA-ER-A193 
      103.56       136.47        54.51        36.95        27.35        31.40 
TCGA-ER-A19C TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3R5 TCGA-GN-A266 
       48.89        49.45        77.88        22.92        10.13 

$`IL5RA WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.57        16.67       112.04       112.57        71.80       133.25 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       28.08        31.59        90.90        95.74        43.43       103.10 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
       65.49        23.77       115.53       168.00        69.90        11.87 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       48.76       113.52        42.08        12.10       171.58        56.19 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 
       66.08        45.11       130.72        58.06        46.98        46.32 
TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO 
      166.52        86.93        60.23        24.53        13.87         9.34 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H 
      103.59        39.75        21.47       161.85        43.69        40.14 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A5GN TCGA-D3-A5GO 
      131.90        18.38        10.03        51.68       135.75       137.92 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW 
      166.19         7.43       125.19       151.53        54.67         3.65 
TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC 
        6.41        11.34         3.25         9.90        25.18        66.25 
TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 
       48.89        36.03       117.21        20.38       194.83       176.55 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB 
       35.93       107.34        61.18        53.92        65.92        23.44 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q 
       68.09        28.60        10.49       215.44        15.68        13.87 
TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17Z 
       10.16        45.11        35.01         3.55        52.01         8.65 
TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 
       94.98        33.73        14.70        26.89        68.15         4.96 
TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A 
      109.64       151.27        78.87       168.26        13.55        63.35 
TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M 
       80.61        47.84        13.97        72.07        32.19        44.35 
TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V 
       18.61        56.42        37.35        14.47        55.92        25.87 
TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 
      171.55        17.92        46.82       102.90        24.43        39.29 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH 
       58.75        47.54        67.43       314.56       135.95       208.04 
TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN 
       48.72        89.33        54.74        79.66        75.48        90.97 
TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU 
      101.95        13.91        14.30        55.59        44.88        94.82 
TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD 
       21.67       129.27        28.83        19.76        61.51        47.28 
TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2ML 
      103.27       103.20        16.96       204.66       144.76       203.05 
TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MT TCGA-EE-A2MU 
      167.90        47.54       248.65        43.23        41.59        53.26 
TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AG 
      124.31       122.73        25.84         3.68        13.81        23.47 
TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA 
      138.81       172.18       127.20        64.08        34.32        53.19 
TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 
       33.40       101.79       148.08        35.44        13.94        50.76 
TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F 
        9.17        77.75        98.40        12.59        13.02        26.37 
TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N 
      268.93       152.35         6.44       131.51        61.05        44.05 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
      162.08        50.89        37.25       148.18        79.99        43.82 
TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES 
       23.34        20.15        16.37        31.27        32.05       247.04 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
       80.32        46.98        33.21        92.98       174.21         4.90 
TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 
      216.92        48.59       228.59       202.65        20.91        28.08 
TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE 
        7.79        27.72        48.85       357.37        53.52        40.27 
TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM 
       15.45         9.70        32.75        47.38        23.93       101.26 
TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU 
       74.73       133.55        11.41       148.80        53.16        26.56 
TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 
       49.48        27.09        27.02        77.82        66.67        28.73 
TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV 
      174.84        12.43        26.73         0.20        47.54         0.16 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 
        2.40         9.90         7.23        14.04       120.46       117.93 
TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS 
       84.72        64.44        62.79        32.48        39.58         6.67 

  IL5RA MUTATED IL5RA WILD-TYPE 
           2.60            0.16 
  IL5RA MUTATED IL5RA WILD-TYPE 
         136.47          357.37 
  IL5RA MUTATED IL5RA WILD-TYPE 
          36.95           48.74 
[1] "2.6 - 136.5 (37.0)" "0.2 - 357.4 (48.7)"
[1] "hr=" "1.5"
D30V3, continuous
                 vv
clus              DISTANT METASTASIS PRIMARY TUMOR
  IL5RA MUTATED                    0             0
  IL5RA WILD-TYPE                 35             4
                 vv
clus              REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  IL5RA MUTATED                                           4                  13
  IL5RA WILD-TYPE                                        54                 157
D30V4, multiclass
                                           clus
vv                                          IL5RA MUTATED IL5RA WILD-TYPE
  DISTANT METASTASIS                                    0              35
  PRIMARY TUMOR                                         0               4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE             4              54
  REGIONAL LYMPH NODE                                  13             157
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  IL5RA MUTATED             0       0       2        2        0        1
  IL5RA WILD-TYPE          10       6      20        8       24       16
                 vv
clus              STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  IL5RA MUTATED           1         1         0         4          0          2
  IL5RA WILD-TYPE         9        13         9        27         13         20
                 vv
clus              STAGE IIIC STAGE IV
  IL5RA MUTATED            3        0
  IL5RA WILD-TYPE         41       12
D30V5, multiclass
             clus
vv            IL5RA MUTATED IL5RA WILD-TYPE
  I OR II NOS             0              10
  STAGE 0                 0               6
  STAGE I                 2              20
  STAGE IA                2               8
  STAGE IB                0              24
  STAGE II                1              16
  STAGE IIA               1               9
  STAGE IIB               1              13
  STAGE IIC               0               9
  STAGE III               4              27
  STAGE IIIA              0              13
  STAGE IIIB              2              20
  STAGE IIIC              3              41
  STAGE IV                0              12
[1] 14  2
[1] 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
  IL5RA MUTATED       2  3  5  4
  IL5RA WILD-TYPE    49 55 48 51
D30V6, multiclass
       clus
vv      IL5RA MUTATED IL5RA WILD-TYPE
  T0+T1             2              49
  T2                3              55
  T3                5              48
  T4                4              51
[1] 4 2
[1] TRUE
[1] "dimension 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
  IL5RA MUTATED     7   4   2   2
  IL5RA WILD-TYPE 131  44  30  31
D30V7, multiclass
    clus
vv   IL5RA MUTATED IL5RA WILD-TYPE
  N0             7             131
  N1             4              44
  N2             2              30
  N3             2              31
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               M0  M1 M1A M1B M1C
  IL5RA MUTATED    16   0   0   0   0
  IL5RA WILD-TYPE 224   4   2   2   5
D30V8, multiclass
     clus
vv    IL5RA MUTATED IL5RA WILD-TYPE
  M0             16             224
  M1              0               4
  M1A             0               2
  M1B             0               2
  M1C             0               5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V9, binary
                 cls
clus               0  1
  IL5RA MUTATED   10  3
  IL5RA WILD-TYPE 92 64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IL5RA MUTATED     10    3
  IL5RA WILD-TYPE   92   64
     clus
vv    IL5RA MUTATED IL5RA WILD-TYPE
  NO             10              92
  YES             3              64
[1] 2 2
[1] FALSE
D30V10, binary
                 cls
clus                0   1
  IL5RA MUTATED     2  15
  IL5RA WILD-TYPE  31 220
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IL5RA MUTATED      2   15
  IL5RA WILD-TYPE   31  220
     clus
vv    IL5RA MUTATED IL5RA WILD-TYPE
  NO              2              31
  YES            15             220
[1] 2 2
[1] FALSE
D30V11, continuous
D30V12, binary
                 cls
clus                0   1
  IL5RA MUTATED     3  14
  IL5RA WILD-TYPE 100 151
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IL5RA MUTATED      3   14
  IL5RA WILD-TYPE  100  151
        clus
vv       IL5RA MUTATED IL5RA WILD-TYPE
  FEMALE             3             100
  MALE              14             151
[1] 2 2
[1] FALSE
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  IL5RA MUTATED       1                         0    16
  IL5RA WILD-TYPE     2                         1   248
D30V13, multiclass
                           clus
vv                          IL5RA MUTATED IL5RA WILD-TYPE
  ASIAN                                 1               2
  BLACK OR AFRICAN AMERICAN             0               1
  WHITE                                16             248
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V14, binary
                 cls
clus                0   1
  IL5RA MUTATED     0  15
  IL5RA WILD-TYPE   3 246
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IL5RA MUTATED      0   15
  IL5RA WILD-TYPE    3  246
                        clus
vv                       IL5RA MUTATED IL5RA WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO            15             246
[1] 2 2
[1] FALSE

Clustering(31) Variable = NBPF7 MUTATION ANALYSIS
D31V1, survival
                 sevent
clus2               0   1
  NBPF7 MUTATED     8   5
  NBPF7 WILD-TYPE 120 125
  NBPF7 MUTATED NBPF7 WILD-TYPE 
             13             245 
  NBPF7 MUTATED NBPF7 WILD-TYPE 
              5             125 
$`NBPF7 MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2JC TCGA-D3-A5GU 
       16.47        45.83        81.24        10.29        69.90        23.11 
TCGA-D9-A6E9 TCGA-D9-A6EC TCGA-EE-A29E TCGA-EE-A2MJ TCGA-EE-A2MQ TCGA-EE-A3J5 
        9.90        13.22        38.63        63.42        21.60        21.60 
TCGA-FW-A3R5 
        0.99 

$`NBPF7 WILD-TYPE`
TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
        8.52       111.09        32.42        70.16       110.79        28.08 
TCGA-D3-A1Q9 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB 
       22.55        85.32         8.38        21.14        88.50        68.22 
TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL 
       11.41        30.87         7.50        36.16         6.31        92.42 
TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 
       56.19        64.44        45.11       114.67        15.25        46.98 
TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML 
       46.32        82.29        61.38        13.32        24.00         6.31 
TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F 
        9.34       103.59        26.37         5.39        80.22        42.71 
TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T 
       15.09        41.10        17.72         8.84        20.48        13.94 
TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D9-A3Z1 TCGA-D9-A3Z3 
       52.01        47.87         1.55         6.97         4.01         2.89 
TCGA-D9-A6EA TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 
       11.31        48.79        35.80        51.12        10.03        39.19 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA 
       13.68         9.99        44.52        36.69        25.15         4.93 
TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 
       22.36         6.64        19.36         7.00        17.56        14.83 
TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EE-A17X 
       13.15         0.20         0.00         0.00        13.22        11.57 
TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 
       10.55         6.31         8.12         1.12         1.35        12.20 
TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H 
        5.13         4.31        36.07         4.34         5.13         9.21 
TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29G 
        1.18         7.99         9.90        37.97        11.15         8.55 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
        4.41         1.08        27.12         9.50        12.03         8.09 
TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 
        8.84         9.99         2.43         8.68         8.09        11.31 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC 
       49.22        23.90         9.67         8.94        39.39        34.29 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK 
       17.98        34.92        47.21        30.08        19.43        16.01 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR 
       35.54        28.31        33.83        30.84         5.42         1.15 
TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 
       13.02        34.98        36.33         8.84        98.27         2.70 
TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH 
        6.18        47.51         9.53        29.46        44.25         7.96 
TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP 
       14.56       111.78       111.91        56.02        25.08        26.99 
TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB 
       29.65        27.16        23.05         5.56       124.31       122.73 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH 
       25.84         3.68        30.15        13.81        15.95        12.72 
TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JD 
        3.22        22.92        21.60        16.14        22.22        27.35 
TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 
        0.46        13.94        33.60        31.40        18.61        12.95 
TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D 
       38.40         5.72        76.41        25.18         3.78         3.52 
TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L 
       11.90        11.11       114.15        34.88         4.21        13.45 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W 
       28.60        42.84        34.68         9.57        36.07        17.72 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG 
       78.44        11.80         1.87         1.51        13.08        12.62 
TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN 
       11.74         9.04         6.58        22.49         1.71        18.41 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 
       85.74         4.90        64.47         3.45        11.01        23.80 
TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC 
       14.24        15.52         7.33         7.30         3.39        20.38 
TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ 
        8.22        19.53        11.08         7.17        30.87        12.92 
TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS 
       12.89        47.38        52.08         8.65         8.81        49.15 
TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 
       40.64         8.68        27.39         0.82         5.23        53.85 
TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC 
        7.36        28.73        14.20        10.78         5.98         6.41 
TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
        2.27         0.20         0.13         0.16         0.43         9.90 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 
        7.23        12.85        24.85        31.33        84.72        10.13 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS 
       16.24        15.42        12.16        14.70         5.79 

  NBPF7 MUTATED NBPF7 WILD-TYPE 
           0.99            0.00 
  NBPF7 MUTATED NBPF7 WILD-TYPE 
          81.24          124.31 
  NBPF7 MUTATED NBPF7 WILD-TYPE 
          21.60           14.24 
[1] "1.0 - 81.2 (21.6)"  "0.0 - 124.3 (14.2)"
[1] "hr=" "1.7"
D31V2, survival
                 sevent
clus2               0   1
  NBPF7 MUTATED     8   5
  NBPF7 WILD-TYPE 124 126
  NBPF7 MUTATED NBPF7 WILD-TYPE 
             13             250 
  NBPF7 MUTATED NBPF7 WILD-TYPE 
              5             126 
$`NBPF7 MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2JC TCGA-D3-A5GU 
       16.57        90.90        95.74        43.43        69.90       125.19 
TCGA-D9-A6E9 TCGA-D9-A6EC TCGA-EE-A29E TCGA-EE-A2MJ TCGA-EE-A2MQ TCGA-EE-A3J5 
        9.90        66.25        39.62        96.23        43.23        36.95 
TCGA-FW-A3R5 
       22.92 

$`NBPF7 WILD-TYPE`
TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       16.67       112.04       112.57        71.80       133.25        28.08 
TCGA-D3-A1Q9 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB 
       31.59       103.10        65.49        23.77       115.53       168.00 
TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL 
       11.87        48.76       113.52        42.08        12.10       171.58 
TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 
       56.19        66.08        45.11       130.72        58.06        46.98 
TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML 
       46.32       166.52        86.93        60.23        24.53        13.87 
TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F 
        9.34       103.59        39.75        21.47       161.85        43.69 
TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T 
       40.14       131.90        18.38        10.03        51.68        15.06 
TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D9-A148 TCGA-D9-A149 
      135.75       137.92       166.19         7.43       151.53        54.67 
TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6EA TCGA-DA-A1HV 
        3.65         6.41        11.34         3.25        25.18        48.89 
TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 
       36.03       117.21        20.38       194.83       176.55        35.93 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC 
      107.34        61.18        53.92        65.92        23.44        68.09 
TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R 
       28.60        10.49       215.44        15.68        13.87        10.16 
TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y 
       45.11        35.01         3.55        52.01        29.82        27.22 
TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 
        8.65        94.98        33.73        14.70        26.89        68.15 
TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I 
        4.96       109.64       151.27        78.87       168.26        13.55 
TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29H 
       63.35        80.61        47.84        13.97        72.07        32.19 
TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R 
        2.60        44.35        18.61        56.42        37.35        14.47 
TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 
       55.92        25.87       171.55        17.92        46.82       102.90 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD 
       24.43        39.29        58.75        47.54        67.43       314.56 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
      135.95       208.04        48.72        89.33        54.74        79.66 
TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS 
       75.48        90.97       101.95        13.91        14.30        55.59 
TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 
       44.88        94.82        21.67       129.27        28.83        19.76 
TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI 
       61.51        47.28       103.27       103.20        16.96       204.66 
TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MR 
      144.76       203.05       167.90        47.54       248.65       103.56 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC 
      136.47        41.59        53.26       124.31       122.73        25.84 
TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 
        3.68        54.51        13.81        23.47       138.81       172.18 
TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE 
      127.20        64.08        34.32        53.19        27.35        33.40 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 
      101.79       148.08        31.40        35.44        13.94        50.76 
TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E 
        9.17        77.75        98.40        48.89        12.59        13.02 
TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M 
       26.37       268.93       152.35         6.44       131.51        61.05 
TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 
       44.05       162.08        50.89        37.25       148.18        79.99 
TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH 
       43.82        23.34        20.15        16.37        31.27        32.05 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A 
      247.04        80.32        46.98        33.21        92.98       174.21 
TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
        4.90       216.92        48.59       228.59       202.65        20.91 
TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD 
       28.08         7.79        27.72        48.85       357.37        53.52 
TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK 
       40.27        15.45         9.70        32.75        47.38        23.93 
TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT 
      101.26        74.73       133.55        11.41       148.80        53.16 
TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 
       26.56        49.48        27.09        27.02        77.82        66.67 
TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD 
       28.73       174.84        12.43        26.73        49.45        77.88 
TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
        0.20        47.54         0.16         2.40         9.90         7.23 
TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 
       14.04       120.46       117.93        84.72        10.13        64.44 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS 
       62.79        32.48        39.58         6.67 

  NBPF7 MUTATED NBPF7 WILD-TYPE 
           9.90            0.16 
  NBPF7 MUTATED NBPF7 WILD-TYPE 
         125.19          357.37 
  NBPF7 MUTATED NBPF7 WILD-TYPE 
         43.430          48.655 
[1] "9.9 - 125.2 (43.4)" "0.2 - 357.4 (48.7)"
[1] "hr=" "1.1"
D31V3, continuous
                 vv
clus              DISTANT METASTASIS PRIMARY TUMOR
  NBPF7 MUTATED                    0             2
  NBPF7 WILD-TYPE                 35             2
                 vv
clus              REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  NBPF7 MUTATED                                           1                  10
  NBPF7 WILD-TYPE                                        57                 160
D31V4, multiclass
                                           clus
vv                                          NBPF7 MUTATED NBPF7 WILD-TYPE
  DISTANT METASTASIS                                    0              35
  PRIMARY TUMOR                                         2               2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE             1              57
  REGIONAL LYMPH NODE                                  10             160
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  NBPF7 MUTATED             0       0       0        0        2        0
  NBPF7 WILD-TYPE          10       6      22       10       22       17
                 vv
clus              STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  NBPF7 MUTATED           0         1         0         5          3          1
  NBPF7 WILD-TYPE        10        13         9        26         10         21
                 vv
clus              STAGE IIIC STAGE IV
  NBPF7 MUTATED            1        0
  NBPF7 WILD-TYPE         43       12
D31V5, multiclass
             clus
vv            NBPF7 MUTATED NBPF7 WILD-TYPE
  I OR II NOS             0              10
  STAGE 0                 0               6
  STAGE I                 0              22
  STAGE IA                0              10
  STAGE IB                2              22
  STAGE II                0              17
  STAGE IIA               0              10
  STAGE IIB               1              13
  STAGE IIC               0               9
  STAGE III               5              26
  STAGE IIIA              3              10
  STAGE IIIB              1              21
  STAGE IIIC              1              43
  STAGE IV                0              12
[1] 14  2
[1] 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
  NBPF7 MUTATED       4  1  5  2
  NBPF7 WILD-TYPE    47 57 48 53
D31V6, multiclass
       clus
vv      NBPF7 MUTATED NBPF7 WILD-TYPE
  T0+T1             4              47
  T2                1              57
  T3                5              48
  T4                2              53
[1] 4 2
[1] TRUE
[1] "dimension 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
  NBPF7 MUTATED     4   4   4   1
  NBPF7 WILD-TYPE 134  44  28  32
D31V7, multiclass
    clus
vv   NBPF7 MUTATED NBPF7 WILD-TYPE
  N0             4             134
  N1             4              44
  N2             4              28
  N3             1              32
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               M0  M1 M1A M1B M1C
  NBPF7 MUTATED    13   0   0   0   0
  NBPF7 WILD-TYPE 227   4   2   2   5
D31V8, multiclass
     clus
vv    NBPF7 MUTATED NBPF7 WILD-TYPE
  M0             13             227
  M1              0               4
  M1A             0               2
  M1B             0               2
  M1C             0               5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V9, binary
                 cls
clus               0  1
  NBPF7 MUTATED    9  1
  NBPF7 WILD-TYPE 93 66
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NBPF7 MUTATED      9    1
  NBPF7 WILD-TYPE   93   66
     clus
vv    NBPF7 MUTATED NBPF7 WILD-TYPE
  NO              9              93
  YES             1              66
[1] 2 2
[1] FALSE
D31V10, binary
                 cls
clus                0   1
  NBPF7 MUTATED     2  11
  NBPF7 WILD-TYPE  31 224
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NBPF7 MUTATED      2   11
  NBPF7 WILD-TYPE   31  224
     clus
vv    NBPF7 MUTATED NBPF7 WILD-TYPE
  NO              2              31
  YES            11             224
[1] 2 2
[1] FALSE
D31V11, continuous
D31V12, binary
                 cls
clus                0   1
  NBPF7 MUTATED     6   7
  NBPF7 WILD-TYPE  97 158
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NBPF7 MUTATED      6    7
  NBPF7 WILD-TYPE   97  158
        clus
vv       NBPF7 MUTATED NBPF7 WILD-TYPE
  FEMALE             6              97
  MALE               7             158
[1] 2 2
[1] FALSE
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  NBPF7 MUTATED       0                         0    13
  NBPF7 WILD-TYPE     3                         1   251
D31V13, multiclass
                           clus
vv                          NBPF7 MUTATED NBPF7 WILD-TYPE
  ASIAN                                 0               3
  BLACK OR AFRICAN AMERICAN             0               1
  WHITE                                13             251
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V14, binary
                 cls
clus                0   1
  NBPF7 MUTATED     0  13
  NBPF7 WILD-TYPE   3 248
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NBPF7 MUTATED      0   13
  NBPF7 WILD-TYPE    3  248
                        clus
vv                       NBPF7 MUTATED NBPF7 WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO            13             248
[1] 2 2
[1] FALSE

Clustering(32) Variable = KEL MUTATION ANALYSIS
D32V1, survival
               sevent
clus2             0   1
  KEL MUTATED    19  15
  KEL WILD-TYPE 109 115
  KEL MUTATED KEL WILD-TYPE 
           34           224 
  KEL MUTATED KEL WILD-TYPE 
           15           115 
$`KEL MUTATED`
TCGA-D3-A2JF TCGA-D3-A2JL TCGA-D3-A3ML TCGA-D3-A3MR TCGA-D3-A5GO TCGA-D9-A6EC 
       30.87        92.42         6.31       103.59        47.87        13.22 
TCGA-DA-A3F8 TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A29C 
       14.83        13.22        11.57         1.12         1.35        37.97 
TCGA-EE-A29D TCGA-EE-A2GI TCGA-EE-A2GR TCGA-EE-A2GU TCGA-EE-A2MD TCGA-EE-A2MJ 
       11.15        30.08         1.15        36.33         9.53        63.42 
TCGA-EE-A2MR TCGA-EE-A2MT TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3J5 TCGA-EE-A3JA 
       29.65        23.05        13.81        15.95        21.60        22.22 
TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A198 TCGA-ER-A3PL TCGA-FR-A44A TCGA-FS-A1ZZ 
       33.60        18.61        38.40         1.71        85.74         5.23 
TCGA-FW-A3R5 TCGA-FW-A3TV TCGA-GN-A265 TCGA-GN-A266 
        0.99         0.16        84.72        10.13 

$`KEL WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.47         8.52       111.09        32.42        70.16       110.79 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       28.08        22.55        45.83        81.24        10.29        85.32 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
        8.38        21.14        88.50        68.22        69.90        11.41 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP 
        7.50        36.16         6.31        56.19        64.44        45.11 
TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC 
      114.67        15.25        46.98        46.32        82.29        61.38 
TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E 
       13.32        24.00         9.34        26.37         5.39        80.22 
TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R 
       42.71        15.09        41.10        17.72         8.84        20.48 
TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 
       13.94        52.01         1.55         6.97        23.11         4.01 
TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY 
        2.89         9.90        11.31        48.79        35.80        51.12 
TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 
       10.03        39.19        13.68         9.99        44.52        36.69 
TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 
       25.15         4.93        22.36         6.64        19.36         7.00 
TCGA-DA-A3F5 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EE-A17Y 
       17.56        13.15         0.20         0.00         0.00        10.55 
TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B 
        6.31         8.12        12.20         5.13         4.31        36.07 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B 
        4.34         5.13         9.21         1.18         7.99         9.90 
TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N 
       38.63         8.55         4.41         1.08        27.12         9.50 
TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W 
       12.03         8.09         8.84         9.99         2.43         8.68 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 
        8.09        11.31        49.22        23.90         9.67         8.94 
TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ 
       39.39        34.29        17.98        34.92        47.21        19.43 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP 
       16.01        35.54        28.31        33.83        30.84         5.42 
TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 
       13.02        34.98         8.84        98.27         2.70         6.18 
TCGA-EE-A2MC TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MK 
       47.51        29.46        44.25         7.96        14.56       111.78 
TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MS 
      111.91        56.02        25.08        26.99        21.60        27.16 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE 
        5.56       124.31       122.73        25.84         3.68        30.15 
TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JD 
       12.72         3.22        22.92        21.60        16.14        27.35 
TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A 
        0.46        13.94        31.40        12.95         5.72        76.41 
TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G 
       25.18         3.78         3.52        11.90        11.11       114.15 
TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P 
       34.88         4.21        13.45        28.60        42.84        34.68 
TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
        9.57        36.07        17.72        78.44        11.80         1.87 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET 
        1.51        13.08        12.62        11.74         9.04         6.58 
TCGA-ER-A3EV TCGA-FR-A3YN TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY 
       22.49        18.41         4.90        64.47         3.45        11.01 
TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB 
       23.80        14.24        15.52         7.33         7.30         3.39 
TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH 
       20.38         8.22        19.53        11.08         7.17        30.87 
TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR 
       12.92        12.89        47.38        52.08         8.65         8.81 
TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A4F0 
       49.15        40.64         8.68        27.39         0.82        53.85 
TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC 
        7.36        28.73        14.20        10.78         5.98         6.41 
TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
        2.27         0.20         0.13         0.43         9.90         7.23 
TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
       12.85        24.85        31.33        16.24        15.42        12.16 
TCGA-GN-A26D TCGA-QB-A6FS 
       14.70         5.79 

  KEL MUTATED KEL WILD-TYPE 
         0.16          0.00 
  KEL MUTATED KEL WILD-TYPE 
       103.59        124.31 
  KEL MUTATED KEL WILD-TYPE 
        17.28         14.40 
[1] "0.2 - 103.6 (17.3)" "0.0 - 124.3 (14.4)"
[1] "hr=" "1.2"
D32V2, survival
               sevent
clus2             0   1
  KEL MUTATED    20  15
  KEL WILD-TYPE 112 116
  KEL MUTATED KEL WILD-TYPE 
           35           228 
  KEL MUTATED KEL WILD-TYPE 
           15           116 
$`KEL MUTATED`
TCGA-D3-A2JF TCGA-D3-A2JL TCGA-D3-A3ML TCGA-D3-A3MR TCGA-D3-A5GO TCGA-D9-A6EC 
       48.76       171.58        13.87       103.59       137.92        66.25 
TCGA-DA-A3F8 TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A181 TCGA-EE-A182 
       15.68         3.55        52.01        29.82        33.73        14.70 
TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A2GI TCGA-EE-A2GR TCGA-EE-A2GU TCGA-EE-A2MD 
       47.84        13.97        48.72        14.30        94.82        47.28 
TCGA-EE-A2MJ TCGA-EE-A2MR TCGA-EE-A2MT TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3J5 
       96.23       103.56        41.59        13.81        23.47        36.95 
TCGA-EE-A3JA TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A198 TCGA-ER-A3PL TCGA-FR-A44A 
       53.19       148.08        35.44        50.76        33.21       174.21 
TCGA-FS-A1ZZ TCGA-FW-A3R5 TCGA-FW-A3TV TCGA-GN-A265 TCGA-GN-A266 
       27.02        22.92         0.16        84.72        10.13 

$`KEL WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.57        16.67       112.04       112.57        71.80       133.25 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       28.08        31.59        90.90        95.74        43.43       103.10 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
       65.49        23.77       115.53       168.00        69.90        11.87 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP 
      113.52        42.08        12.10        56.19        66.08        45.11 
TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC 
      130.72        58.06        46.98        46.32       166.52        86.93 
TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E 
       60.23        24.53         9.34        39.75        21.47       161.85 
TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R 
       43.69        40.14       131.90        18.38        10.03        51.68 
TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 
       15.06       135.75       166.19         7.43       125.19       151.53 
TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 
       54.67         3.65         6.41        11.34         3.25         9.90 
TCGA-D9-A6EA TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 
       25.18        48.89        36.03       117.21        20.38       194.83 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA 
      176.55        35.93       107.34        61.18        53.92        65.92 
TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-EB-A44Q 
       23.44        68.09        28.60        10.49       215.44        13.87 
TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 
       10.16        45.11        35.01        27.22         8.65        94.98 
TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F 
       26.89        68.15         4.96       109.64       151.27        78.87 
TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29E TCGA-EE-A29G 
      168.26        13.55        63.35        80.61        39.62        72.07 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
       32.19         2.60        44.35        18.61        56.42        37.35 
TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 
       14.47        55.92        25.87       171.55        17.92        46.82 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC 
      102.90        24.43        39.29        58.75        47.54        67.43 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
      314.56       135.95       208.04        89.33        54.74        79.66 
TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GS TCGA-EE-A2GT 
       75.48        90.97       101.95        13.91        55.59        44.88 
TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2ME 
       21.67       129.27        28.83        19.76        61.51       103.27 
TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM 
      103.20        16.96       204.66       144.76       203.05       167.90 
TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3AA 
       47.54       248.65        43.23       136.47        53.26       124.31 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AH TCGA-EE-A3J3 
      122.73        25.84         3.68        54.51       138.81       172.18 
TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH 
      127.20        64.08        34.32        27.35        33.40       101.79 
TCGA-ER-A193 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C 
       31.40        13.94         9.17        77.75        98.40        48.89 
TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J 
       12.59        13.02        26.37       268.93       152.35         6.44 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S 
      131.51        61.05        44.05       162.08        50.89        37.25 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF 
      148.18        79.99        43.82        23.34        20.15        16.37 
TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-FR-A3YN 
       31.27        32.05       247.04        80.32        46.98        92.98 
TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
        4.90       216.92        48.59       228.59       202.65        20.91 
TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD 
       28.08         7.79        27.72        48.85       357.37        53.52 
TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK 
       40.27        15.45         9.70        32.75        47.38        23.93 
TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT 
      101.26        74.73       133.55        11.41       148.80        53.16 
TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 
       26.56        49.48        27.09        77.82        66.67        28.73 
TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 
      174.84        12.43        26.73        49.45        77.88         0.20 
TCGA-FW-A3TU TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 
       47.54         2.40         9.90         7.23        14.04       120.46 
TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS 
      117.93        64.44        62.79        32.48        39.58         6.67 

  KEL MUTATED KEL WILD-TYPE 
         0.16          0.20 
  KEL MUTATED KEL WILD-TYPE 
       174.21        357.37 
  KEL MUTATED KEL WILD-TYPE 
        41.59         48.89 
[1] "0.2 - 174.2 (41.6)" "0.2 - 357.4 (48.9)"
[1] "hr=" "1.1"
D32V3, continuous
               vv
clus            DISTANT METASTASIS PRIMARY TUMOR
  KEL MUTATED                    5             1
  KEL WILD-TYPE                 30             3
               vv
clus            REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  KEL MUTATED                                           7                  22
  KEL WILD-TYPE                                        51                 148
D32V4, multiclass
                                           clus
vv                                          KEL MUTATED KEL WILD-TYPE
  DISTANT METASTASIS                                  5            30
  PRIMARY TUMOR                                       1             3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE           7            51
  REGIONAL LYMPH NODE                                22           148
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  KEL MUTATED             1       0       2        4        3        5
  KEL WILD-TYPE           9       6      20        6       21       12
               vv
clus            STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  KEL MUTATED           0         1         1         7          2          1
  KEL WILD-TYPE        10        13         8        24         11         21
               vv
clus            STAGE IIIC STAGE IV
  KEL MUTATED            3        1
  KEL WILD-TYPE         41       11
D32V5, multiclass
             clus
vv            KEL MUTATED KEL WILD-TYPE
  I OR II NOS           1             9
  STAGE 0               0             6
  STAGE I               2            20
  STAGE IA              4             6
  STAGE IB              3            21
  STAGE II              5            12
  STAGE IIA             0            10
  STAGE IIB             1            13
  STAGE IIC             1             8
  STAGE III             7            24
  STAGE IIIA            2            11
  STAGE IIIB            1            21
  STAGE IIIC            3            41
  STAGE IV              1            11
[1] 14  2
[1] 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
  KEL MUTATED       8  6  8  6
  KEL WILD-TYPE    43 52 45 49
D32V6, multiclass
       clus
vv      KEL MUTATED KEL WILD-TYPE
  T0+T1           8            43
  T2              6            52
  T3              8            45
  T4              6            49
[1] 4 2
[1] TRUE
[1] "dimension 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
  KEL MUTATED    19   6   5   1
  KEL WILD-TYPE 119  42  27  32
D32V7, multiclass
    clus
vv   KEL MUTATED KEL WILD-TYPE
  N0          19           119
  N1           6            42
  N2           5            27
  N3           1            32
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             M0  M1 M1A M1B M1C
  KEL MUTATED    32   0   1   0   0
  KEL WILD-TYPE 208   4   1   2   5
D32V8, multiclass
     clus
vv    KEL MUTATED KEL WILD-TYPE
  M0           32           208
  M1            0             4
  M1A           1             1
  M1B           0             2
  M1C           0             5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V9, binary
               cls
clus             0  1
  KEL MUTATED   15  7
  KEL WILD-TYPE 87 60
[1] "tbl2"
               cls
clus            [,1] [,2]
  KEL MUTATED     15    7
  KEL WILD-TYPE   87   60
     clus
vv    KEL MUTATED KEL WILD-TYPE
  NO           15            87
  YES           7            60
[1] 2 2
[1] FALSE
D32V10, binary
               cls
clus              0   1
  KEL MUTATED     5  30
  KEL WILD-TYPE  28 205
[1] "tbl2"
               cls
clus            [,1] [,2]
  KEL MUTATED      5   30
  KEL WILD-TYPE   28  205
     clus
vv    KEL MUTATED KEL WILD-TYPE
  NO            5            28
  YES          30           205
[1] 2 2
[1] FALSE
D32V11, continuous
D32V12, binary
               cls
clus              0   1
  KEL MUTATED     9  26
  KEL WILD-TYPE  94 139
[1] "tbl2"
               cls
clus            [,1] [,2]
  KEL MUTATED      9   26
  KEL WILD-TYPE   94  139
        clus
vv       KEL MUTATED KEL WILD-TYPE
  FEMALE           9            94
  MALE            26           139
[1] 2 2
[1] FALSE
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  KEL MUTATED       0                         0    35
  KEL WILD-TYPE     3                         1   229
D32V13, multiclass
                           clus
vv                          KEL MUTATED KEL WILD-TYPE
  ASIAN                               0             3
  BLACK OR AFRICAN AMERICAN           0             1
  WHITE                              35           229
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V14, binary
               cls
clus              0   1
  KEL MUTATED     1  33
  KEL WILD-TYPE   2 228
[1] "tbl2"
               cls
clus            [,1] [,2]
  KEL MUTATED      1   33
  KEL WILD-TYPE    2  228
                        clus
vv                       KEL MUTATED KEL WILD-TYPE
  HISPANIC OR LATINO               1             2
  NOT HISPANIC OR LATINO          33           228
[1] 2 2
[1] FALSE

Clustering(33) Variable = C7ORF58 MUTATION ANALYSIS
D33V1, survival
                   sevent
clus2                 0   1
  C7ORF58 MUTATED    14  16
  C7ORF58 WILD-TYPE 114 114
  C7ORF58 MUTATED C7ORF58 WILD-TYPE 
               30               228 
  C7ORF58 MUTATED C7ORF58 WILD-TYPE 
               16               114 
$`C7ORF58 MUTATED`
TCGA-D3-A1Q4 TCGA-D3-A3C7 TCGA-D3-A5GO TCGA-DA-A1HV TCGA-DA-A1I0 TCGA-DA-A3F3 
      111.09        46.98        47.87        48.79        10.03         7.00 
TCGA-EE-A29E TCGA-EE-A29P TCGA-EE-A2GB TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GU 
       38.63        12.03        39.39        30.84         5.42        36.33 
TCGA-EE-A2M7 TCGA-EE-A2MD TCGA-EE-A2MR TCGA-EE-A3AA TCGA-EE-A3AE TCGA-EE-A3AF 
        2.70         9.53        29.65       124.31        30.15        13.81 
TCGA-EE-A3AH TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3JD TCGA-ER-A193 TCGA-ER-A198 
       12.72        22.92        21.60        27.35        31.40        38.40 
TCGA-FS-A1ZC TCGA-FS-A4FB TCGA-FW-A3R5 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
       20.38         5.98         0.99        16.24        15.42        12.16 

$`C7ORF58 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       16.47         8.52        32.42        70.16       110.79        28.08 
TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 
       22.55        45.83        81.24        10.29        85.32         8.38 
TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF 
       21.14        88.50        68.22        69.90        11.41        30.87 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO 
        7.50        36.16         6.31        92.42        56.19        64.44 
TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC 
       45.11       114.67        15.25        46.32        82.29        61.38 
TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU 
       13.32        24.00         6.31         9.34       103.59        26.37 
TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K 
        5.39        80.22        42.71        15.09        41.10        17.72 
TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS 
        8.84        20.48        13.94        52.01         1.55         6.97 
TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC 
       23.11         4.01         2.89         9.90        11.31        13.22 
TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 
       35.80        51.12        39.19        13.68         9.99        44.52 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
       36.69        25.15         4.93        22.36         6.64        19.36 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH 
       17.56        14.83        13.15         0.20         0.00         0.00 
TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 
       13.22        11.57        10.55         6.31         8.12         1.12 
TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C 
        1.35        12.20         5.13         4.31        36.07         4.34 
TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C 
        5.13         9.21         1.18         7.99         9.90        37.97 
TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N 
       11.15         8.55         4.41         1.08        27.12         9.50 
TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X 
        8.09         8.84         9.99         2.43         8.68         8.09 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GC 
       11.31        49.22        23.90         9.67         8.94        34.29 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK 
       17.98        34.92        47.21        30.08        19.43        16.01 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT 
       35.54        28.31        33.83         1.15        13.02        34.98 
TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2ME TCGA-EE-A2MG 
        8.84        98.27         6.18        47.51        29.46        44.25 
TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM 
        7.96        14.56        63.42       111.78       111.91        56.02 
TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU 
       25.08        26.99        21.60        27.16        23.05         5.56 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AG TCGA-EE-A3J3 TCGA-EE-A3J5 
      122.73        25.84         3.68        15.95         3.22        21.60 
TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 
       16.14        22.22         0.46        13.94        33.60        18.61 
TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D 
       12.95         5.72        76.41        25.18         3.78         3.52 
TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L 
       11.90        11.11       114.15        34.88         4.21        13.45 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W 
       28.60        42.84        34.68         9.57        36.07        17.72 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG 
       78.44        11.80         1.87         1.51        13.08        12.62 
TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN 
       11.74         9.04         6.58        22.49         1.71        18.41 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 
       85.74         4.90        64.47         3.45        11.01        23.80 
TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZD 
       14.24        15.52         7.33         7.30         3.39         8.22 
TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK 
       19.53        11.08         7.17        30.87        12.92        12.89 
TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT 
       47.38        52.08         8.65         8.81        49.15        40.64 
TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 
        8.68        27.39         0.82         5.23        53.85         7.36 
TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 
       28.73        14.20        10.78         6.41         2.27         0.20 
TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 
        0.13         0.16         0.43         9.90         7.23        12.85 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A26D TCGA-QB-A6FS 
       24.85        31.33        84.72        10.13        14.70         5.79 

  C7ORF58 MUTATED C7ORF58 WILD-TYPE 
             0.99              0.00 
  C7ORF58 MUTATED C7ORF58 WILD-TYPE 
           124.31            122.73 
  C7ORF58 MUTATED C7ORF58 WILD-TYPE 
            22.26             14.07 
[1] "1.0 - 124.3 (22.3)" "0.0 - 122.7 (14.1)"
[1] "hr=" "1.1"
D33V2, survival
                   sevent
clus2                 0   1
  C7ORF58 MUTATED    15  16
  C7ORF58 WILD-TYPE 117 115
  C7ORF58 MUTATED C7ORF58 WILD-TYPE 
               31               232 
  C7ORF58 MUTATED C7ORF58 WILD-TYPE 
               16               115 
$`C7ORF58 MUTATED`
TCGA-D3-A1Q4 TCGA-D3-A3C7 TCGA-D3-A5GO TCGA-D9-A149 TCGA-DA-A1HV TCGA-DA-A1I0 
      112.04        46.98       137.92        54.67        48.89        20.38 
TCGA-DA-A3F3 TCGA-EE-A29E TCGA-EE-A29P TCGA-EE-A2GB TCGA-EE-A2GO TCGA-EE-A2GP 
       10.49        39.62        56.42        47.54       101.95        13.91 
TCGA-EE-A2GU TCGA-EE-A2M7 TCGA-EE-A2MD TCGA-EE-A2MR TCGA-EE-A3AA TCGA-EE-A3AE 
       94.82        28.83        47.28       103.56       124.31        54.51 
TCGA-EE-A3AF TCGA-EE-A3AH TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3JD TCGA-ER-A193 
       13.81       138.81       127.20        64.08        27.35        31.40 
TCGA-ER-A198 TCGA-FS-A1ZC TCGA-FS-A4FB TCGA-FW-A3R5 TCGA-GN-A267 TCGA-GN-A268 
       50.76       357.37        26.73        22.92        64.44        62.79 
TCGA-GN-A26A 
       32.48 

$`C7ORF58 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       16.57        16.67       112.57        71.80       133.25        28.08 
TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 
       31.59        90.90        95.74        43.43       103.10        65.49 
TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF 
       23.77       115.53       168.00        69.90        11.87        48.76 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO 
      113.52        42.08        12.10       171.58        56.19        66.08 
TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC 
       45.11       130.72        58.06        46.32       166.52        86.93 
TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU 
       60.23        24.53        13.87         9.34       103.59        39.75 
TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K 
       21.47       161.85        43.69        40.14       131.90        18.38 
TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS 
       10.03        51.68        15.06       135.75       166.19         7.43 
TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 
      125.19       151.53         3.65         6.41        11.34         3.25 
TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I1 
        9.90        25.18        66.25        36.03       117.21       194.83 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA 
      176.55        35.93       107.34        61.18        53.92        65.92 
TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q 
       23.44        68.09        28.60       215.44        15.68        13.87 
TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X 
       10.16        45.11        35.01         3.55        52.01        29.82 
TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 
       27.22         8.65        94.98        33.73        14.70        26.89 
TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H 
       68.15         4.96       109.64       151.27        78.87       168.26 
TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29G 
       13.55        63.35        80.61        47.84        13.97        72.07 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A29R 
       32.19         2.60        44.35        18.61        37.35        14.47 
TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 
       55.92        25.87       171.55        17.92        46.82       102.90 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE 
       24.43        39.29        58.75        67.43       314.56       135.95 
TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM 
      208.04        48.72        89.33        54.74        79.66        75.48 
TCGA-EE-A2GN TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2M5 TCGA-EE-A2M6 
       90.97        14.30        55.59        44.88        21.67       129.27 
TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI 
       19.76        61.51       103.27       103.20        16.96       204.66 
TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP 
       96.23       144.76       203.05       167.90        47.54       248.65 
TCGA-EE-A2MQ TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AC 
       43.23       136.47        41.59        53.26       122.73        25.84 
TCGA-EE-A3AD TCGA-EE-A3AG TCGA-EE-A3J3 TCGA-EE-A3J5 TCGA-EE-A3J8 TCGA-EE-A3JA 
        3.68        23.47       172.18        36.95        34.32        53.19 
TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 
       33.40       101.79       148.08        35.44        13.94         9.17 
TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F 
       77.75        98.40        48.89        12.59        13.02        26.37 
TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N 
      268.93       152.35         6.44       131.51        61.05        44.05 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
      162.08        50.89        37.25       148.18        79.99        43.82 
TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES 
       23.34        20.15        16.37        31.27        32.05       247.04 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
       80.32        46.98        33.21        92.98       174.21         4.90 
TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 
      216.92        48.59       228.59       202.65        20.91        28.08 
TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF 
        7.79        27.72        48.85        53.52        40.27        15.45 
TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP 
        9.70        32.75        47.38        23.93       101.26        74.73 
TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW 
      133.55        11.41       148.80        53.16        26.56        49.48 
TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 
       27.09        27.02        77.82        66.67        28.73       174.84 
TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV 
       12.43        49.45        77.88         0.20        47.54         0.16 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 
        2.40         9.90         7.23        14.04       120.46       117.93 
TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A26D TCGA-QB-A6FS 
       84.72        10.13        39.58         6.67 

  C7ORF58 MUTATED C7ORF58 WILD-TYPE 
            10.49              0.16 
  C7ORF58 MUTATED C7ORF58 WILD-TYPE 
           357.37            314.56 
  C7ORF58 MUTATED C7ORF58 WILD-TYPE 
            50.76             47.69 
[1] "10.5 - 357.4 (50.8)" "0.2 - 314.6 (47.7)" 
[1] "hr=" "1"  
D33V3, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  C7ORF58 MUTATED                    3             0
  C7ORF58 WILD-TYPE                 32             4
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  C7ORF58 MUTATED                                           8
  C7ORF58 WILD-TYPE                                        50
                   vv
clus                REGIONAL LYMPH NODE
  C7ORF58 MUTATED                    21
  C7ORF58 WILD-TYPE                 149
D33V4, multiclass
                                           clus
vv                                          C7ORF58 MUTATED C7ORF58 WILD-TYPE
  DISTANT METASTASIS                                      3                32
  PRIMARY TUMOR                                           0                 4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE               8                50
  REGIONAL LYMPH NODE                                    21               149
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  C7ORF58 MUTATED             2       0       2        2        0        6
  C7ORF58 WILD-TYPE           8       6      20        8       24       11
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  C7ORF58 MUTATED           0         2         1         5          2
  C7ORF58 WILD-TYPE        10        12         8        26         11
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  C7ORF58 MUTATED            5          2        1
  C7ORF58 WILD-TYPE         17         42       11
D33V5, multiclass
             clus
vv            C7ORF58 MUTATED C7ORF58 WILD-TYPE
  I OR II NOS               2                 8
  STAGE 0                   0                 6
  STAGE I                   2                20
  STAGE IA                  2                 8
  STAGE IB                  0                24
  STAGE II                  6                11
  STAGE IIA                 0                10
  STAGE IIB                 2                12
  STAGE IIC                 1                 8
  STAGE III                 5                26
  STAGE IIIA                2                11
  STAGE IIIB                5                17
  STAGE IIIC                2                42
  STAGE IV                  1                11
[1] 14  2
[1] 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
  C7ORF58 MUTATED       7  6  8  6
  C7ORF58 WILD-TYPE    44 52 45 49
D33V6, multiclass
       clus
vv      C7ORF58 MUTATED C7ORF58 WILD-TYPE
  T0+T1               7                44
  T2                  6                52
  T3                  8                45
  T4                  6                49
[1] 4 2
[1] TRUE
[1] "dimension 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
  C7ORF58 MUTATED    15  10   4   2
  C7ORF58 WILD-TYPE 123  38  28  31
D33V7, multiclass
    clus
vv   C7ORF58 MUTATED C7ORF58 WILD-TYPE
  N0              15               123
  N1              10                38
  N2               4                28
  N3               2                31
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1 M1A M1B M1C
  C7ORF58 MUTATED    31   0   1   0   0
  C7ORF58 WILD-TYPE 209   4   1   2   5
D33V8, multiclass
     clus
vv    C7ORF58 MUTATED C7ORF58 WILD-TYPE
  M0               31               209
  M1                0                 4
  M1A               1                 1
  M1B               0                 2
  M1C               0                 5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V9, binary
                   cls
clus                 0  1
  C7ORF58 MUTATED   11  9
  C7ORF58 WILD-TYPE 91 58
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C7ORF58 MUTATED     11    9
  C7ORF58 WILD-TYPE   91   58
     clus
vv    C7ORF58 MUTATED C7ORF58 WILD-TYPE
  NO               11                91
  YES               9                58
[1] 2 2
[1] FALSE
D33V10, binary
                   cls
clus                  0   1
  C7ORF58 MUTATED     6  26
  C7ORF58 WILD-TYPE  27 209
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C7ORF58 MUTATED      6   26
  C7ORF58 WILD-TYPE   27  209
     clus
vv    C7ORF58 MUTATED C7ORF58 WILD-TYPE
  NO                6                27
  YES              26               209
[1] 2 2
[1] FALSE
D33V11, continuous
D33V12, binary
                   cls
clus                  0   1
  C7ORF58 MUTATED    13  19
  C7ORF58 WILD-TYPE  90 146
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C7ORF58 MUTATED     13   19
  C7ORF58 WILD-TYPE   90  146
        clus
vv       C7ORF58 MUTATED C7ORF58 WILD-TYPE
  FEMALE              13                90
  MALE                19               146
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  C7ORF58 MUTATED       0                         0    32
  C7ORF58 WILD-TYPE     3                         1   232
D33V13, multiclass
                           clus
vv                          C7ORF58 MUTATED C7ORF58 WILD-TYPE
  ASIAN                                   0                 3
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  32               232
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V14, binary
                   cls
clus                  0   1
  C7ORF58 MUTATED     0  32
  C7ORF58 WILD-TYPE   3 229
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C7ORF58 MUTATED      0   32
  C7ORF58 WILD-TYPE    3  229
                        clus
vv                       C7ORF58 MUTATED C7ORF58 WILD-TYPE
  HISPANIC OR LATINO                   0                 3
  NOT HISPANIC OR LATINO              32               229
[1] 2 2
[1] FALSE

Clustering(34) Variable = NBPF1 MUTATION ANALYSIS
D34V1, survival
                 sevent
clus2               0   1
  NBPF1 MUTATED    21  16
  NBPF1 WILD-TYPE 107 114
  NBPF1 MUTATED NBPF1 WILD-TYPE 
             37             221 
  NBPF1 MUTATED NBPF1 WILD-TYPE 
             16             114 
$`NBPF1 MUTATED`
TCGA-D3-A1QA TCGA-D3-A2J6 TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D9-A6EC TCGA-DA-A1HV 
       45.83        10.29        88.50        69.90        13.22        48.79 
TCGA-DA-A1I4 TCGA-DA-A3F3 TCGA-EE-A17X TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A20C 
        9.99         7.00        11.57         1.12         1.35         4.34 
TCGA-EE-A20F TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29S 
        5.13        11.15        38.63         4.41         1.08         9.99 
TCGA-EE-A2GB TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GR TCGA-EE-A2M6 TCGA-EE-A2MR 
       39.39        33.83        30.84         1.15        98.27        29.65 
TCGA-EE-A3AA TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3J7 TCGA-EE-A3JD TCGA-EE-A3JI 
      124.31         3.68        13.81        21.60        27.35        33.60 
TCGA-ER-A19F TCGA-ER-A19G TCGA-FS-A1ZA TCGA-FS-A1ZK TCGA-FW-A3R5 TCGA-GN-A265 
       11.11       114.15         7.30        12.89         0.99        84.72 
TCGA-GN-A266 
       10.13 

$`NBPF1 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.47         8.52       111.09        32.42        70.16       110.79 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QB TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 
       28.08        22.55        81.24        85.32         8.38        21.14 
TCGA-D3-A2JB TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK 
       68.22        11.41        30.87         7.50        36.16         6.31 
TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 
       92.42        56.19        64.44        45.11       114.67        15.25 
TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF 
       46.98        46.32        82.29        61.38        13.32        24.00 
TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E 
        6.31         9.34       103.59        26.37         5.39        80.22 
TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R 
       42.71        15.09        41.10        17.72         8.84        20.48 
TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU 
       13.94        52.01        47.87         1.55         6.97        23.11 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-DA-A1HW TCGA-DA-A1HY 
        4.01         2.89         9.90        11.31        35.80        51.12 
TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 
       10.03        39.19        13.68        44.52        36.69        25.15 
TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 
        4.93        22.36         6.64        19.36        17.56        14.83 
TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EE-A17Y 
       13.15         0.20         0.00         0.00        13.22        10.55 
TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B 
        6.31         8.12        12.20         5.13         4.31        36.07 
TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29G 
        9.21         1.18         7.99         9.90        37.97         8.55 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29V 
       27.12         9.50        12.03         8.09         8.84         2.43 
TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 
        8.68         8.09        11.31        49.22        23.90         9.67 
TCGA-EE-A2A6 TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI 
        8.94        34.29        17.98        34.92        47.21        30.08 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GP TCGA-EE-A2GS 
       19.43        16.01        35.54        28.31         5.42        13.02 
TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC 
       34.98        36.33         8.84         2.70         6.18        47.51 
TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ 
        9.53        29.46        44.25         7.96        14.56        63.42 
TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ 
      111.78       111.91        56.02        25.08        26.99        21.60 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AE 
       27.16        23.05         5.56       122.73        25.84        30.15 
TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J8 
       15.95        12.72         3.22        22.92        21.60        16.14 
TCGA-EE-A3JA TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 
       22.22         0.46        13.94        31.40        18.61        12.95 
TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D 
       38.40         5.72        76.41        25.18         3.78         3.52 
TCGA-ER-A19E TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N 
       11.90        34.88         4.21        13.45        28.60        42.84 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
       34.68         9.57        36.07        17.72        78.44        11.80 
TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES 
        1.87         1.51        13.08        12.62        11.74         9.04 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
        6.58        22.49         1.71        18.41        85.74         4.90 
TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 
       64.47         3.45        11.01        23.80        14.24        15.52 
TCGA-FS-A1Z7 TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF 
        7.33         3.39        20.38         8.22        19.53        11.08 
TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ 
        7.17        30.87        12.92        47.38        52.08         8.65 
TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY 
        8.81        49.15        40.64         8.68        27.39         0.82 
TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 
        5.23        53.85         7.36        28.73        14.20        10.78 
TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV 
        5.98         6.41         2.27         0.20         0.13         0.16 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 
        0.43         9.90         7.23        12.85        24.85        31.33 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS 
       16.24        15.42        12.16        14.70         5.79 

  NBPF1 MUTATED NBPF1 WILD-TYPE 
           0.99            0.00 
  NBPF1 MUTATED NBPF1 WILD-TYPE 
         124.31          122.73 
  NBPF1 MUTATED NBPF1 WILD-TYPE 
          12.89           15.25 
[1] "1.0 - 124.3 (12.9)" "0.0 - 122.7 (15.2)"
[1] "hr=" "1.2"
D34V2, survival
                 sevent
clus2               0   1
  NBPF1 MUTATED    21  16
  NBPF1 WILD-TYPE 111 115
  NBPF1 MUTATED NBPF1 WILD-TYPE 
             37             226 
  NBPF1 MUTATED NBPF1 WILD-TYPE 
             16             115 
$`NBPF1 MUTATED`
TCGA-D3-A1QA TCGA-D3-A2J6 TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D9-A6EC TCGA-DA-A1HV 
       90.90        43.43       115.53        69.90        66.25        48.89 
TCGA-DA-A1I4 TCGA-DA-A3F3 TCGA-EE-A17X TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A20C 
       35.93        10.49        29.82        33.73        14.70       151.27 
TCGA-EE-A20F TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29S 
       78.87        13.97        39.62        32.19         2.60        55.92 
TCGA-EE-A2GB TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GR TCGA-EE-A2M6 TCGA-EE-A2MR 
       47.54        90.97       101.95        14.30       129.27       103.56 
TCGA-EE-A3AA TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3J7 TCGA-EE-A3JD TCGA-EE-A3JI 
      124.31         3.68        13.81        64.08        27.35       148.08 
TCGA-ER-A19F TCGA-ER-A19G TCGA-FS-A1ZA TCGA-FS-A1ZK TCGA-FW-A3R5 TCGA-GN-A265 
       26.37       268.93        27.72        23.93        22.92        84.72 
TCGA-GN-A266 
       10.13 

$`NBPF1 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.57        16.67       112.04       112.57        71.80       133.25 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QB TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 
       28.08        31.59        95.74       103.10        65.49        23.77 
TCGA-D3-A2JB TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK 
      168.00        11.87        48.76       113.52        42.08        12.10 
TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 
      171.58        56.19        66.08        45.11       130.72        58.06 
TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF 
       46.98        46.32       166.52        86.93        60.23        24.53 
TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E 
       13.87         9.34       103.59        39.75        21.47       161.85 
TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R 
       43.69        40.14       131.90        18.38        10.03        51.68 
TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU 
       15.06       135.75       137.92       166.19         7.43       125.19 
TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 
      151.53        54.67         3.65         6.41        11.34         3.25 
TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 
        9.90        25.18        36.03       117.21        20.38       194.83 
TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB 
      176.55       107.34        61.18        53.92        65.92        23.44 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R 
       68.09        28.60       215.44        15.68        13.87        10.16 
TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17Y TCGA-EE-A17Z 
       45.11        35.01         3.55        52.01        27.22         8.65 
TCGA-EE-A180 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20H 
       94.98        26.89        68.15         4.96       109.64       168.26 
TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29G TCGA-EE-A29M 
       13.55        63.35        80.61        47.84        72.07        44.35 
TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29V TCGA-EE-A29W 
       18.61        56.42        37.35        14.47        25.87       171.55 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 
       17.92        46.82       102.90        24.43        39.29        58.75 
TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ 
       67.43       314.56       135.95       208.04        48.72        89.33 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GP TCGA-EE-A2GS TCGA-EE-A2GT 
       54.74        79.66        75.48        13.91        55.59        44.88 
TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD 
       94.82        21.67        28.83        19.76        61.51        47.28 
TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK 
      103.27       103.20        16.96       204.66        96.23       144.76 
TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MS 
      203.05       167.90        47.54       248.65        43.23       136.47 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AE TCGA-EE-A3AG 
       41.59        53.26       122.73        25.84        54.51        23.47 
TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J8 TCGA-EE-A3JA 
      138.81       172.18       127.20        36.95        34.32        53.19 
TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 
       33.40       101.79        31.40        35.44        13.94        50.76 
TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E 
        9.17        77.75        98.40        48.89        12.59        13.02 
TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P 
      152.35         6.44       131.51        61.05        44.05       162.08 
TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
       50.89        37.25       148.18        79.99        43.82        23.34 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET 
       20.15        16.37        31.27        32.05       247.04        80.32 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW 
       46.98        33.21        92.98       174.21         4.90       216.92 
TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 
       48.59       228.59       202.65        20.91        28.08         7.79 
TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG 
       48.85       357.37        53.52        40.27        15.45         9.70 
TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR 
       32.75        47.38       101.26        74.73       133.55        11.41 
TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ 
      148.80        53.16        26.56        49.48        27.09        27.02 
TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB 
       77.82        66.67        28.73       174.84        12.43        26.73 
TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY 
       49.45        77.88         0.20        47.54         0.16         2.40 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A267 
        9.90         7.23        14.04       120.46       117.93        64.44 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS 
       62.79        32.48        39.58         6.67 

  NBPF1 MUTATED NBPF1 WILD-TYPE 
           2.60            0.16 
  NBPF1 MUTATED NBPF1 WILD-TYPE 
         268.93          357.37 
  NBPF1 MUTATED NBPF1 WILD-TYPE 
          43.43           48.74 
[1] "2.6 - 268.9 (43.4)" "0.2 - 357.4 (48.7)"
[1] "hr=" "1"  
D34V3, continuous
                 vv
clus              DISTANT METASTASIS PRIMARY TUMOR
  NBPF1 MUTATED                    4             1
  NBPF1 WILD-TYPE                 31             3
                 vv
clus              REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  NBPF1 MUTATED                                           8                  25
  NBPF1 WILD-TYPE                                        50                 145
D34V4, multiclass
                                           clus
vv                                          NBPF1 MUTATED NBPF1 WILD-TYPE
  DISTANT METASTASIS                                    4              31
  PRIMARY TUMOR                                         1               3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE             8              50
  REGIONAL LYMPH NODE                                  25             145
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  NBPF1 MUTATED             0       2       5        2        1        4
  NBPF1 WILD-TYPE          10       4      17        8       23       13
                 vv
clus              STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  NBPF1 MUTATED           2         1         0         5          2          5
  NBPF1 WILD-TYPE         8        13         9        26         11         17
                 vv
clus              STAGE IIIC STAGE IV
  NBPF1 MUTATED            5        0
  NBPF1 WILD-TYPE         39       12
D34V5, multiclass
             clus
vv            NBPF1 MUTATED NBPF1 WILD-TYPE
  I OR II NOS             0              10
  STAGE 0                 2               4
  STAGE I                 5              17
  STAGE IA                2               8
  STAGE IB                1              23
  STAGE II                4              13
  STAGE IIA               2               8
  STAGE IIB               1              13
  STAGE IIC               0               9
  STAGE III               5              26
  STAGE IIIA              2              11
  STAGE IIIB              5              17
  STAGE IIIC              5              39
  STAGE IV                0              12
[1] 14  2
[1] 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
  NBPF1 MUTATED      10  7  8  5
  NBPF1 WILD-TYPE    41 51 45 50
D34V6, multiclass
       clus
vv      NBPF1 MUTATED NBPF1 WILD-TYPE
  T0+T1            10              41
  T2                7              51
  T3                8              45
  T4                5              50
[1] 4 2
[1] TRUE
[1] "dimension 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
  NBPF1 MUTATED    19   8   7   2
  NBPF1 WILD-TYPE 119  40  25  31
D34V7, multiclass
    clus
vv   NBPF1 MUTATED NBPF1 WILD-TYPE
  N0            19             119
  N1             8              40
  N2             7              25
  N3             2              31
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               M0  M1 M1A M1B M1C
  NBPF1 MUTATED    36   0   0   0   0
  NBPF1 WILD-TYPE 204   4   2   2   5
D34V8, multiclass
     clus
vv    NBPF1 MUTATED NBPF1 WILD-TYPE
  M0             36             204
  M1              0               4
  M1A             0               2
  M1B             0               2
  M1C             0               5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V9, binary
                 cls
clus               0  1
  NBPF1 MUTATED   12  9
  NBPF1 WILD-TYPE 90 58
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NBPF1 MUTATED     12    9
  NBPF1 WILD-TYPE   90   58
     clus
vv    NBPF1 MUTATED NBPF1 WILD-TYPE
  NO             12              90
  YES             9              58
[1] 2 2
[1] FALSE
D34V10, binary
                 cls
clus                0   1
  NBPF1 MUTATED     9  29
  NBPF1 WILD-TYPE  24 206
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NBPF1 MUTATED      9   29
  NBPF1 WILD-TYPE   24  206
     clus
vv    NBPF1 MUTATED NBPF1 WILD-TYPE
  NO              9              24
  YES            29             206
[1] 2 2
[1] FALSE
D34V11, continuous
D34V12, binary
                 cls
clus                0   1
  NBPF1 MUTATED    10  28
  NBPF1 WILD-TYPE  93 137
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NBPF1 MUTATED     10   28
  NBPF1 WILD-TYPE   93  137
        clus
vv       NBPF1 MUTATED NBPF1 WILD-TYPE
  FEMALE            10              93
  MALE              28             137
[1] 2 2
[1] FALSE
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  NBPF1 MUTATED       0                         0    38
  NBPF1 WILD-TYPE     3                         1   226
D34V13, multiclass
                           clus
vv                          NBPF1 MUTATED NBPF1 WILD-TYPE
  ASIAN                                 0               3
  BLACK OR AFRICAN AMERICAN             0               1
  WHITE                                38             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"
D34V14, binary
                 cls
clus                0   1
  NBPF1 MUTATED     0  37
  NBPF1 WILD-TYPE   3 224
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NBPF1 MUTATED      0   37
  NBPF1 WILD-TYPE    3  224
                        clus
vv                       NBPF1 MUTATED NBPF1 WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO            37             224
[1] 2 2
[1] FALSE

Clustering(35) Variable = TMEM216 MUTATION ANALYSIS
D35V1, survival
                   sevent
clus2                 0   1
  TMEM216 MUTATED     4   4
  TMEM216 WILD-TYPE 124 126
  TMEM216 MUTATED TMEM216 WILD-TYPE 
                8               250 
  TMEM216 MUTATED TMEM216 WILD-TYPE 
                4               126 
$`TMEM216 MUTATED`
TCGA-D3-A1Q6 TCGA-D3-A3CB TCGA-DA-A1I8 TCGA-EE-A17Y TCGA-EE-A2A6 TCGA-EE-A2GR 
       70.16        82.29        25.15        10.55         8.94         1.15 
TCGA-ER-A2ND TCGA-ER-A2NH 
        1.87        11.74 

$`TMEM216 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       16.47         8.52       111.09        32.42       110.79        28.08 
TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 
       22.55        45.83        81.24        10.29        85.32         8.38 
TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF 
       21.14        88.50        68.22        69.90        11.41        30.87 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO 
        7.50        36.16         6.31        92.42        56.19        64.44 
TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CC 
       45.11       114.67        15.25        46.98        46.32        61.38 
TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU 
       13.32        24.00         6.31         9.34       103.59        26.37 
TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K 
        5.39        80.22        42.71        15.09        41.10        17.72 
TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR 
        8.84        20.48        13.94        52.01        47.87         1.55 
TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA 
        6.97        23.11         4.01         2.89         9.90        11.31 
TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 
       13.22        48.79        35.80        51.12        10.03        39.19 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IB 
       13.68         9.99        44.52        36.69         4.93        22.36 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q 
        6.64        19.36         7.00        17.56        14.83        13.15 
TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Z 
        0.20         0.00         0.00        13.22        11.57         6.31 
TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 
        8.12         1.12         1.35        12.20         5.13         4.31 
TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A 
       36.07         4.34         5.13         9.21         1.18         7.99 
TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H 
        9.90        37.97        11.15        38.63         8.55         4.41 
TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R 
        1.08        27.12         9.50        12.03         8.09         8.84 
TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 
        9.99         2.43         8.68         8.09        11.31        49.22 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE 
       23.90         9.67        39.39        34.29        17.98        34.92 
TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM 
       47.21        30.08        19.43        16.01        35.54        28.31 
TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU 
       33.83        30.84         5.42        13.02        34.98        36.33 
TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD 
        8.84        98.27         2.70         6.18        47.51         9.53 
TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK 
       29.46        44.25         7.96        14.56        63.42       111.78 
TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR 
      111.91        56.02        25.08        26.99        21.60        29.65 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC 
       27.16        23.05         5.56       124.31       122.73        25.84 
TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 
        3.68        30.15        13.81        15.95        12.72         3.22 
TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JD 
       22.92        21.60        21.60        16.14        22.22        27.35 
TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 
        0.46        13.94        33.60        31.40        18.61        12.95 
TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D 
       38.40         5.72        76.41        25.18         3.78         3.52 
TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L 
       11.90        11.11       114.15        34.88         4.21        13.45 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W 
       28.60        42.84        34.68         9.57        36.07        17.72 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES 
       78.44        11.80         1.51        13.08        12.62         9.04 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
        6.58        22.49         1.71        18.41        85.74         4.90 
TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 
       64.47         3.45        11.01        23.80        14.24        15.52 
TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE 
        7.33         7.30         3.39        20.38         8.22        19.53 
TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM 
       11.08         7.17        30.87        12.92        12.89        47.38 
TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU 
       52.08         8.65         8.81        49.15        40.64         8.68 
TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 
       27.39         0.82         5.23        53.85         7.36        28.73 
TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 
       14.20        10.78         5.98         6.41         2.27         0.20 
TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
        0.99         0.13         0.16         0.43         9.90         7.23 
TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 
       12.85        24.85        31.33        84.72        10.13        16.24 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS 
       15.42        12.16        14.70         5.79 

  TMEM216 MUTATED TMEM216 WILD-TYPE 
             1.15              0.00 
  TMEM216 MUTATED TMEM216 WILD-TYPE 
            82.29            124.31 
  TMEM216 MUTATED TMEM216 WILD-TYPE 
           11.145            14.960 
[1] "1.1 - 82.3 (11.1)"  "0.0 - 124.3 (15.0)"
[1] "hr=" "1"  
D35V2, survival
                   sevent
clus2                 0   1
  TMEM216 MUTATED     4   4
  TMEM216 WILD-TYPE 128 127
  TMEM216 MUTATED TMEM216 WILD-TYPE 
                8               255 
  TMEM216 MUTATED TMEM216 WILD-TYPE 
                4               127 
$`TMEM216 MUTATED`
TCGA-D3-A1Q6 TCGA-D3-A3CB TCGA-DA-A1I8 TCGA-EE-A17Y TCGA-EE-A2A6 TCGA-EE-A2GR 
       71.80       166.52        53.92        27.22        58.75        14.30 
TCGA-ER-A2ND TCGA-ER-A2NH 
       23.34        32.05 

$`TMEM216 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       16.57        16.67       112.04       112.57       133.25        28.08 
TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 
       31.59        90.90        95.74        43.43       103.10        65.49 
TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF 
       23.77       115.53       168.00        69.90        11.87        48.76 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO 
      113.52        42.08        12.10       171.58        56.19        66.08 
TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CC 
       45.11       130.72        58.06        46.98        46.32        86.93 
TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU 
       60.23        24.53        13.87         9.34       103.59        39.75 
TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K 
       21.47       161.85        43.69        40.14       131.90        18.38 
TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR 
       10.03        51.68        15.06       135.75       137.92       166.19 
TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX 
        7.43       125.19       151.53        54.67         3.65         6.41 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1HV 
       11.34         3.25         9.90        25.18        66.25        48.89 
TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 
       36.03       117.21        20.38       194.83       176.55        35.93 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
      107.34        61.18        65.92        23.44        68.09        28.60 
TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG 
       10.49       215.44        15.68        13.87        10.16        45.11 
TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A180 
       35.01         3.55        52.01        29.82         8.65        94.98 
TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B 
       33.73        14.70        26.89        68.15         4.96       109.64 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B 
      151.27        78.87       168.26        13.55        63.35        80.61 
TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L 
       47.84        13.97        39.62        72.07        32.19         2.60 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S 
       44.35        18.61        56.42        37.35        14.47        55.92 
TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 
       25.87       171.55        17.92        46.82       102.90        24.43 
TCGA-EE-A2A5 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH 
       39.29        47.54        67.43       314.56       135.95       208.04 
TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN 
       48.72        89.33        54.74        79.66        75.48        90.97 
TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 
      101.95        13.91        55.59        44.88        94.82        21.67 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME 
      129.27        28.83        19.76        61.51        47.28       103.27 
TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML 
      103.20        16.96       204.66        96.23       144.76       203.05 
TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS 
      167.90        47.54       248.65        43.23       103.56       136.47 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD 
       41.59        53.26       124.31       122.73        25.84         3.68 
TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 
       54.51        13.81        23.47       138.81       172.18       127.20 
TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE 
       36.95        64.08        34.32        53.19        27.35        33.40 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 
      101.79       148.08        31.40        35.44        13.94        50.76 
TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E 
        9.17        77.75        98.40        48.89        12.59        13.02 
TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M 
       26.37       268.93       152.35         6.44       131.51        61.05 
TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 
       44.05       162.08        50.89        37.25       148.18        79.99 
TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET 
       43.82        20.15        16.37        31.27       247.04        80.32 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW 
       46.98        33.21        92.98       174.21         4.90       216.92 
TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 
       48.59       228.59       202.65        20.91        28.08         7.79 
TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF 
       27.72        48.85       357.37        53.52        40.27        15.45 
TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP 
        9.70        32.75        47.38        23.93       101.26        74.73 
TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW 
      133.55        11.41       148.80        53.16        26.56        49.48 
TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 
       27.09        27.02        77.82        66.67        28.73       174.84 
TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 
       12.43        26.73        49.45        77.88         0.20        22.92 
TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 
       47.54         0.16         2.40         9.90         7.23        14.04 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 
      120.46       117.93        84.72        10.13        64.44        62.79 
TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS 
       32.48        39.58         6.67 

  TMEM216 MUTATED TMEM216 WILD-TYPE 
            14.30              0.16 
  TMEM216 MUTATED TMEM216 WILD-TYPE 
           166.52            357.37 
  TMEM216 MUTATED TMEM216 WILD-TYPE 
           42.985            48.590 
[1] "14.3 - 166.5 (43.0)" "0.2 - 357.4 (48.6)" 
[1] "hr=" "1.2"
D35V3, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  TMEM216 MUTATED                    1             0
  TMEM216 WILD-TYPE                 34             4
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  TMEM216 MUTATED                                           4
  TMEM216 WILD-TYPE                                        54
                   vv
clus                REGIONAL LYMPH NODE
  TMEM216 MUTATED                     3
  TMEM216 WILD-TYPE                 167
D35V4, multiclass
                                           clus
vv                                          TMEM216 MUTATED TMEM216 WILD-TYPE
  DISTANT METASTASIS                                      1                34
  PRIMARY TUMOR                                           0                 4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE               4                54
  REGIONAL LYMPH NODE                                     3               167
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  TMEM216 MUTATED             1       0       0        1        0        1
  TMEM216 WILD-TYPE           9       6      22        9       24       16
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  TMEM216 MUTATED           0         0         0         1          0
  TMEM216 WILD-TYPE        10        14         9        30         13
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  TMEM216 MUTATED            1          3        0
  TMEM216 WILD-TYPE         21         41       12
D35V5, multiclass
             clus
vv            TMEM216 MUTATED TMEM216 WILD-TYPE
  I OR II NOS               1                 9
  STAGE 0                   0                 6
  STAGE I                   0                22
  STAGE IA                  1                 9
  STAGE IB                  0                24
  STAGE II                  1                16
  STAGE IIA                 0                10
  STAGE IIB                 0                14
  STAGE IIC                 0                 9
  STAGE III                 1                30
  STAGE IIIA                0                13
  STAGE IIIB                1                21
  STAGE IIIC                3                41
  STAGE IV                  0                12
[1] 14  2
[1] 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
  TMEM216 MUTATED       2  1  1  4
  TMEM216 WILD-TYPE    49 57 52 51
D35V6, multiclass
       clus
vv      TMEM216 MUTATED TMEM216 WILD-TYPE
  T0+T1               2                49
  T2                  1                57
  T3                  1                52
  T4                  4                51
[1] 4 2
[1] TRUE
[1] "dimension 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
  TMEM216 MUTATED     3   2   0   3
  TMEM216 WILD-TYPE 135  46  32  30
D35V7, multiclass
    clus
vv   TMEM216 MUTATED TMEM216 WILD-TYPE
  N0               3               135
  N1               2                46
  N2               0                32
  N3               3                30
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1 M1A M1B M1C
  TMEM216 MUTATED     8   0   0   0   0
  TMEM216 WILD-TYPE 232   4   2   2   5
D35V8, multiclass
     clus
vv    TMEM216 MUTATED TMEM216 WILD-TYPE
  M0                8               232
  M1                0                 4
  M1A               0                 2
  M1B               0                 2
  M1C               0                 5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V9, binary
                   cls
clus                 0  1
  TMEM216 MUTATED    3  2
  TMEM216 WILD-TYPE 99 65
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM216 MUTATED      3    2
  TMEM216 WILD-TYPE   99   65
     clus
vv    TMEM216 MUTATED TMEM216 WILD-TYPE
  NO                3                99
  YES               2                65
[1] 2 2
[1] FALSE
D35V10, binary
                   cls
clus                  0   1
  TMEM216 MUTATED     0   8
  TMEM216 WILD-TYPE  33 227
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM216 MUTATED      0    8
  TMEM216 WILD-TYPE   33  227
     clus
vv    TMEM216 MUTATED TMEM216 WILD-TYPE
  NO                0                33
  YES               8               227
[1] 2 2
[1] FALSE
D35V11, continuous
D35V12, binary
                   cls
clus                  0   1
  TMEM216 MUTATED     2   6
  TMEM216 WILD-TYPE 101 159
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM216 MUTATED      2    6
  TMEM216 WILD-TYPE  101  159
        clus
vv       TMEM216 MUTATED TMEM216 WILD-TYPE
  FEMALE               2               101
  MALE                 6               159
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TMEM216 MUTATED       1                         0     7
  TMEM216 WILD-TYPE     2                         1   257
D35V13, multiclass
                           clus
vv                          TMEM216 MUTATED TMEM216 WILD-TYPE
  ASIAN                                   1                 2
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                   7               257
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V14, binary
                   cls
clus                  0   1
  TMEM216 MUTATED     0   7
  TMEM216 WILD-TYPE   3 254
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM216 MUTATED      0    7
  TMEM216 WILD-TYPE    3  254
                        clus
vv                       TMEM216 MUTATED TMEM216 WILD-TYPE
  HISPANIC OR LATINO                   0                 3
  NOT HISPANIC OR LATINO               7               254
[1] 2 2
[1] FALSE

Clustering(36) Variable = DOM3Z MUTATION ANALYSIS
D36V1, survival
                 sevent
clus2               0   1
  DOM3Z MUTATED     2   4
  DOM3Z WILD-TYPE 126 126
  DOM3Z MUTATED DOM3Z WILD-TYPE 
              6             252 
  DOM3Z MUTATED DOM3Z WILD-TYPE 
              4             126 
$`DOM3Z MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1QA TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D9-A6EC TCGA-EE-A29L 
       16.47        45.83         6.31        15.25        13.22         1.08 

$`DOM3Z WILD-TYPE`
TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
        8.52       111.09        32.42        70.16       110.79        28.08 
TCGA-D3-A1Q9 TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 
       22.55        81.24        10.29        85.32         8.38        21.14 
TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JG 
       88.50        68.22        69.90        11.41        30.87         7.50 
TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ 
       36.16        92.42        56.19        64.44        45.11       114.67 
TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF 
       46.98        46.32        82.29        61.38        13.32        24.00 
TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E 
        6.31         9.34       103.59        26.37         5.39        80.22 
TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R 
       42.71        15.09        41.10        17.72         8.84        20.48 
TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU 
       13.94        52.01        47.87         1.55         6.97        23.11 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-DA-A1HV TCGA-DA-A1HW 
        4.01         2.89         9.90        11.31        48.79        35.80 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 
       51.12        10.03        39.19        13.68         9.99        44.52 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
       36.69        25.15         4.93        22.36         6.64        19.36 
TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG 
        7.00        17.56        14.83        13.15         0.20         0.00 
TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 
        0.00        13.22        11.57        10.55         6.31         8.12 
TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B 
        1.12         1.35        12.20         5.13         4.31        36.07 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B 
        4.34         5.13         9.21         1.18         7.99         9.90 
TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M 
       37.97        11.15        38.63         8.55         4.41        27.12 
TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V 
        9.50        12.03         8.09         8.84         9.99         2.43 
TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 
        8.68         8.09        11.31        49.22        23.90         9.67 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH 
        8.94        39.39        34.29        17.98        34.92        47.21 
TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN 
       30.08        19.43        16.01        35.54        28.31        33.83 
TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU 
       30.84         5.42         1.15        13.02        34.98        36.33 
TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD 
        8.84        98.27         2.70         6.18        47.51         9.53 
TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK 
       29.46        44.25         7.96        14.56        63.42       111.78 
TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR 
      111.91        56.02        25.08        26.99        21.60        29.65 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC 
       27.16        23.05         5.56       124.31       122.73        25.84 
TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 
        3.68        30.15        13.81        15.95        12.72         3.22 
TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JD 
       22.92        21.60        21.60        16.14        22.22        27.35 
TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 
        0.46        13.94        33.60        31.40        18.61        12.95 
TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D 
       38.40         5.72        76.41        25.18         3.78         3.52 
TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L 
       11.90        11.11       114.15        34.88         4.21        13.45 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W 
       28.60        42.84        34.68         9.57        36.07        17.72 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG 
       78.44        11.80         1.87         1.51        13.08        12.62 
TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN 
       11.74         9.04         6.58        22.49         1.71        18.41 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 
       85.74         4.90        64.47         3.45        11.01        23.80 
TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC 
       14.24        15.52         7.33         7.30         3.39        20.38 
TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ 
        8.22        19.53        11.08         7.17        30.87        12.92 
TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS 
       12.89        47.38        52.08         8.65         8.81        49.15 
TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 
       40.64         8.68        27.39         0.82         5.23        53.85 
TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC 
        7.36        28.73        14.20        10.78         5.98         6.41 
TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY 
        2.27         0.20         0.99         0.13         0.16         0.43 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        9.90         7.23        12.85        24.85        31.33        84.72 
TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS 
       10.13        16.24        15.42        12.16        14.70         5.79 

  DOM3Z MUTATED DOM3Z WILD-TYPE 
           1.08            0.00 
  DOM3Z MUTATED DOM3Z WILD-TYPE 
          45.83          124.31 
  DOM3Z MUTATED DOM3Z WILD-TYPE 
         14.235          14.765 
[1] "1.1 - 45.8 (14.2)"  "0.0 - 124.3 (14.8)"
[1] "hr=" "1.7"
D36V2, survival
                 sevent
clus2               0   1
  DOM3Z MUTATED     3   4
  DOM3Z WILD-TYPE 129 127
  DOM3Z MUTATED DOM3Z WILD-TYPE 
              7             256 
  DOM3Z MUTATED DOM3Z WILD-TYPE 
              4             127 
$`DOM3Z MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1QA TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D9-A149 TCGA-D9-A6EC 
       16.57        90.90        12.10        58.06        54.67        66.25 
TCGA-EE-A29L 
        2.60 

$`DOM3Z WILD-TYPE`
TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       16.67       112.04       112.57        71.80       133.25        28.08 
TCGA-D3-A1Q9 TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 
       31.59        95.74        43.43       103.10        65.49        23.77 
TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JG 
      115.53       168.00        69.90        11.87        48.76       113.52 
TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ 
       42.08       171.58        56.19        66.08        45.11       130.72 
TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF 
       46.98        46.32       166.52        86.93        60.23        24.53 
TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E 
       13.87         9.34       103.59        39.75        21.47       161.85 
TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R 
       43.69        40.14       131.90        18.38        10.03        51.68 
TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU 
       15.06       135.75       137.92       166.19         7.43       125.19 
TCGA-D9-A148 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 
      151.53         3.65         6.41        11.34         3.25         9.90 
TCGA-D9-A6EA TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 
       25.18        48.89        36.03       117.21        20.38       194.83 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA 
      176.55        35.93       107.34        61.18        53.92        65.92 
TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 
       23.44        68.09        28.60        10.49       215.44        15.68 
TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN 
       13.87        10.16        45.11        35.01         3.55        52.01 
TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 
       29.82        27.22         8.65        94.98        33.73        14.70 
TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F 
       26.89        68.15         4.96       109.64       151.27        78.87 
TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D 
      168.26        13.55        63.35        80.61        47.84        13.97 
TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P 
       39.62        72.07        32.19        44.35        18.61        56.42 
TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X 
       37.35        14.47        55.92        25.87       171.55        17.92 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB 
       46.82       102.90        24.43        39.29        58.75        47.54 
TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ 
       67.43       314.56       135.95       208.04        48.72        89.33 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP 
       54.74        79.66        75.48        90.97       101.95        13.91 
TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 
       14.30        55.59        44.88        94.82        21.67       129.27 
TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG 
       28.83        19.76        61.51        47.28       103.27       103.20 
TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM 
       16.96       204.66        96.23       144.76       203.05       167.90 
TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT 
       47.54       248.65        43.23       103.56       136.47        41.59 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE 
       53.26       124.31       122.73        25.84         3.68        54.51 
TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 
       13.81        23.47       138.81       172.18       127.20        36.95 
TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH 
       64.08        34.32        53.19        27.35        33.40       101.79 
TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 
      148.08        31.40        35.44        13.94        50.76         9.17 
TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F 
       77.75        98.40        48.89        12.59        13.02        26.37 
TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N 
      268.93       152.35         6.44       131.51        61.05        44.05 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
      162.08        50.89        37.25       148.18        79.99        43.82 
TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES 
       23.34        20.15        16.37        31.27        32.05       247.04 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
       80.32        46.98        33.21        92.98       174.21         4.90 
TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 
      216.92        48.59       228.59       202.65        20.91        28.08 
TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE 
        7.79        27.72        48.85       357.37        53.52        40.27 
TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM 
       15.45         9.70        32.75        47.38        23.93       101.26 
TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU 
       74.73       133.55        11.41       148.80        53.16        26.56 
TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 
       49.48        27.09        27.02        77.82        66.67        28.73 
TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 
      174.84        12.43        26.73        49.45        77.88         0.20 
TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
       22.92        47.54         0.16         2.40         9.90         7.23 
TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 
       14.04       120.46       117.93        84.72        10.13        64.44 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS 
       62.79        32.48        39.58         6.67 

  DOM3Z MUTATED DOM3Z WILD-TYPE 
           2.60            0.16 
  DOM3Z MUTATED DOM3Z WILD-TYPE 
          90.90          357.37 
  DOM3Z MUTATED DOM3Z WILD-TYPE 
         54.670          48.215 
[1] "2.6 - 90.9 (54.7)"  "0.2 - 357.4 (48.2)"
[1] "hr=" "1.8"
D36V3, continuous
                 vv
clus              DISTANT METASTASIS PRIMARY TUMOR
  DOM3Z MUTATED                    0             1
  DOM3Z WILD-TYPE                 35             3
                 vv
clus              REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  DOM3Z MUTATED                                           1                   5
  DOM3Z WILD-TYPE                                        57                 165
D36V4, multiclass
                                           clus
vv                                          DOM3Z MUTATED DOM3Z WILD-TYPE
  DISTANT METASTASIS                                    0              35
  PRIMARY TUMOR                                         1               3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE             1              57
  REGIONAL LYMPH NODE                                   5             165
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  DOM3Z MUTATED             0       0       0        0        2        0
  DOM3Z WILD-TYPE          10       6      22       10       22       17
                 vv
clus              STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DOM3Z MUTATED           0         0         0         0          1          0
  DOM3Z WILD-TYPE        10        14         9        31         12         22
                 vv
clus              STAGE IIIC STAGE IV
  DOM3Z MUTATED            3        0
  DOM3Z WILD-TYPE         41       12
D36V5, multiclass
             clus
vv            DOM3Z MUTATED DOM3Z WILD-TYPE
  I OR II NOS             0              10
  STAGE 0                 0               6
  STAGE I                 0              22
  STAGE IA                0              10
  STAGE IB                2              22
  STAGE II                0              17
  STAGE IIA               0              10
  STAGE IIB               0              14
  STAGE IIC               0               9
  STAGE III               0              31
  STAGE IIIA              1              12
  STAGE IIIB              0              22
  STAGE IIIC              3              41
  STAGE IV                0              12
[1] 14  2
[1] 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
  DOM3Z MUTATED       1  2  1  2
  DOM3Z WILD-TYPE    50 56 52 53
D36V6, multiclass
       clus
vv      DOM3Z MUTATED DOM3Z WILD-TYPE
  T0+T1             1              50
  T2                2              56
  T3                1              52
  T4                2              53
[1] 4 2
[1] TRUE
[1] "dimension 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
  DOM3Z MUTATED     2   2   1   2
  DOM3Z WILD-TYPE 136  46  31  31
D36V7, multiclass
    clus
vv   DOM3Z MUTATED DOM3Z WILD-TYPE
  N0             2             136
  N1             2              46
  N2             1              31
  N3             2              31
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               M0  M1 M1A M1B M1C
  DOM3Z MUTATED     7   0   0   0   0
  DOM3Z WILD-TYPE 233   4   2   2   5
D36V8, multiclass
     clus
vv    DOM3Z MUTATED DOM3Z WILD-TYPE
  M0              7             233
  M1              0               4
  M1A             0               2
  M1B             0               2
  M1C             0               5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V9, binary
                 cls
clus               0  1
  DOM3Z MUTATED    5  2
  DOM3Z WILD-TYPE 97 65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DOM3Z MUTATED      5    2
  DOM3Z WILD-TYPE   97   65
     clus
vv    DOM3Z MUTATED DOM3Z WILD-TYPE
  NO              5              97
  YES             2              65
[1] 2 2
[1] FALSE
D36V10, binary
                 cls
clus                0   1
  DOM3Z MUTATED     0   7
  DOM3Z WILD-TYPE  33 228
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DOM3Z MUTATED      0    7
  DOM3Z WILD-TYPE   33  228
     clus
vv    DOM3Z MUTATED DOM3Z WILD-TYPE
  NO              0              33
  YES             7             228
[1] 2 2
[1] FALSE
D36V11, continuous
D36V12, binary
                 cls
clus                0   1
  DOM3Z MUTATED     4   3
  DOM3Z WILD-TYPE  99 162
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DOM3Z MUTATED      4    3
  DOM3Z WILD-TYPE   99  162
        clus
vv       DOM3Z MUTATED DOM3Z WILD-TYPE
  FEMALE             4              99
  MALE               3             162
[1] 2 2
[1] FALSE
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DOM3Z MUTATED       0                         0     7
  DOM3Z WILD-TYPE     3                         1   257
D36V13, multiclass
                           clus
vv                          DOM3Z MUTATED DOM3Z WILD-TYPE
  ASIAN                                 0               3
  BLACK OR AFRICAN AMERICAN             0               1
  WHITE                                 7             257
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V14, binary
                 cls
clus                0   1
  DOM3Z MUTATED     0   7
  DOM3Z WILD-TYPE   3 254
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DOM3Z MUTATED      0    7
  DOM3Z WILD-TYPE    3  254
                        clus
vv                       DOM3Z MUTATED DOM3Z WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO             7             254
[1] 2 2
[1] FALSE

Clustering(37) Variable = BCLAF1 MUTATION ANALYSIS
D37V1, survival
                  sevent
clus2                0   1
  BCLAF1 MUTATED    25  20
  BCLAF1 WILD-TYPE 103 110
  BCLAF1 MUTATED BCLAF1 WILD-TYPE 
              45              213 
  BCLAF1 MUTATED BCLAF1 WILD-TYPE 
              20              110 
$`BCLAF1 MUTATED`
TCGA-D3-A1Q6 TCGA-D3-A3C7 TCGA-D3-A3ML TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51T 
       70.16        46.98         6.31       103.59        26.37        13.94 
TCGA-D3-A5GO TCGA-D9-A3Z1 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1HY 
       47.87         4.01        11.31        13.22        48.79        51.12 
TCGA-EE-A181 TCGA-EE-A20C TCGA-EE-A29B TCGA-EE-A29E TCGA-EE-A29L TCGA-EE-A29M 
        1.12         4.34         9.90        38.63         1.08        27.12 
TCGA-EE-A2A0 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GJ 
       11.31        23.90         8.94        34.29        17.98        19.43 
TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2M5 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2MS 
        5.42         1.15         8.84        47.51         9.53        27.16 
TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3JD TCGA-EE-A3JI TCGA-ER-A198 TCGA-ER-A19N 
       13.81        15.95        27.35        33.60        38.40        42.84 
TCGA-ER-A2NC TCGA-FS-A1Z3 TCGA-FS-A1Z7 TCGA-FS-A1ZD TCGA-FS-A4FC TCGA-FW-A3R5 
       11.80        14.24         7.33         8.22         6.41         0.99 
TCGA-FW-A3TU TCGA-GF-A3OT TCGA-GN-A266 
        0.13         9.90        10.13 

$`BCLAF1 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       16.47         8.52       111.09        32.42       110.79        28.08 
TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 
       22.55        45.83        81.24        10.29        85.32         8.38 
TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF 
       21.14        88.50        68.22        69.90        11.41        30.87 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO 
        7.50        36.16         6.31        92.42        56.19        64.44 
TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC 
       45.11       114.67        15.25        46.32        82.29        61.38 
TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F 
       13.32        24.00         9.34         5.39        80.22        42.71 
TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A5GN 
       15.09        41.10        17.72         8.84        20.48        52.01 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-DA-A1HW 
        1.55         6.97        23.11         2.89         9.90        35.80 
TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 
       10.03        39.19        13.68         9.99        44.52        36.69 
TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 
       25.15         4.93        22.36         6.64        19.36         7.00 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH 
       17.56        14.83        13.15         0.20         0.00         0.00 
TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A182 
       13.22        11.57        10.55         6.31         8.12         1.35 
TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H 
       12.20         5.13         4.31        36.07         5.13         9.21 
TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29H 
        1.18         7.99        37.97        11.15         8.55         4.41 
TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V 
        9.50        12.03         8.09         8.84         9.99         2.43 
TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A1 TCGA-EE-A2A5 TCGA-EE-A2GB TCGA-EE-A2GE 
        8.68         8.09        49.22         9.67        39.39        34.92 
TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN 
       47.21        30.08        16.01        35.54        28.31        33.83 
TCGA-EE-A2GO TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 
       30.84        13.02        34.98        36.33        98.27         2.70 
TCGA-EE-A2M8 TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ 
        6.18        29.46        44.25         7.96        14.56        63.42 
TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ 
      111.78       111.91        56.02        25.08        26.99        21.60 
TCGA-EE-A2MR TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC 
       29.65        23.05         5.56       124.31       122.73        25.84 
TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 
        3.68        30.15        12.72         3.22        22.92        21.60 
TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A193 
       21.60        16.14        22.22         0.46        13.94        31.40 
TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C 
       18.61        12.95         5.72        76.41        25.18         3.78 
TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J 
        3.52        11.90        11.11       114.15        34.88         4.21 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W 
       13.45        28.60        34.68         9.57        36.07        17.72 
TCGA-ER-A1A1 TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH 
       78.44         1.87         1.51        13.08        12.62        11.74 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A 
        9.04         6.58        22.49         1.71        18.41        85.74 
TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z4 
        4.90        64.47         3.45        11.01        23.80        15.52 
TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG 
        7.30         3.39        20.38        19.53        11.08         7.17 
TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ 
       30.87        12.92        12.89        47.38        52.08         8.65 
TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY 
        8.81        49.15        40.64         8.68        27.39         0.82 
TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 
        5.23        53.85         7.36        28.73        14.20        10.78 
TCGA-FS-A4FB TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A4EO 
        5.98         2.27         0.20         0.16         0.43         7.23 
TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 
       12.85        24.85        31.33        84.72        16.24        15.42 
TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS 
       12.16        14.70         5.79 

  BCLAF1 MUTATED BCLAF1 WILD-TYPE 
            0.13             0.00 
  BCLAF1 MUTATED BCLAF1 WILD-TYPE 
          103.59           124.31 
  BCLAF1 MUTATED BCLAF1 WILD-TYPE 
           13.81            15.25 
[1] "0.1 - 103.6 (13.8)" "0.0 - 124.3 (15.2)"
[1] "hr=" "1"  
D37V2, survival
                  sevent
clus2                0   1
  BCLAF1 MUTATED    26  20
  BCLAF1 WILD-TYPE 106 111
  BCLAF1 MUTATED BCLAF1 WILD-TYPE 
              46              217 
  BCLAF1 MUTATED BCLAF1 WILD-TYPE 
              20              111 
$`BCLAF1 MUTATED`
TCGA-D3-A1Q6 TCGA-D3-A3C7 TCGA-D3-A3ML TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51T 
       71.80        46.98        13.87       103.59        39.75        15.06 
TCGA-D3-A5GO TCGA-D9-A148 TCGA-D9-A3Z1 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1HV 
      137.92       151.53        11.34        25.18        66.25        48.89 
TCGA-DA-A1HY TCGA-EE-A181 TCGA-EE-A20C TCGA-EE-A29B TCGA-EE-A29E TCGA-EE-A29L 
      117.21        33.73       151.27        80.61        39.62         2.60 
TCGA-EE-A29M TCGA-EE-A2A0 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GC TCGA-EE-A2GD 
       44.35        46.82        24.43        58.75        67.43       314.56 
TCGA-EE-A2GJ TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2M5 TCGA-EE-A2MC TCGA-EE-A2MD 
       89.33        13.91        14.30        21.67        61.51        47.28 
TCGA-EE-A2MS TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3JD TCGA-EE-A3JI TCGA-ER-A198 
      136.47        13.81        23.47        27.35       148.08        50.76 
TCGA-ER-A19N TCGA-ER-A2NC TCGA-FS-A1Z3 TCGA-FS-A1Z7 TCGA-FS-A1ZD TCGA-FS-A4FC 
       44.05        43.82        20.91         7.79        53.52        49.45 
TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-GF-A3OT TCGA-GN-A266 
       22.92        47.54         9.90        10.13 

$`BCLAF1 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       16.57        16.67       112.04       112.57       133.25        28.08 
TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 
       31.59        90.90        95.74        43.43       103.10        65.49 
TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF 
       23.77       115.53       168.00        69.90        11.87        48.76 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO 
      113.52        42.08        12.10       171.58        56.19        66.08 
TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC 
       45.11       130.72        58.06        46.32       166.52        86.93 
TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F 
       60.23        24.53         9.34        21.47       161.85        43.69 
TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A5GN 
       40.14       131.90        18.38        10.03        51.68       135.75 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX 
      166.19         7.43       125.19        54.67         3.65         6.41 
TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-DA-A1HW TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 
        3.25         9.90        36.03        20.38       194.83       176.55 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB 
       35.93       107.34        61.18        53.92        65.92        23.44 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q 
       68.09        28.60        10.49       215.44        15.68        13.87 
TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X 
       10.16        45.11        35.01         3.55        52.01        29.82 
TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 
       27.22         8.65        94.98        14.70        26.89        68.15 
TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A 
        4.96       109.64        78.87       168.26        13.55        63.35 
TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29N TCGA-EE-A29P 
       47.84        13.97        72.07        32.19        18.61        56.42 
TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X 
       37.35        14.47        55.92        25.87       171.55        17.92 
TCGA-EE-A2A1 TCGA-EE-A2A5 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI 
      102.90        39.29        47.54       135.95       208.04        48.72 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GS 
       54.74        79.66        75.48        90.97       101.95        55.59 
TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2ME 
       44.88        94.82       129.27        28.83        19.76       103.27 
TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML 
      103.20        16.96       204.66        96.23       144.76       203.05 
TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MT 
      167.90        47.54       248.65        43.23       103.56        41.59 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE 
       53.26       124.31       122.73        25.84         3.68        54.51 
TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 
      138.81       172.18       127.20        36.95        64.08        34.32 
TCGA-EE-A3JA TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 
       53.19        33.40       101.79        31.40        35.44        13.94 
TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E 
        9.17        77.75        98.40        48.89        12.59        13.02 
TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M 
       26.37       268.93       152.35         6.44       131.51        61.05 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2ND 
      162.08        50.89        37.25       148.18        79.99        23.34 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET 
       20.15        16.37        31.27        32.05       247.04        80.32 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW 
       46.98        33.21        92.98       174.21         4.90       216.92 
TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1ZA TCGA-FS-A1ZB 
       48.59       228.59       202.65        28.08        27.72        48.85 
TCGA-FS-A1ZC TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ 
      357.37        40.27        15.45         9.70        32.75        47.38 
TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS 
       23.93       101.26        74.73       133.55        11.41       148.80 
TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 
       53.16        26.56        49.48        27.09        27.02        77.82 
TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FD 
       66.67        28.73       174.84        12.43        26.73        77.88 
TCGA-FW-A3I3 TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 
        0.20         0.16         2.40         7.23        14.04       120.46 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D 
      117.93        84.72        64.44        62.79        32.48        39.58 
TCGA-QB-A6FS 
        6.67 

  BCLAF1 MUTATED BCLAF1 WILD-TYPE 
            2.60             0.16 
  BCLAF1 MUTATED BCLAF1 WILD-TYPE 
          314.56           357.37 
  BCLAF1 MUTATED BCLAF1 WILD-TYPE 
          45.585           48.890 
[1] "2.6 - 314.6 (45.6)" "0.2 - 357.4 (48.9)"
[1] "hr=" "1"  
D37V3, continuous
                  vv
clus               DISTANT METASTASIS PRIMARY TUMOR
  BCLAF1 MUTATED                    6             2
  BCLAF1 WILD-TYPE                 29             2
                  vv
clus               REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  BCLAF1 MUTATED                                           9
  BCLAF1 WILD-TYPE                                        49
                  vv
clus               REGIONAL LYMPH NODE
  BCLAF1 MUTATED                    29
  BCLAF1 WILD-TYPE                 141
D37V4, multiclass
                                           clus
vv                                          BCLAF1 MUTATED BCLAF1 WILD-TYPE
  DISTANT METASTASIS                                     6               29
  PRIMARY TUMOR                                          2                2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE              9               49
  REGIONAL LYMPH NODE                                   29              141
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  BCLAF1 MUTATED             0       1       3        2        2        5
  BCLAF1 WILD-TYPE          10       5      19        8       22       12
                  vv
clus               STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  BCLAF1 MUTATED           3         3         0         6          3
  BCLAF1 WILD-TYPE         7        11         9        25         10
                  vv
clus               STAGE IIIB STAGE IIIC STAGE IV
  BCLAF1 MUTATED            3          9        1
  BCLAF1 WILD-TYPE         19         35       11
D37V5, multiclass
             clus
vv            BCLAF1 MUTATED BCLAF1 WILD-TYPE
  I OR II NOS              0               10
  STAGE 0                  1                5
  STAGE I                  3               19
  STAGE IA                 2                8
  STAGE IB                 2               22
  STAGE II                 5               12
  STAGE IIA                3                7
  STAGE IIB                3               11
  STAGE IIC                0                9
  STAGE III                6               25
  STAGE IIIA               3               10
  STAGE IIIB               3               19
  STAGE IIIC               9               35
  STAGE IV                 1               11
[1] 14  2
[1] 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
  BCLAF1 MUTATED       7  8 12 10
  BCLAF1 WILD-TYPE    44 50 41 45
D37V6, multiclass
       clus
vv      BCLAF1 MUTATED BCLAF1 WILD-TYPE
  T0+T1              7               44
  T2                 8               50
  T3                12               41
  T4                10               45
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  BCLAF1 MUTATED    20   9   6   7
  BCLAF1 WILD-TYPE 118  39  26  26
D37V7, multiclass
    clus
vv   BCLAF1 MUTATED BCLAF1 WILD-TYPE
  N0             20              118
  N1              9               39
  N2              6               26
  N3              7               26
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                M0  M1 M1A M1B M1C
  BCLAF1 MUTATED    41   1   0   1   0
  BCLAF1 WILD-TYPE 199   3   2   1   5
D37V8, multiclass
     clus
vv    BCLAF1 MUTATED BCLAF1 WILD-TYPE
  M0              41              199
  M1               1                3
  M1A              0                2
  M1B              1                1
  M1C              0                5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V9, binary
                  cls
clus                0  1
  BCLAF1 MUTATED   16 12
  BCLAF1 WILD-TYPE 86 55
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BCLAF1 MUTATED     16   12
  BCLAF1 WILD-TYPE   86   55
     clus
vv    BCLAF1 MUTATED BCLAF1 WILD-TYPE
  NO              16               86
  YES             12               55
[1] 2 2
[1] FALSE
D37V10, binary
                  cls
clus                 0   1
  BCLAF1 MUTATED     9  37
  BCLAF1 WILD-TYPE  24 198
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BCLAF1 MUTATED      9   37
  BCLAF1 WILD-TYPE   24  198
     clus
vv    BCLAF1 MUTATED BCLAF1 WILD-TYPE
  NO               9               24
  YES             37              198
[1] 2 2
[1] FALSE
D37V11, continuous
D37V12, binary
                  cls
clus                 0   1
  BCLAF1 MUTATED    13  33
  BCLAF1 WILD-TYPE  90 132
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BCLAF1 MUTATED     13   33
  BCLAF1 WILD-TYPE   90  132
        clus
vv       BCLAF1 MUTATED BCLAF1 WILD-TYPE
  FEMALE             13               90
  MALE               33              132
[1] 2 2
[1] FALSE
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  BCLAF1 MUTATED       0                         0    46
  BCLAF1 WILD-TYPE     3                         1   218
D37V13, multiclass
                           clus
vv                          BCLAF1 MUTATED BCLAF1 WILD-TYPE
  ASIAN                                  0                3
  BLACK OR AFRICAN AMERICAN              0                1
  WHITE                                 46              218
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V14, binary
                  cls
clus                 0   1
  BCLAF1 MUTATED     0  46
  BCLAF1 WILD-TYPE   3 215
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BCLAF1 MUTATED      0   46
  BCLAF1 WILD-TYPE    3  215
                        clus
vv                       BCLAF1 MUTATED BCLAF1 WILD-TYPE
  HISPANIC OR LATINO                  0                3
  NOT HISPANIC OR LATINO             46              215
[1] 2 2
[1] FALSE

Clustering(38) Variable = ZFX MUTATION ANALYSIS
D38V1, survival
               sevent
clus2             0   1
  ZFX MUTATED     8   5
  ZFX WILD-TYPE 120 125
  ZFX MUTATED ZFX WILD-TYPE 
           13           245 
  ZFX MUTATED ZFX WILD-TYPE 
            5           125 
$`ZFX MUTATED`
TCGA-D3-A2JF TCGA-DA-A1I0 TCGA-EE-A17Z TCGA-EE-A2GC TCGA-EE-A2GO TCGA-EE-A2GR 
       30.87        10.03         6.31        34.29        30.84         1.15 
TCGA-EE-A2GT TCGA-EE-A2MJ TCGA-EE-A3JA TCGA-FS-A1ZT TCGA-FS-A1ZW TCGA-FS-A1ZZ 
       34.98        63.42        22.22        40.64        27.39         5.23 
TCGA-QB-A6FS 
        5.79 

$`ZFX WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.47         8.52       111.09        32.42        70.16       110.79 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       28.08        22.55        45.83        81.24        10.29        85.32 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
        8.38        21.14        88.50        68.22        69.90        11.41 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO 
        7.50        36.16         6.31        92.42        56.19        64.44 
TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB 
       45.11       114.67        15.25        46.98        46.32        82.29 
TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR 
       61.38        13.32        24.00         6.31         9.34       103.59 
TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J 
       26.37         5.39        80.22        42.71        15.09        41.10 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO 
       17.72         8.84        20.48        13.94        52.01        47.87 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 
        1.55         6.97        23.11         4.01         2.89         9.90 
TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I1 
       11.31        13.22        48.79        35.80        51.12        39.19 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA 
       13.68         9.99        44.52        36.69        25.15         4.93 
TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 
       22.36         6.64        19.36         7.00        17.56        14.83 
TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EE-A17X 
       13.15         0.20         0.00         0.00        13.22        11.57 
TCGA-EE-A17Y TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 
       10.55         8.12         1.12         1.35        12.20         5.13 
TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I 
        4.31        36.07         4.34         5.13         9.21         1.18 
TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G 
        7.99         9.90        37.97        11.15        38.63         8.55 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
        4.41         1.08        27.12         9.50        12.03         8.09 
TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 
        8.84         9.99         2.43         8.68         8.09        11.31 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD 
       49.22        23.90         9.67         8.94        39.39        17.98 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
       34.92        47.21        30.08        19.43        16.01        35.54 
TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M5 
       28.31        33.83         5.42        13.02        36.33         8.84 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME 
       98.27         2.70         6.18        47.51         9.53        29.46 
TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM 
       44.25         7.96        14.56       111.78       111.91        56.02 
TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT 
       25.08        26.99        21.60        29.65        27.16        23.05 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE 
        5.56       124.31       122.73        25.84         3.68        30.15 
TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 
       13.81        15.95        12.72         3.22        22.92        21.60 
TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI 
       21.60        16.14        27.35         0.46        13.94        33.60 
TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A 
       31.40        18.61        12.95        38.40         5.72        76.41 
TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G 
       25.18         3.78         3.52        11.90        11.11       114.15 
TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P 
       34.88         4.21        13.45        28.60        42.84        34.68 
TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
        9.57        36.07        17.72        78.44        11.80         1.87 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET 
        1.51        13.08        12.62        11.74         9.04         6.58 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW 
       22.49         1.71        18.41        85.74         4.90        64.47 
TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 
        3.45        11.01        23.80        14.24        15.52         7.33 
TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF 
        7.30         3.39        20.38         8.22        19.53        11.08 
TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP 
        7.17        30.87        12.92        12.89        47.38        52.08 
TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZU TCGA-FS-A1ZY TCGA-FS-A4F0 
        8.65         8.81        49.15         8.68         0.82        53.85 
TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC 
        7.36        28.73        14.20        10.78         5.98         6.41 
TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY 
        2.27         0.20         0.99         0.13         0.16         0.43 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        9.90         7.23        12.85        24.85        31.33        84.72 
TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D 
       10.13        16.24        15.42        12.16        14.70 

  ZFX MUTATED ZFX WILD-TYPE 
         1.15          0.00 
  ZFX MUTATED ZFX WILD-TYPE 
        63.42        124.31 
  ZFX MUTATED ZFX WILD-TYPE 
        27.39         14.56 
[1] "1.1 - 63.4 (27.4)"  "0.0 - 124.3 (14.6)"
[1] "hr=" "1.4"
D38V2, survival
               sevent
clus2             0   1
  ZFX MUTATED     8   5
  ZFX WILD-TYPE 124 126
  ZFX MUTATED ZFX WILD-TYPE 
           13           250 
  ZFX MUTATED ZFX WILD-TYPE 
            5           126 
$`ZFX MUTATED`
TCGA-D3-A2JF TCGA-DA-A1I0 TCGA-EE-A17Z TCGA-EE-A2GC TCGA-EE-A2GO TCGA-EE-A2GR 
       48.76        20.38         8.65        67.43       101.95        14.30 
TCGA-EE-A2GT TCGA-EE-A2MJ TCGA-EE-A3JA TCGA-FS-A1ZT TCGA-FS-A1ZW TCGA-FS-A1ZZ 
       44.88        96.23        53.19        53.16        49.48        27.02 
TCGA-QB-A6FS 
        6.67 

$`ZFX WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.57        16.67       112.04       112.57        71.80       133.25 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       28.08        31.59        90.90        95.74        43.43       103.10 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
       65.49        23.77       115.53       168.00        69.90        11.87 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO 
      113.52        42.08        12.10       171.58        56.19        66.08 
TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB 
       45.11       130.72        58.06        46.98        46.32       166.52 
TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR 
       86.93        60.23        24.53        13.87         9.34       103.59 
TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J 
       39.75        21.47       161.85        43.69        40.14       131.90 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO 
       18.38        10.03        51.68        15.06       135.75       137.92 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW 
      166.19         7.43       125.19       151.53        54.67         3.65 
TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC 
        6.41        11.34         3.25         9.90        25.18        66.25 
TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 
       48.89        36.03       117.21       194.83       176.55        35.93 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC 
      107.34        61.18        53.92        65.92        23.44        68.09 
TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R 
       28.60        10.49       215.44        15.68        13.87        10.16 
TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y 
       45.11        35.01         3.55        52.01        29.82        27.22 
TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 
       94.98        33.73        14.70        26.89        68.15         4.96 
TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A 
      109.64       151.27        78.87       168.26        13.55        63.35 
TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H 
       80.61        47.84        13.97        39.62        72.07        32.19 
TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R 
        2.60        44.35        18.61        56.42        37.35        14.47 
TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 
       55.92        25.87       171.55        17.92        46.82       102.90 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE 
       24.43        39.29        58.75        47.54       314.56       135.95 
TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM 
      208.04        48.72        89.33        54.74        79.66        75.48 
TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 
       90.97        13.91        55.59        94.82        21.67       129.27 
TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG 
       28.83        19.76        61.51        47.28       103.27       103.20 
TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN 
       16.96       204.66       144.76       203.05       167.90        47.54 
TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU 
      248.65        43.23       103.56       136.47        41.59        53.26 
TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF 
      124.31       122.73        25.84         3.68        54.51        13.81 
TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 
       23.47       138.81       172.18       127.20        36.95        64.08 
TCGA-EE-A3J8 TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 
       34.32        27.35        33.40       101.79       148.08        31.40 
TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B 
       35.44        13.94        50.76         9.17        77.75        98.40 
TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H 
       48.89        12.59        13.02        26.37       268.93       152.35 
TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q 
        6.44       131.51        61.05        44.05       162.08        50.89 
TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE 
       37.25       148.18        79.99        43.82        23.34        20.15 
TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV 
       16.37        31.27        32.05       247.04        80.32        46.98 
TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX 
       33.21        92.98       174.21         4.90       216.92        48.59 
TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA 
      228.59       202.65        20.91        28.08         7.79        27.72 
TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG 
       48.85       357.37        53.52        40.27        15.45         9.70 
TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ 
       32.75        47.38        23.93       101.26        74.73       133.55 
TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZU TCGA-FS-A1ZY TCGA-FS-A4F0 TCGA-FS-A4F4 
       11.41       148.80        26.56        27.09        77.82        66.67 
TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD 
       28.73       174.84        12.43        26.73        49.45        77.88 
TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
        0.20        22.92        47.54         0.16         2.40         9.90 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 
        7.23        14.04       120.46       117.93        84.72        10.13 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D 
       64.44        62.79        32.48        39.58 

  ZFX MUTATED ZFX WILD-TYPE 
         6.67          0.16 
  ZFX MUTATED ZFX WILD-TYPE 
       101.95        357.37 
  ZFX MUTATED ZFX WILD-TYPE 
       48.760        48.215 
[1] "6.7 - 102.0 (48.8)" "0.2 - 357.4 (48.2)"
[1] "hr=" "1.1"
D38V3, continuous
               vv
clus            DISTANT METASTASIS PRIMARY TUMOR
  ZFX MUTATED                    3             0
  ZFX WILD-TYPE                 32             4
               vv
clus            REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  ZFX MUTATED                                           3                   7
  ZFX WILD-TYPE                                        55                 163
D38V4, multiclass
                                           clus
vv                                          ZFX MUTATED ZFX WILD-TYPE
  DISTANT METASTASIS                                  3            32
  PRIMARY TUMOR                                       0             4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE           3            55
  REGIONAL LYMPH NODE                                 7           163
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  ZFX MUTATED             0       0       0        1        1        2
  ZFX WILD-TYPE          10       6      22        9       23       15
               vv
clus            STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  ZFX MUTATED           1         3         0         2          0          1
  ZFX WILD-TYPE         9        11         9        29         13         21
               vv
clus            STAGE IIIC STAGE IV
  ZFX MUTATED            1        1
  ZFX WILD-TYPE         43       11
D38V5, multiclass
             clus
vv            ZFX MUTATED ZFX WILD-TYPE
  I OR II NOS           0            10
  STAGE 0               0             6
  STAGE I               0            22
  STAGE IA              1             9
  STAGE IB              1            23
  STAGE II              2            15
  STAGE IIA             1             9
  STAGE IIB             3            11
  STAGE IIC             0             9
  STAGE III             2            29
  STAGE IIIA            0            13
  STAGE IIIB            1            21
  STAGE IIIC            1            43
  STAGE IV              1            11
[1] 14  2
[1] 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
  ZFX MUTATED       2  3  4  4
  ZFX WILD-TYPE    49 55 49 51
D38V6, multiclass
       clus
vv      ZFX MUTATED ZFX WILD-TYPE
  T0+T1           2            49
  T2              3            55
  T3              4            49
  T4              4            51
[1] 4 2
[1] TRUE
[1] "dimension 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
  ZFX MUTATED     9   2   0   2
  ZFX WILD-TYPE 129  46  32  31
D38V7, multiclass
    clus
vv   ZFX MUTATED ZFX WILD-TYPE
  N0           9           129
  N1           2            46
  N2           0            32
  N3           2            31
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             M0  M1 M1A M1B M1C
  ZFX MUTATED    12   0   1   0   0
  ZFX WILD-TYPE 228   4   1   2   5
D38V8, multiclass
     clus
vv    ZFX MUTATED ZFX WILD-TYPE
  M0           12           228
  M1            0             4
  M1A           1             1
  M1B           0             2
  M1C           0             5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V9, binary
               cls
clus             0  1
  ZFX MUTATED    6  4
  ZFX WILD-TYPE 96 63
[1] "tbl2"
               cls
clus            [,1] [,2]
  ZFX MUTATED      6    4
  ZFX WILD-TYPE   96   63
     clus
vv    ZFX MUTATED ZFX WILD-TYPE
  NO            6            96
  YES           4            63
[1] 2 2
[1] FALSE
D38V10, binary
               cls
clus              0   1
  ZFX MUTATED     1  12
  ZFX WILD-TYPE  32 223
[1] "tbl2"
               cls
clus            [,1] [,2]
  ZFX MUTATED      1   12
  ZFX WILD-TYPE   32  223
     clus
vv    ZFX MUTATED ZFX WILD-TYPE
  NO            1            32
  YES          12           223
[1] 2 2
[1] FALSE
D38V11, continuous
D38V12, binary
               cls
clus              0   1
  ZFX MUTATED     2  11
  ZFX WILD-TYPE 101 154
[1] "tbl2"
               cls
clus            [,1] [,2]
  ZFX MUTATED      2   11
  ZFX WILD-TYPE  101  154
        clus
vv       ZFX MUTATED ZFX WILD-TYPE
  FEMALE           2           101
  MALE            11           154
[1] 2 2
[1] FALSE
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ZFX MUTATED       0                         0    13
  ZFX WILD-TYPE     3                         1   251
D38V13, multiclass
                           clus
vv                          ZFX MUTATED ZFX WILD-TYPE
  ASIAN                               0             3
  BLACK OR AFRICAN AMERICAN           0             1
  WHITE                              13           251
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V14, binary
               cls
clus              0   1
  ZFX MUTATED     1  12
  ZFX WILD-TYPE   2 249
[1] "tbl2"
               cls
clus            [,1] [,2]
  ZFX MUTATED      1   12
  ZFX WILD-TYPE    2  249
                        clus
vv                       ZFX MUTATED ZFX WILD-TYPE
  HISPANIC OR LATINO               1             2
  NOT HISPANIC OR LATINO          12           249
[1] 2 2
[1] FALSE

Clustering(39) Variable = BRAF MUTATION ANALYSIS
D39V1, survival
                sevent
clus2             0  1
  BRAF MUTATED   68 61
  BRAF WILD-TYPE 60 69
  BRAF MUTATED BRAF WILD-TYPE 
           129            129 
  BRAF MUTATED BRAF WILD-TYPE 
            61             69 
$`BRAF MUTATED`
TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A1QA 
      111.09        32.42        70.16       110.79        22.55        45.83 
TCGA-D3-A2J7 TCGA-D3-A2JA TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK 
       85.32        88.50        11.41         7.50        36.16         6.31 
TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3CB TCGA-D3-A3CE 
       56.19        45.11        15.25        46.98        82.29        13.32 
TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51F TCGA-D3-A51J TCGA-D3-A51N 
        9.34       103.59        26.37        42.71        41.10         8.84 
TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z3 
       13.94        52.01         1.55         6.97        23.11         2.89 
TCGA-D9-A6E9 TCGA-D9-A6EC TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I2 
        9.90        13.22        35.80        51.12        10.03        13.68 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IB TCGA-DA-A3F5 
        9.99        44.52        36.69        25.15        22.36        17.56 
TCGA-DA-A3F8 TCGA-EB-A5UN TCGA-EE-A17Y TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A20B 
       14.83        13.22        10.55         1.12        12.20        36.07 
TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29H 
        5.13         9.21         7.99        37.97        38.63         4.41 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29W TCGA-EE-A2A0 TCGA-EE-A2A6 
       27.12         9.50        12.03         8.68        11.31         8.94 
TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GM 
       39.39        34.29        34.92        47.21        19.43        28.31 
TCGA-EE-A2GO TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 
       30.84        13.02        34.98         8.84        98.27         2.70 
TCGA-EE-A2M8 TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MK TCGA-EE-A2MP 
        6.18        29.46        44.25         7.96       111.78        26.99 
TCGA-EE-A2MQ TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AG 
       21.60       124.31       122.73         3.68        13.81        15.95 
TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH 
       12.72         3.22        22.92        27.35         0.46        13.94 
TCGA-ER-A193 TCGA-ER-A198 TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19E TCGA-ER-A19F 
       31.40        38.40        25.18         3.78        11.90        11.11 
TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19M TCGA-ER-A19P TCGA-ER-A19Q 
      114.15        34.88         4.21        28.60        34.68         9.57 
TCGA-ER-A19S TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NG TCGA-ER-A3PL TCGA-FR-A44A 
       36.07        11.80         1.87        12.62         1.71        85.74 
TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z7 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZF 
        3.45        11.01         7.33        20.38         8.22        11.08 
TCGA-FS-A1ZH TCGA-FS-A1ZM TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZZ TCGA-FS-A4F8 
       30.87        47.38         8.81        49.15         5.23        14.20 
TCGA-FS-A4FB TCGA-FW-A3R5 TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A4EO TCGA-GF-A6C8 
        5.98         0.99         0.16         0.43         7.23        12.85 
TCGA-GN-A262 TCGA-GN-A265 TCGA-QB-A6FS 
       24.85        84.72         5.79 

$`BRAF WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q8 TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J8 
       16.47         8.52        28.08        81.24        10.29         8.38 
TCGA-D3-A2J9 TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JF TCGA-D3-A2JL TCGA-D3-A2JO 
       21.14        68.22        69.90        30.87        92.42        64.44 
TCGA-D3-A3BZ TCGA-D3-A3C8 TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MV 
      114.67        46.32        61.38        24.00         6.31         5.39 
TCGA-D3-A51E TCGA-D3-A51H TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A5GO TCGA-D9-A3Z1 
       80.22        15.09        17.72        20.48        47.87         4.01 
TCGA-D9-A6EA TCGA-DA-A1HV TCGA-DA-A1I1 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 
       11.31        48.79        39.19         4.93         6.64        19.36 
TCGA-DA-A3F3 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EE-A17X 
        7.00        13.15         0.20         0.00         0.00        11.57 
TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A182 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20C 
        6.31         8.12         1.35         5.13         4.31         4.34 
TCGA-EE-A20I TCGA-EE-A29B TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29L TCGA-EE-A29Q 
        1.18         9.90        11.15         8.55         1.08         8.09 
TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A1 TCGA-EE-A2A2 
        8.84         9.99         2.43         8.09        49.22        23.90 
TCGA-EE-A2A5 TCGA-EE-A2GD TCGA-EE-A2GI TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GN 
        9.67        17.98        30.08        16.01        35.54        33.83 
TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GU TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2MI 
        5.42         1.15        36.33        47.51         9.53        14.56 
TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MR TCGA-EE-A2MS 
       63.42       111.91        56.02        25.08        29.65        27.16 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AC TCGA-EE-A3AE TCGA-EE-A3J5 TCGA-EE-A3J7 
       23.05         5.56        25.84        30.15        21.60        21.60 
TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 
       16.14        22.22        33.60        18.61        12.95         5.72 
TCGA-ER-A19A TCGA-ER-A19D TCGA-ER-A19L TCGA-ER-A19N TCGA-ER-A19W TCGA-ER-A1A1 
       76.41         3.52        13.45        42.84        17.72        78.44 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV 
        1.51        13.08        11.74         9.04         6.58        22.49 
TCGA-FR-A3YN TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 
       18.41         4.90        64.47        23.80        14.24        15.52 
TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZK 
        7.30         3.39        19.53         7.17        12.92        12.89 
TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY 
       52.08         8.65        40.64         8.68        27.39         0.82 
TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FS-A4FD 
       53.85         7.36        28.73        10.78         6.41         2.27 
TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-GF-A3OT TCGA-GN-A264 TCGA-GN-A266 TCGA-GN-A267 
        0.20         0.13         9.90        31.33        10.13        16.24 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D 
       15.42        12.16        14.70 

  BRAF MUTATED BRAF WILD-TYPE 
          0.16           0.00 
  BRAF MUTATED BRAF WILD-TYPE 
        124.31         114.67 
  BRAF MUTATED BRAF WILD-TYPE 
         15.25          14.56 
[1] "0.2 - 124.3 (15.2)" "0.0 - 114.7 (14.6)"
[1] "hr=" "1.3"
D39V2, survival
                sevent
clus2             0  1
  BRAF MUTATED   70 62
  BRAF WILD-TYPE 62 69
  BRAF MUTATED BRAF WILD-TYPE 
           132            131 
  BRAF MUTATED BRAF WILD-TYPE 
            62             69 
$`BRAF MUTATED`
TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A1QA 
      112.04       112.57        71.80       133.25        31.59        90.90 
TCGA-D3-A2J7 TCGA-D3-A2JA TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK 
      103.10       115.53        11.87       113.52        42.08        12.10 
TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3CB TCGA-D3-A3CE 
       56.19        45.11        58.06        46.98       166.52        60.23 
TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51F TCGA-D3-A51J TCGA-D3-A51N 
        9.34       103.59        39.75        43.69       131.90        10.03 
TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 
       15.06       135.75       166.19         7.43       125.19       151.53 
TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EC TCGA-DA-A1HW 
        3.65         6.41         3.25         9.90        66.25        36.03 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 
      117.21        20.38       176.55        35.93       107.34        61.18 
TCGA-DA-A1I8 TCGA-DA-A1IB TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A5UN TCGA-EE-A17Y 
       53.92        23.44       215.44        15.68        52.01        27.22 
TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29A 
       33.73        26.89       109.64        78.87       168.26        63.35 
TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P 
       47.84        39.62        32.19        44.35        18.61        56.42 
TCGA-EE-A29W TCGA-EE-A2A0 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GE 
      171.55        46.82        58.75        47.54        67.43       135.95 
TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GM TCGA-EE-A2GO TCGA-EE-A2GS TCGA-EE-A2GT 
      208.04        89.33        75.48       101.95        55.59        44.88 
TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2ME TCGA-EE-A2MG 
       21.67       129.27        28.83        19.76       103.27       103.20 
TCGA-EE-A2MH TCGA-EE-A2MK TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A3AA TCGA-EE-A3AB 
       16.96       144.76       248.65        43.23       124.31       122.73 
TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 
        3.68        13.81        23.47       138.81       172.18       127.20 
TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A198 TCGA-ER-A19B 
       27.35        33.40       101.79        31.40        50.76        98.40 
TCGA-ER-A19C TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J 
       48.89        13.02        26.37       268.93       152.35         6.44 
TCGA-ER-A19M TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A2NC TCGA-ER-A2ND 
       61.05       162.08        50.89        37.25        43.82        23.34 
TCGA-ER-A2NG TCGA-ER-A3PL TCGA-FR-A44A TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z7 
       31.27        33.21       174.21        48.59       228.59         7.79 
TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZF TCGA-FS-A1ZH TCGA-FS-A1ZM TCGA-FS-A1ZR 
      357.37        53.52        15.45        32.75       101.26        11.41 
TCGA-FS-A1ZS TCGA-FS-A1ZZ TCGA-FS-A4F8 TCGA-FS-A4FB TCGA-FW-A3R5 TCGA-FW-A3TV 
      148.80        27.02       174.84        26.73        22.92         0.16 
TCGA-FW-A5DY TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A265 TCGA-QB-A6FS 
        2.40         7.23        14.04       120.46        84.72         6.67 

$`BRAF WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q8 TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J8 
       16.57        16.67        28.08        95.74        43.43        65.49 
TCGA-D3-A2J9 TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JF TCGA-D3-A2JL TCGA-D3-A2JO 
       23.77       168.00        69.90        48.76       171.58        66.08 
TCGA-D3-A3BZ TCGA-D3-A3C8 TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MV 
      130.72        46.32        86.93        24.53        13.87        21.47 
TCGA-D3-A51E TCGA-D3-A51H TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A5GO TCGA-D9-A149 
      161.85        40.14        18.38        51.68       137.92        54.67 
TCGA-D9-A3Z1 TCGA-D9-A6EA TCGA-DA-A1HV TCGA-DA-A1I1 TCGA-DA-A1IA TCGA-DA-A1IC 
       11.34        25.18        48.89       194.83        65.92        68.09 
TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH 
       28.60        10.49        13.87        10.16        45.11        35.01 
TCGA-EB-A5UL TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A182 TCGA-EE-A184 
        3.55        29.82         8.65        94.98        14.70        68.15 
TCGA-EE-A185 TCGA-EE-A20C TCGA-EE-A20I TCGA-EE-A29B TCGA-EE-A29D TCGA-EE-A29G 
        4.96       151.27        13.55        80.61        13.97        72.07 
TCGA-EE-A29L TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29X 
        2.60        37.35        14.47        55.92        25.87        17.92 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2GD TCGA-EE-A2GI TCGA-EE-A2GK 
      102.90        24.43        39.29       314.56        48.72        54.74 
TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GU TCGA-EE-A2MC 
       79.66        90.97        13.91        14.30        94.82        61.51 
TCGA-EE-A2MD TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN 
       47.28       204.66        96.23       203.05       167.90        47.54 
TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AC TCGA-EE-A3AE 
      103.56       136.47        41.59        53.26        25.84        54.51 
TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JI TCGA-ER-A195 
       36.95        64.08        34.32        53.19       148.08        35.44 
TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19D TCGA-ER-A19L TCGA-ER-A19N 
       13.94         9.17        77.75        12.59       131.51        44.05 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NH TCGA-ER-A3ES 
      148.18        79.99        20.15        16.37        32.05       247.04 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-FR-A3YN TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1Z0 
       80.32        46.98        92.98         4.90       216.92       202.65 
TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZE TCGA-FS-A1ZG 
       20.91        28.08        27.72        48.85        40.27         9.70 
TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZT TCGA-FS-A1ZU 
       47.38        23.93        74.73       133.55        53.16        26.56 
TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F9 
       49.48        27.09        77.82        66.67        28.73        12.43 
TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-GF-A3OT TCGA-GN-A264 
       49.45        77.88         0.20        47.54         9.90       117.93 
TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D 
       10.13        64.44        62.79        32.48        39.58 

  BRAF MUTATED BRAF WILD-TYPE 
          0.16           0.20 
  BRAF MUTATED BRAF WILD-TYPE 
        357.37         314.56 
  BRAF MUTATED BRAF WILD-TYPE 
        50.825         47.380 
[1] "0.2 - 357.4 (50.8)" "0.2 - 314.6 (47.4)"
[1] "hr=" "1.3"
D39V3, continuous
                vv
clus             DISTANT METASTASIS PRIMARY TUMOR
  BRAF MUTATED                   11             2
  BRAF WILD-TYPE                 24             2
                vv
clus             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  BRAF MUTATED                                          26                  97
  BRAF WILD-TYPE                                        32                  73
D39V4, multiclass
                                           clus
vv                                          BRAF MUTATED BRAF WILD-TYPE
  DISTANT METASTASIS                                  11             24
  PRIMARY TUMOR                                        2              2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE           26             32
  REGIONAL LYMPH NODE                                 97             73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  BRAF MUTATED             7       2      13        3       13        9
  BRAF WILD-TYPE           3       4       9        7       11        8
                vv
clus             STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  BRAF MUTATED           4         4         4        21          7         10
  BRAF WILD-TYPE         6        10         5        10          6         12
                vv
clus             STAGE IIIC STAGE IV
  BRAF MUTATED           18        7
  BRAF WILD-TYPE         26        5
D39V5, multiclass
             clus
vv            BRAF MUTATED BRAF WILD-TYPE
  I OR II NOS            7              3
  STAGE 0                2              4
  STAGE I               13              9
  STAGE IA               3              7
  STAGE IB              13             11
  STAGE II               9              8
  STAGE IIA              4              6
  STAGE IIB              4             10
  STAGE IIC              4              5
  STAGE III             21             10
  STAGE IIIA             7              6
  STAGE IIIB            10             12
  STAGE IIIC            18             26
  STAGE IV               7              5
[1] 14  2
[1] 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
  BRAF MUTATED      32 32 32 16
  BRAF WILD-TYPE    19 26 21 39
D39V6, multiclass
       clus
vv      BRAF MUTATED BRAF WILD-TYPE
  T0+T1           32             19
  T2              32             26
  T3              32             21
  T4              16             39
[1] 4 2
[1] TRUE
[1] "dimension 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
  BRAF MUTATED   66 31 18 12
  BRAF WILD-TYPE 72 17 14 21
D39V7, multiclass
    clus
vv   BRAF MUTATED BRAF WILD-TYPE
  N0           66             72
  N1           31             17
  N2           18             14
  N3           12             21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              M0  M1 M1A M1B M1C
  BRAF MUTATED   123   1   2   1   4
  BRAF WILD-TYPE 117   3   0   1   1
D39V8, multiclass
     clus
vv    BRAF MUTATED BRAF WILD-TYPE
  M0           123            117
  M1             1              3
  M1A            2              0
  M1B            1              1
  M1C            4              1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V9, binary
                cls
clus              0  1
  BRAF MUTATED   49 30
  BRAF WILD-TYPE 53 37
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRAF MUTATED     49   30
  BRAF WILD-TYPE   53   37
     clus
vv    BRAF MUTATED BRAF WILD-TYPE
  NO            49             53
  YES           30             37
[1] 2 2
[1] FALSE
D39V10, binary
                cls
clus               0   1
  BRAF MUTATED    19 117
  BRAF WILD-TYPE  14 118
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRAF MUTATED     19  117
  BRAF WILD-TYPE   14  118
     clus
vv    BRAF MUTATED BRAF WILD-TYPE
  NO            19             14
  YES          117            118
[1] 2 2
[1] FALSE
D39V11, continuous
D39V12, binary
                cls
clus              0  1
  BRAF MUTATED   54 82
  BRAF WILD-TYPE 49 83
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRAF MUTATED     54   82
  BRAF WILD-TYPE   49   83
        clus
vv       BRAF MUTATED BRAF WILD-TYPE
  FEMALE           54             49
  MALE             82             83
[1] 2 2
[1] FALSE
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  BRAF MUTATED       1                         0   135
  BRAF WILD-TYPE     2                         1   129
D39V13, multiclass
                           clus
vv                          BRAF MUTATED BRAF WILD-TYPE
  ASIAN                                1              2
  BLACK OR AFRICAN AMERICAN            0              1
  WHITE                              135            129
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V14, binary
                cls
clus               0   1
  BRAF MUTATED     1 133
  BRAF WILD-TYPE   2 128
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRAF MUTATED      1  133
  BRAF WILD-TYPE    2  128
                        clus
vv                       BRAF MUTATED BRAF WILD-TYPE
  HISPANIC OR LATINO                1              2
  NOT HISPANIC OR LATINO          133            128
[1] 2 2
[1] FALSE

Clustering(40) Variable = SAG MUTATION ANALYSIS
D40V1, survival
               sevent
clus2             0   1
  SAG MUTATED     5   4
  SAG WILD-TYPE 123 126
  SAG MUTATED SAG WILD-TYPE 
            9           249 
  SAG MUTATED SAG WILD-TYPE 
            4           126 
$`SAG MUTATED`
TCGA-D9-A6EA TCGA-EE-A29M TCGA-EE-A29V TCGA-EE-A2GI TCGA-EE-A2GO TCGA-EE-A2M5 
       11.31        27.12         2.43        30.08        30.84         8.84 
TCGA-EE-A2MC TCGA-EE-A2MR TCGA-FS-A1ZZ 
       47.51        29.65         5.23 

$`SAG WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.47         8.52       111.09        32.42        70.16       110.79 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       28.08        22.55        45.83        81.24        10.29        85.32 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
        8.38        21.14        88.50        68.22        69.90        11.41 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       30.87         7.50        36.16         6.31        92.42        56.19 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 
       64.44        45.11       114.67        15.25        46.98        46.32 
TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO 
       82.29        61.38        13.32        24.00         6.31         9.34 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H 
      103.59        26.37         5.39        80.22        42.71        15.09 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN 
       41.10        17.72         8.84        20.48        13.94        52.01 
TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 
       47.87         1.55         6.97        23.11         4.01         2.89 
TCGA-D9-A6E9 TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 
        9.90        13.22        48.79        35.80        51.12        10.03 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 
       39.19        13.68         9.99        44.52        36.69        25.15 
TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 
        4.93        22.36         6.64        19.36         7.00        17.56 
TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN 
       14.83        13.15         0.20         0.00         0.00        13.22 
TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 
       11.57        10.55         6.31         8.12         1.12         1.35 
TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F 
       12.20         5.13         4.31        36.07         4.34         5.13 
TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D 
        9.21         1.18         7.99         9.90        37.97        11.15 
TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P 
       38.63         8.55         4.41         1.08         9.50        12.03 
TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 
        8.09         8.84         9.99         8.68         8.09        11.31 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC 
       49.22        23.90         9.67         8.94        39.39        34.29 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
       17.98        34.92        47.21        19.43        16.01        35.54 
TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT 
       28.31        33.83         5.42         1.15        13.02        34.98 
TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MD TCGA-EE-A2ME 
       36.33        98.27         2.70         6.18         9.53        29.46 
TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML 
       44.25         7.96        14.56        63.42       111.78       111.91 
TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MS TCGA-EE-A2MT 
       56.02        25.08        26.99        21.60        27.16        23.05 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE 
        5.56       124.31       122.73        25.84         3.68        30.15 
TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 
       13.81        15.95        12.72         3.22        22.92        21.60 
TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH 
       21.60        16.14        22.22        27.35         0.46        13.94 
TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 
       33.60        31.40        18.61        12.95        38.40         5.72 
TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F 
       76.41        25.18         3.78         3.52        11.90        11.11 
TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N 
      114.15        34.88         4.21        13.45        28.60        42.84 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
       34.68         9.57        36.07        17.72        78.44        11.80 
TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES 
        1.87         1.51        13.08        12.62        11.74         9.04 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
        6.58        22.49         1.71        18.41        85.74         4.90 
TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 
       64.47         3.45        11.01        23.80        14.24        15.52 
TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE 
        7.33         7.30         3.39        20.38         8.22        19.53 
TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM 
       11.08         7.17        30.87        12.92        12.89        47.38 
TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU 
       52.08         8.65         8.81        49.15        40.64         8.68 
TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 
       27.39         0.82        53.85         7.36        28.73        14.20 
TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 
       10.78         5.98         6.41         2.27         0.20         0.99 
TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 
        0.13         0.16         0.43         9.90         7.23        12.85 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 
       24.85        31.33        84.72        10.13        16.24        15.42 
TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS 
       12.16        14.70         5.79 

  SAG MUTATED SAG WILD-TYPE 
         2.43          0.00 
  SAG MUTATED SAG WILD-TYPE 
        47.51        124.31 
  SAG MUTATED SAG WILD-TYPE 
        27.12         14.70 
[1] "2.4 - 47.5 (27.1)"  "0.0 - 124.3 (14.7)"
[1] "hr=" "1.1"
D40V2, survival
               sevent
clus2             0   1
  SAG MUTATED     5   4
  SAG WILD-TYPE 127 127
  SAG MUTATED SAG WILD-TYPE 
            9           254 
  SAG MUTATED SAG WILD-TYPE 
            4           127 
$`SAG MUTATED`
TCGA-D9-A6EA TCGA-EE-A29M TCGA-EE-A29V TCGA-EE-A2GI TCGA-EE-A2GO TCGA-EE-A2M5 
       25.18        44.35        25.87        48.72       101.95        21.67 
TCGA-EE-A2MC TCGA-EE-A2MR TCGA-FS-A1ZZ 
       61.51       103.56        27.02 

$`SAG WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.57        16.67       112.04       112.57        71.80       133.25 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       28.08        31.59        90.90        95.74        43.43       103.10 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
       65.49        23.77       115.53       168.00        69.90        11.87 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       48.76       113.52        42.08        12.10       171.58        56.19 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 
       66.08        45.11       130.72        58.06        46.98        46.32 
TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO 
      166.52        86.93        60.23        24.53        13.87         9.34 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H 
      103.59        39.75        21.47       161.85        43.69        40.14 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN 
      131.90        18.38        10.03        51.68        15.06       135.75 
TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 
      137.92       166.19         7.43       125.19       151.53        54.67 
TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EC 
        3.65         6.41        11.34         3.25         9.90        66.25 
TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 
       48.89        36.03       117.21        20.38       194.83       176.55 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB 
       35.93       107.34        61.18        53.92        65.92        23.44 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q 
       68.09        28.60        10.49       215.44        15.68        13.87 
TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X 
       10.16        45.11        35.01         3.55        52.01        29.82 
TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 
       27.22         8.65        94.98        33.73        14.70        26.89 
TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H 
       68.15         4.96       109.64       151.27        78.87       168.26 
TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E 
       13.55        63.35        80.61        47.84        13.97        39.62 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
       72.07        32.19         2.60        18.61        56.42        37.35 
TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 
       14.47        55.92       171.55        17.92        46.82       102.90 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD 
       24.43        39.29        58.75        47.54        67.43       314.56 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM 
      135.95       208.04        89.33        54.74        79.66        75.48 
TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU 
       90.97        13.91        14.30        55.59        44.88        94.82 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG 
      129.27        28.83        19.76        47.28       103.27       103.20 
TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM 
       16.96       204.66        96.23       144.76       203.05       167.90 
TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU 
       47.54       248.65        43.23       136.47        41.59        53.26 
TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF 
      124.31       122.73        25.84         3.68        54.51        13.81 
TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 
       23.47       138.81       172.18       127.20        36.95        64.08 
TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI 
       34.32        53.19        27.35        33.40       101.79       148.08 
TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A 
       31.40        35.44        13.94        50.76         9.17        77.75 
TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G 
       98.40        48.89        12.59        13.02        26.37       268.93 
TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P 
      152.35         6.44       131.51        61.05        44.05       162.08 
TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
       50.89        37.25       148.18        79.99        43.82        23.34 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET 
       20.15        16.37        31.27        32.05       247.04        80.32 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW 
       46.98        33.21        92.98       174.21         4.90       216.92 
TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 
       48.59       228.59       202.65        20.91        28.08         7.79 
TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF 
       27.72        48.85       357.37        53.52        40.27        15.45 
TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP 
        9.70        32.75        47.38        23.93       101.26        74.73 
TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW 
      133.55        11.41       148.80        53.16        26.56        49.48 
TCGA-FS-A1ZY TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 
       27.09        77.82        66.67        28.73       174.84        12.43 
TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU 
       26.73        49.45        77.88         0.20        22.92        47.54 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 
        0.16         2.40         9.90         7.23        14.04       120.46 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
      117.93        84.72        10.13        64.44        62.79        32.48 
TCGA-GN-A26D TCGA-QB-A6FS 
       39.58         6.67 

  SAG MUTATED SAG WILD-TYPE 
        21.67          0.16 
  SAG MUTATED SAG WILD-TYPE 
       103.56        357.37 
  SAG MUTATED SAG WILD-TYPE 
       44.350        48.675 
[1] "21.7 - 103.6 (44.4)" "0.2 - 357.4 (48.7)" 
[1] "hr=" "1.2"
D40V3, continuous
               vv
clus            DISTANT METASTASIS PRIMARY TUMOR
  SAG MUTATED                    2             1
  SAG WILD-TYPE                 33             3
               vv
clus            REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  SAG MUTATED                                           2                   6
  SAG WILD-TYPE                                        56                 164
D40V4, multiclass
                                           clus
vv                                          SAG MUTATED SAG WILD-TYPE
  DISTANT METASTASIS                                  2            33
  PRIMARY TUMOR                                       1             3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE           2            56
  REGIONAL LYMPH NODE                                 6           164
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  SAG MUTATED             1       1       3        1        1        1
  SAG WILD-TYPE           9       5      19        9       23       16
               vv
clus            STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  SAG MUTATED           0         1         0         0          0          0
  SAG WILD-TYPE        10        13         9        31         13         22
               vv
clus            STAGE IIIC STAGE IV
  SAG MUTATED            2        0
  SAG WILD-TYPE         42       12
D40V5, multiclass
             clus
vv            SAG MUTATED SAG WILD-TYPE
  I OR II NOS           1             9
  STAGE 0               1             5
  STAGE I               3            19
  STAGE IA              1             9
  STAGE IB              1            23
  STAGE II              1            16
  STAGE IIA             0            10
  STAGE IIB             1            13
  STAGE IIC             0             9
  STAGE III             0            31
  STAGE IIIA            0            13
  STAGE IIIB            0            22
  STAGE IIIC            2            42
  STAGE IV              0            12
[1] 14  2
[1] 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
  SAG MUTATED       1  4  3  1
  SAG WILD-TYPE    50 54 50 54
D40V6, multiclass
       clus
vv      SAG MUTATED SAG WILD-TYPE
  T0+T1           1            50
  T2              4            54
  T3              3            50
  T4              1            54
[1] 4 2
[1] TRUE
[1] "dimension 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
  SAG MUTATED     9   1   0   1
  SAG WILD-TYPE 129  47  32  32
D40V7, multiclass
    clus
vv   SAG MUTATED SAG WILD-TYPE
  N0           9           129
  N1           1            47
  N2           0            32
  N3           1            32
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             M0  M1 M1A M1B M1C
  SAG MUTATED    11   0   0   0   0
  SAG WILD-TYPE 229   4   2   2   5
D40V8, multiclass
     clus
vv    SAG MUTATED SAG WILD-TYPE
  M0           11           229
  M1            0             4
  M1A           0             2
  M1B           0             2
  M1C           0             5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V9, binary
               cls
clus             0  1
  SAG MUTATED    7  2
  SAG WILD-TYPE 95 65
[1] "tbl2"
               cls
clus            [,1] [,2]
  SAG MUTATED      7    2
  SAG WILD-TYPE   95   65
     clus
vv    SAG MUTATED SAG WILD-TYPE
  NO            7            95
  YES           2            65
[1] 2 2
[1] FALSE
D40V10, binary
               cls
clus              0   1
  SAG MUTATED     0  11
  SAG WILD-TYPE  33 224
[1] "tbl2"
               cls
clus            [,1] [,2]
  SAG MUTATED      0   11
  SAG WILD-TYPE   33  224
     clus
vv    SAG MUTATED SAG WILD-TYPE
  NO            0            33
  YES          11           224
[1] 2 2
[1] FALSE
D40V11, continuous
D40V12, binary
               cls
clus              0   1
  SAG MUTATED     3   8
  SAG WILD-TYPE 100 157
[1] "tbl2"
               cls
clus            [,1] [,2]
  SAG MUTATED      3    8
  SAG WILD-TYPE  100  157
        clus
vv       SAG MUTATED SAG WILD-TYPE
  FEMALE           3           100
  MALE             8           157
[1] 2 2
[1] FALSE
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SAG MUTATED       0                         0    11
  SAG WILD-TYPE     3                         1   253
D40V13, multiclass
                           clus
vv                          SAG MUTATED SAG WILD-TYPE
  ASIAN                               0             3
  BLACK OR AFRICAN AMERICAN           0             1
  WHITE                              11           253
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V14, binary
               cls
clus              0   1
  SAG MUTATED     1  10
  SAG WILD-TYPE   2 251
[1] "tbl2"
               cls
clus            [,1] [,2]
  SAG MUTATED      1   10
  SAG WILD-TYPE    2  251
                        clus
vv                       SAG MUTATED SAG WILD-TYPE
  HISPANIC OR LATINO               1             2
  NOT HISPANIC OR LATINO          10           251
[1] 2 2
[1] FALSE

Clustering(41) Variable = OR51S1 MUTATION ANALYSIS
D41V1, survival
                  sevent
clus2                0   1
  OR51S1 MUTATED    16  13
  OR51S1 WILD-TYPE 112 117
  OR51S1 MUTATED OR51S1 WILD-TYPE 
              29              229 
  OR51S1 MUTATED OR51S1 WILD-TYPE 
              13              117 
$`OR51S1 MUTATED`
TCGA-D3-A2JO TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A51J TCGA-D9-A6EC TCGA-EE-A183 
       64.44        46.98        46.32        41.10        13.22        12.20 
TCGA-EE-A20C TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A2GC TCGA-EE-A2GI 
        4.34         4.41        27.12         9.50        34.29        30.08 
TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2MS TCGA-EE-A2MT 
       30.84         5.42        63.42       111.78        27.16        23.05 
TCGA-EE-A3J5 TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JI TCGA-ER-A19H TCGA-FS-A1Z3 
       21.60        27.35         0.46        33.60        34.88        14.24 
TCGA-FS-A1ZK TCGA-FS-A4F5 TCGA-FW-A3R5 TCGA-GN-A266 TCGA-GN-A268 
       12.89        28.73         0.99        10.13        15.42 

$`OR51S1 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.47         8.52       111.09        32.42        70.16       110.79 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       28.08        22.55        45.83        81.24        10.29        85.32 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
        8.38        21.14        88.50        68.22        69.90        11.41 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       30.87         7.50        36.16         6.31        92.42        56.19 
TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE 
       45.11       114.67        15.25        82.29        61.38        13.32 
TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV 
       24.00         6.31         9.34       103.59        26.37         5.39 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R 
       80.22        42.71        15.09        17.72         8.84        20.48 
TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU 
       13.94        52.01        47.87         1.55         6.97        23.11 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-DA-A1HV TCGA-DA-A1HW 
        4.01         2.89         9.90        11.31        48.79        35.80 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 
       51.12        10.03        39.19        13.68         9.99        44.52 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
       36.69        25.15         4.93        22.36         6.64        19.36 
TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG 
        7.00        17.56        14.83        13.15         0.20         0.00 
TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 
        0.00        13.22        11.57        10.55         6.31         8.12 
TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20F 
        1.12         1.35         5.13         4.31        36.07         5.13 
TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D 
        9.21         1.18         7.99         9.90        37.97        11.15 
TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29L TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R 
       38.63         8.55         1.08        12.03         8.09         8.84 
TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 
        9.99         2.43         8.68         8.09        11.31        49.22 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE 
       23.90         9.67         8.94        39.39        17.98        34.92 
TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN 
       47.21        19.43        16.01        35.54        28.31        33.83 
TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 
        1.15        13.02        34.98        36.33         8.84        98.27 
TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG 
        2.70         6.18        47.51         9.53        29.46        44.25 
TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP 
        7.96        14.56       111.91        56.02        25.08        26.99 
TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC 
       21.60        29.65         5.56       124.31       122.73        25.84 
TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 
        3.68        30.15        13.81        15.95        12.72         3.22 
TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JH TCGA-ER-A193 
       22.92        21.60        16.14        22.22        13.94        31.40 
TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B 
       18.61        12.95        38.40         5.72        76.41        25.18 
TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19J 
        3.78         3.52        11.90        11.11       114.15         4.21 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S 
       13.45        28.60        42.84        34.68         9.57        36.07 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF 
       17.72        78.44        11.80         1.87         1.51        13.08 
TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL 
       12.62        11.74         9.04         6.58        22.49         1.71 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY 
       18.41        85.74         4.90        64.47         3.45        11.01 
TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC 
       23.80        15.52         7.33         7.30         3.39        20.38 
TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ 
        8.22        19.53        11.08         7.17        30.87        12.92 
TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT 
       47.38        52.08         8.65         8.81        49.15        40.64 
TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 
        8.68        27.39         0.82         5.23        53.85         7.36 
TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 
       14.20        10.78         5.98         6.41         2.27         0.20 
TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 
        0.13         0.16         0.43         9.90         7.23        12.85 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A26D 
       24.85        31.33        84.72        16.24        12.16        14.70 
TCGA-QB-A6FS 
        5.79 

  OR51S1 MUTATED OR51S1 WILD-TYPE 
            0.46             0.00 
  OR51S1 MUTATED OR51S1 WILD-TYPE 
          111.78           124.31 
  OR51S1 MUTATED OR51S1 WILD-TYPE 
           27.12            13.94 
[1] "0.5 - 111.8 (27.1)" "0.0 - 124.3 (13.9)"
[1] "hr=" "1.3"
D41V2, survival
                  sevent
clus2                0   1
  OR51S1 MUTATED    16  13
  OR51S1 WILD-TYPE 116 118
  OR51S1 MUTATED OR51S1 WILD-TYPE 
              29              234 
  OR51S1 MUTATED OR51S1 WILD-TYPE 
              13              118 
$`OR51S1 MUTATED`
TCGA-D3-A2JO TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A51J TCGA-D9-A6EC TCGA-EE-A183 
       66.08        46.98        46.32       131.90        66.25        26.89 
TCGA-EE-A20C TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A2GC TCGA-EE-A2GI 
      151.27        32.19        44.35        18.61        67.43        48.72 
TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2MS TCGA-EE-A2MT 
      101.95        13.91        96.23       144.76       136.47        41.59 
TCGA-EE-A3J5 TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JI TCGA-ER-A19H TCGA-FS-A1Z3 
       36.95        27.35        33.40       148.08       152.35        20.91 
TCGA-FS-A1ZK TCGA-FS-A4F5 TCGA-FW-A3R5 TCGA-GN-A266 TCGA-GN-A268 
       23.93        28.73        22.92        10.13        62.79 

$`OR51S1 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.57        16.67       112.04       112.57        71.80       133.25 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       28.08        31.59        90.90        95.74        43.43       103.10 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
       65.49        23.77       115.53       168.00        69.90        11.87 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       48.76       113.52        42.08        12.10       171.58        56.19 
TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE 
       45.11       130.72        58.06       166.52        86.93        60.23 
TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV 
       24.53        13.87         9.34       103.59        39.75        21.47 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R 
      161.85        43.69        40.14        18.38        10.03        51.68 
TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU 
       15.06       135.75       137.92       166.19         7.43       125.19 
TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 
      151.53        54.67         3.65         6.41        11.34         3.25 
TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 
        9.90        25.18        48.89        36.03       117.21        20.38 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 
      194.83       176.55        35.93       107.34        61.18        53.92 
TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 
       65.92        23.44        68.09        28.60        10.49       215.44 
TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL 
       15.68        13.87        10.16        45.11        35.01         3.55 
TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 
       52.01        29.82        27.22         8.65        94.98        33.73 
TCGA-EE-A182 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H 
       14.70        68.15         4.96       109.64        78.87       168.26 
TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E 
       13.55        63.35        80.61        47.84        13.97        39.62 
TCGA-EE-A29G TCGA-EE-A29L TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S 
       72.07         2.60        56.42        37.35        14.47        55.92 
TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 
       25.87       171.55        17.92        46.82       102.90        24.43 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH 
       39.29        58.75        47.54       314.56       135.95       208.04 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GR 
       89.33        54.74        79.66        75.48        90.97        14.30 
TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 
       55.59        44.88        94.82        21.67       129.27        28.83 
TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH 
       19.76        61.51        47.28       103.27       103.20        16.96 
TCGA-EE-A2MI TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ 
      204.66       203.05       167.90        47.54       248.65        43.23 
TCGA-EE-A2MR TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD 
      103.56        53.26       124.31       122.73        25.84         3.68 
TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 
       54.51        13.81        23.47       138.81       172.18       127.20 
TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A195 
       64.08        34.32        53.19       101.79        31.40        35.44 
TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C 
       13.94        50.76         9.17        77.75        98.40        48.89 
TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19J TCGA-ER-A19L 
       12.59        13.02        26.37       268.93         6.44       131.51 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W 
       61.05        44.05       162.08        50.89        37.25       148.18 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG 
       79.99        43.82        23.34        20.15        16.37        31.27 
TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN 
       32.05       247.04        80.32        46.98        33.21        92.98 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 
      174.21         4.90       216.92        48.59       228.59       202.65 
TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD 
       28.08         7.79        27.72        48.85       357.37        53.52 
TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZM 
       40.27        15.45         9.70        32.75        47.38       101.26 
TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU 
       74.73       133.55        11.41       148.80        53.16        26.56 
TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 
       49.48        27.09        27.02        77.82        66.67       174.84 
TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU 
       12.43        26.73        49.45        77.88         0.20        47.54 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 
        0.16         2.40         9.90         7.23        14.04       120.46 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS 
      117.93        84.72        64.44        32.48        39.58         6.67 

  OR51S1 MUTATED OR51S1 WILD-TYPE 
           10.13             0.16 
  OR51S1 MUTATED OR51S1 WILD-TYPE 
          152.35           357.37 
  OR51S1 MUTATED OR51S1 WILD-TYPE 
          46.320           48.805 
[1] "10.1 - 152.3 (46.3)" "0.2 - 357.4 (48.8)" 
[1] "hr=" "1"  
D41V3, continuous
                  vv
clus               DISTANT METASTASIS PRIMARY TUMOR
  OR51S1 MUTATED                    3             1
  OR51S1 WILD-TYPE                 32             3
                  vv
clus               REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  OR51S1 MUTATED                                          10
  OR51S1 WILD-TYPE                                        48
                  vv
clus               REGIONAL LYMPH NODE
  OR51S1 MUTATED                    15
  OR51S1 WILD-TYPE                 155
D41V4, multiclass
                                           clus
vv                                          OR51S1 MUTATED OR51S1 WILD-TYPE
  DISTANT METASTASIS                                     3               32
  PRIMARY TUMOR                                          1                3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE             10               48
  REGIONAL LYMPH NODE                                   15              155
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  OR51S1 MUTATED             1       2       1        2        3        3
  OR51S1 WILD-TYPE           9       4      21        8       21       14
                  vv
clus               STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  OR51S1 MUTATED           0         2         0         7          1
  OR51S1 WILD-TYPE        10        12         9        24         12
                  vv
clus               STAGE IIIB STAGE IIIC STAGE IV
  OR51S1 MUTATED            2          2        1
  OR51S1 WILD-TYPE         20         42       11
D41V5, multiclass
             clus
vv            OR51S1 MUTATED OR51S1 WILD-TYPE
  I OR II NOS              1                9
  STAGE 0                  2                4
  STAGE I                  1               21
  STAGE IA                 2                8
  STAGE IB                 3               21
  STAGE II                 3               14
  STAGE IIA                0               10
  STAGE IIB                2               12
  STAGE IIC                0                9
  STAGE III                7               24
  STAGE IIIA               1               12
  STAGE IIIB               2               20
  STAGE IIIC               2               42
  STAGE IV                 1               11
[1] 14  2
[1] 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
  OR51S1 MUTATED       4  4  5  6
  OR51S1 WILD-TYPE    47 54 48 49
D41V6, multiclass
       clus
vv      OR51S1 MUTATED OR51S1 WILD-TYPE
  T0+T1              4               47
  T2                 4               54
  T3                 5               48
  T4                 6               49
[1] 4 2
[1] TRUE
[1] "dimension 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
  OR51S1 MUTATED    18   6   2   2
  OR51S1 WILD-TYPE 120  42  30  31
D41V7, multiclass
    clus
vv   OR51S1 MUTATED OR51S1 WILD-TYPE
  N0             18              120
  N1              6               42
  N2              2               30
  N3              2               31
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                M0  M1 M1A M1B M1C
  OR51S1 MUTATED    27   1   0   0   0
  OR51S1 WILD-TYPE 213   3   2   2   5
D41V8, multiclass
     clus
vv    OR51S1 MUTATED OR51S1 WILD-TYPE
  M0              27              213
  M1               1                3
  M1A              0                2
  M1B              0                2
  M1C              0                5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V9, binary
                  cls
clus                0  1
  OR51S1 MUTATED   13  4
  OR51S1 WILD-TYPE 89 63
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR51S1 MUTATED     13    4
  OR51S1 WILD-TYPE   89   63
     clus
vv    OR51S1 MUTATED OR51S1 WILD-TYPE
  NO              13               89
  YES              4               63
[1] 2 2
[1] FALSE
D41V10, binary
                  cls
clus                 0   1
  OR51S1 MUTATED     5  24
  OR51S1 WILD-TYPE  28 211
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR51S1 MUTATED      5   24
  OR51S1 WILD-TYPE   28  211
     clus
vv    OR51S1 MUTATED OR51S1 WILD-TYPE
  NO               5               28
  YES             24              211
[1] 2 2
[1] FALSE
D41V11, continuous
D41V12, binary
                  cls
clus                 0   1
  OR51S1 MUTATED    11  18
  OR51S1 WILD-TYPE  92 147
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR51S1 MUTATED     11   18
  OR51S1 WILD-TYPE   92  147
        clus
vv       OR51S1 MUTATED OR51S1 WILD-TYPE
  FEMALE             11               92
  MALE               18              147
[1] 2 2
[1] FALSE
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  OR51S1 MUTATED       0                         0    29
  OR51S1 WILD-TYPE     3                         1   235
D41V13, multiclass
                           clus
vv                          OR51S1 MUTATED OR51S1 WILD-TYPE
  ASIAN                                  0                3
  BLACK OR AFRICAN AMERICAN              0                1
  WHITE                                 29              235
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V14, binary
                  cls
clus                 0   1
  OR51S1 MUTATED     0  29
  OR51S1 WILD-TYPE   3 232
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR51S1 MUTATED      0   29
  OR51S1 WILD-TYPE    3  232
                        clus
vv                       OR51S1 MUTATED OR51S1 WILD-TYPE
  HISPANIC OR LATINO                  0                3
  NOT HISPANIC OR LATINO             29              232
[1] 2 2
[1] FALSE

Clustering(42) Variable = USP17L2 MUTATION ANALYSIS
D42V1, survival
                   sevent
clus2                 0   1
  USP17L2 MUTATED    11  10
  USP17L2 WILD-TYPE 117 120
  USP17L2 MUTATED USP17L2 WILD-TYPE 
               21               237 
  USP17L2 MUTATED USP17L2 WILD-TYPE 
               10               120 
$`USP17L2 MUTATED`
TCGA-D3-A1Q6 TCGA-D3-A2JF TCGA-D3-A3CB TCGA-D9-A6EC TCGA-DA-A1I4 TCGA-EE-A181 
       70.16        30.87        82.29        13.22         9.99         1.12 
TCGA-EE-A20B TCGA-EE-A29M TCGA-EE-A2A2 TCGA-EE-A2GI TCGA-EE-A2MJ TCGA-EE-A2MR 
       36.07        27.12        23.90        30.08        63.42        29.65 
TCGA-EE-A2MU TCGA-EE-A3AH TCGA-ER-A193 TCGA-ER-A199 TCGA-FS-A1ZD TCGA-FS-A4F5 
        5.56        12.72        31.40         5.72         8.22        28.73 
TCGA-FS-A4F9 TCGA-FW-A3R5 TCGA-GN-A266 
       10.78         0.99        10.13 

$`USP17L2 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       16.47         8.52       111.09        32.42       110.79        28.08 
TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 
       22.55        45.83        81.24        10.29        85.32         8.38 
TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JG 
       21.14        88.50        68.22        69.90        11.41         7.50 
TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP 
       36.16         6.31        92.42        56.19        64.44        45.11 
TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CC TCGA-D3-A3CE 
      114.67        15.25        46.98        46.32        61.38        13.32 
TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV 
       24.00         6.31         9.34       103.59        26.37         5.39 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N 
       80.22        42.71        15.09        41.10        17.72         8.84 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS 
       20.48        13.94        52.01        47.87         1.55         6.97 
TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-DA-A1HV 
       23.11         4.01         2.89         9.90        11.31        48.79 
TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I5 
       35.80        51.12        10.03        39.19        13.68        44.52 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
       36.69        25.15         4.93        22.36         6.64        19.36 
TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG 
        7.00        17.56        14.83        13.15         0.20         0.00 
TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 
        0.00        13.22        11.57        10.55         6.31         8.12 
TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20C TCGA-EE-A20F 
        1.35        12.20         5.13         4.31         4.34         5.13 
TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D 
        9.21         1.18         7.99         9.90        37.97        11.15 
TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P 
       38.63         8.55         4.41         1.08         9.50        12.03 
TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X 
        8.09         8.84         9.99         2.43         8.68         8.09 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC 
       11.31        49.22         9.67         8.94        39.39        34.29 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
       17.98        34.92        47.21        19.43        16.01        35.54 
TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS 
       28.31        33.83        30.84         5.42         1.15        13.02 
TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 
       34.98        36.33         8.84        98.27         2.70         6.18 
TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI 
       47.51         9.53        29.46        44.25         7.96        14.56 
TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ 
      111.78       111.91        56.02        25.08        26.99        21.60 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD 
       27.16        23.05       124.31       122.73        25.84         3.68 
TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 
       30.15        13.81        15.95         3.22        22.92        21.60 
TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH 
       21.60        16.14        22.22        27.35         0.46        13.94 
TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19B 
       33.60        18.61        12.95        38.40        76.41        25.18 
TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H 
        3.78         3.52        11.90        11.11       114.15        34.88 
TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q 
        4.21        13.45        28.60        42.84        34.68         9.57 
TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE 
       36.07        17.72        78.44        11.80         1.87         1.51 
TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV 
       13.08        12.62        11.74         9.04         6.58        22.49 
TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX 
        1.71        18.41        85.74         4.90        64.47         3.45 
TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA 
       11.01        23.80        14.24        15.52         7.33         7.30 
TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH 
        3.39        20.38        19.53        11.08         7.17        30.87 
TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR 
       12.92        12.89        47.38        52.08         8.65         8.81 
TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ 
       49.15        40.64         8.68        27.39         0.82         5.23 
TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD 
       53.85         7.36        14.20         5.98         6.41         2.27 
TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
        0.20         0.13         0.16         0.43         9.90         7.23 
TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 
       12.85        24.85        31.33        84.72        16.24        15.42 
TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS 
       12.16        14.70         5.79 

  USP17L2 MUTATED USP17L2 WILD-TYPE 
             0.99              0.00 
  USP17L2 MUTATED USP17L2 WILD-TYPE 
            82.29            124.31 
  USP17L2 MUTATED USP17L2 WILD-TYPE 
             23.9              14.7 
[1] "1.0 - 82.3 (23.9)"  "0.0 - 124.3 (14.7)"
[1] "hr=" "1.1"
D42V2, survival
                   sevent
clus2                 0   1
  USP17L2 MUTATED    11  10
  USP17L2 WILD-TYPE 121 121
  USP17L2 MUTATED USP17L2 WILD-TYPE 
               21               242 
  USP17L2 MUTATED USP17L2 WILD-TYPE 
               10               121 
$`USP17L2 MUTATED`
TCGA-D3-A1Q6 TCGA-D3-A2JF TCGA-D3-A3CB TCGA-D9-A6EC TCGA-DA-A1I4 TCGA-EE-A181 
       71.80        48.76       166.52        66.25        35.93        33.73 
TCGA-EE-A20B TCGA-EE-A29M TCGA-EE-A2A2 TCGA-EE-A2GI TCGA-EE-A2MJ TCGA-EE-A2MR 
      109.64        44.35        24.43        48.72        96.23       103.56 
TCGA-EE-A2MU TCGA-EE-A3AH TCGA-ER-A193 TCGA-ER-A199 TCGA-FS-A1ZD TCGA-FS-A4F5 
       53.26       138.81        31.40         9.17        53.52        28.73 
TCGA-FS-A4F9 TCGA-FW-A3R5 TCGA-GN-A266 
       12.43        22.92        10.13 

$`USP17L2 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       16.57        16.67       112.04       112.57       133.25        28.08 
TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 
       31.59        90.90        95.74        43.43       103.10        65.49 
TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JG 
       23.77       115.53       168.00        69.90        11.87       113.52 
TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP 
       42.08        12.10       171.58        56.19        66.08        45.11 
TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CC TCGA-D3-A3CE 
      130.72        58.06        46.98        46.32        86.93        60.23 
TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV 
       24.53        13.87         9.34       103.59        39.75        21.47 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N 
      161.85        43.69        40.14       131.90        18.38        10.03 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS 
       51.68        15.06       135.75       137.92       166.19         7.43 
TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 
      125.19       151.53        54.67         3.65         6.41        11.34 
TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY 
        3.25         9.90        25.18        48.89        36.03       117.21 
TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 
       20.38       194.83       176.55       107.34        61.18        53.92 
TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 
       65.92        23.44        68.09        28.60        10.49       215.44 
TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL 
       15.68        13.87        10.16        45.11        35.01         3.55 
TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A182 
       52.01        29.82        27.22         8.65        94.98        14.70 
TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H 
       26.89        68.15         4.96       151.27        78.87       168.26 
TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E 
       13.55        63.35        80.61        47.84        13.97        39.62 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
       72.07        32.19         2.60        18.61        56.42        37.35 
TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 
       14.47        55.92        25.87       171.55        17.92        46.82 
TCGA-EE-A2A1 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD 
      102.90        39.29        58.75        47.54        67.43       314.56 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM 
      135.95       208.04        89.33        54.74        79.66        75.48 
TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT 
       90.97       101.95        13.91        14.30        55.59        44.88 
TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC 
       94.82        21.67       129.27        28.83        19.76        61.51 
TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MK 
       47.28       103.27       103.20        16.96       204.66       144.76 
TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MS 
      203.05       167.90        47.54       248.65        43.23       136.47 
TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE 
       41.59       124.31       122.73        25.84         3.68        54.51 
TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 
       13.81        23.47       172.18       127.20        36.95        64.08 
TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI 
       34.32        53.19        27.35        33.40       101.79       148.08 
TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C 
       35.44        13.94        50.76        77.75        98.40        48.89 
TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J 
       12.59        13.02        26.37       268.93       152.35         6.44 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S 
      131.51        61.05        44.05       162.08        50.89        37.25 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF 
      148.18        79.99        43.82        23.34        20.15        16.37 
TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL 
       31.27        32.05       247.04        80.32        46.98        33.21 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY 
       92.98       174.21         4.90       216.92        48.59       228.59 
TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB 
      202.65        20.91        28.08         7.79        27.72        48.85 
TCGA-FS-A1ZC TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ 
      357.37        40.27        15.45         9.70        32.75        47.38 
TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS 
       23.93       101.26        74.73       133.55        11.41       148.80 
TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 
       53.16        26.56        49.48        27.09        27.02        77.82 
TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 
       66.67       174.84        26.73        49.45        77.88         0.20 
TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 
       47.54         0.16         2.40         9.90         7.23        14.04 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
      120.46       117.93        84.72        64.44        62.79        32.48 
TCGA-GN-A26D TCGA-QB-A6FS 
       39.58         6.67 

  USP17L2 MUTATED USP17L2 WILD-TYPE 
             9.17              0.16 
  USP17L2 MUTATED USP17L2 WILD-TYPE 
           166.52            357.37 
  USP17L2 MUTATED USP17L2 WILD-TYPE 
           48.720            48.215 
[1] "9.2 - 166.5 (48.7)" "0.2 - 357.4 (48.2)"
[1] "hr=" "1.1"
D42V3, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  USP17L2 MUTATED                    1             1
  USP17L2 WILD-TYPE                 34             3
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  USP17L2 MUTATED                                           6
  USP17L2 WILD-TYPE                                        52
                   vv
clus                REGIONAL LYMPH NODE
  USP17L2 MUTATED                    13
  USP17L2 WILD-TYPE                 157
D42V4, multiclass
                                           clus
vv                                          USP17L2 MUTATED USP17L2 WILD-TYPE
  DISTANT METASTASIS                                      1                34
  PRIMARY TUMOR                                           1                 3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE               6                52
  REGIONAL LYMPH NODE                                    13               157
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  USP17L2 MUTATED             1       0       1        3        2        3
  USP17L2 WILD-TYPE           9       6      21        7       22       14
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  USP17L2 MUTATED           1         1         0         3          1
  USP17L2 WILD-TYPE         9        13         9        28         12
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  USP17L2 MUTATED            0          4        0
  USP17L2 WILD-TYPE         22         40       12
D42V5, multiclass
             clus
vv            USP17L2 MUTATED USP17L2 WILD-TYPE
  I OR II NOS               1                 9
  STAGE 0                   0                 6
  STAGE I                   1                21
  STAGE IA                  3                 7
  STAGE IB                  2                22
  STAGE II                  3                14
  STAGE IIA                 1                 9
  STAGE IIB                 1                13
  STAGE IIC                 0                 9
  STAGE III                 3                28
  STAGE IIIA                1                12
  STAGE IIIB                0                22
  STAGE IIIC                4                40
  STAGE IV                  0                12
[1] 14  2
[1] 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
  USP17L2 MUTATED       3  5  6  5
  USP17L2 WILD-TYPE    48 53 47 50
D42V6, multiclass
       clus
vv      USP17L2 MUTATED USP17L2 WILD-TYPE
  T0+T1               3                48
  T2                  5                53
  T3                  6                47
  T4                  5                50
[1] 4 2
[1] TRUE
[1] "dimension 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
  USP17L2 MUTATED    13   3   2   2
  USP17L2 WILD-TYPE 125  45  30  31
D42V7, multiclass
    clus
vv   USP17L2 MUTATED USP17L2 WILD-TYPE
  N0              13               125
  N1               3                45
  N2               2                30
  N3               2                31
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1 M1A M1B M1C
  USP17L2 MUTATED    20   0   0   0   0
  USP17L2 WILD-TYPE 220   4   2   2   5
D42V8, multiclass
     clus
vv    USP17L2 MUTATED USP17L2 WILD-TYPE
  M0               20               220
  M1                0                 4
  M1A               0                 2
  M1B               0                 2
  M1C               0                 5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V9, binary
                   cls
clus                 0  1
  USP17L2 MUTATED   10  5
  USP17L2 WILD-TYPE 92 62
[1] "tbl2"
                   cls
clus                [,1] [,2]
  USP17L2 MUTATED     10    5
  USP17L2 WILD-TYPE   92   62
     clus
vv    USP17L2 MUTATED USP17L2 WILD-TYPE
  NO               10                92
  YES               5                62
[1] 2 2
[1] FALSE
D42V10, binary
                   cls
clus                  0   1
  USP17L2 MUTATED     1  20
  USP17L2 WILD-TYPE  32 215
[1] "tbl2"
                   cls
clus                [,1] [,2]
  USP17L2 MUTATED      1   20
  USP17L2 WILD-TYPE   32  215
     clus
vv    USP17L2 MUTATED USP17L2 WILD-TYPE
  NO                1                32
  YES              20               215
[1] 2 2
[1] FALSE
D42V11, continuous
D42V12, binary
                   cls
clus                  0   1
  USP17L2 MUTATED     6  15
  USP17L2 WILD-TYPE  97 150
[1] "tbl2"
                   cls
clus                [,1] [,2]
  USP17L2 MUTATED      6   15
  USP17L2 WILD-TYPE   97  150
        clus
vv       USP17L2 MUTATED USP17L2 WILD-TYPE
  FEMALE               6                97
  MALE                15               150
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  USP17L2 MUTATED       0                         0    21
  USP17L2 WILD-TYPE     3                         1   243
D42V13, multiclass
                           clus
vv                          USP17L2 MUTATED USP17L2 WILD-TYPE
  ASIAN                                   0                 3
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  21               243
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V14, binary
                   cls
clus                  0   1
  USP17L2 MUTATED     0  21
  USP17L2 WILD-TYPE   3 240
[1] "tbl2"
                   cls
clus                [,1] [,2]
  USP17L2 MUTATED      0   21
  USP17L2 WILD-TYPE    3  240
                        clus
vv                       USP17L2 MUTATED USP17L2 WILD-TYPE
  HISPANIC OR LATINO                   0                 3
  NOT HISPANIC OR LATINO              21               240
[1] 2 2
[1] FALSE

Clustering(43) Variable = LRPPRC MUTATION ANALYSIS
D43V1, survival
                  sevent
clus2                0   1
  LRPPRC MUTATED     6   8
  LRPPRC WILD-TYPE 122 122
  LRPPRC MUTATED LRPPRC WILD-TYPE 
              14              244 
  LRPPRC MUTATED LRPPRC WILD-TYPE 
               8              122 
$`LRPPRC MUTATED`
TCGA-D3-A1Q6 TCGA-D3-A2JO TCGA-D3-A3CE TCGA-EE-A20H TCGA-EE-A29E TCGA-EE-A29L 
       70.16        64.44        13.32         9.21        38.63         1.08 
TCGA-EE-A2GC TCGA-EE-A2GS TCGA-EE-A2MS TCGA-EE-A3AA TCGA-ER-A193 TCGA-ER-A19F 
       34.29        13.02        27.16       124.31        31.40        11.11 
TCGA-ER-A19M TCGA-FS-A1ZD 
       28.60         8.22 

$`LRPPRC WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       16.47         8.52       111.09        32.42       110.79        28.08 
TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 
       22.55        45.83        81.24        10.29        85.32         8.38 
TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF 
       21.14        88.50        68.22        69.90        11.41        30.87 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JP 
        7.50        36.16         6.31        92.42        56.19        45.11 
TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC 
      114.67        15.25        46.98        46.32        82.29        61.38 
TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV 
       24.00         6.31         9.34       103.59        26.37         5.39 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N 
       80.22        42.71        15.09        41.10        17.72         8.84 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS 
       20.48        13.94        52.01        47.87         1.55         6.97 
TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC 
       23.11         4.01         2.89         9.90        11.31        13.22 
TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 
       48.79        35.80        51.12        10.03        39.19        13.68 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB 
        9.99        44.52        36.69        25.15         4.93        22.36 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q 
        6.64        19.36         7.00        17.56        14.83        13.15 
TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y 
        0.20         0.00         0.00        13.22        11.57        10.55 
TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 
        6.31         8.12         1.12         1.35        12.20         5.13 
TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29A 
        4.31        36.07         4.34         5.13         1.18         7.99 
TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M 
        9.90        37.97        11.15         8.55         4.41        27.12 
TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V 
        9.50        12.03         8.09         8.84         9.99         2.43 
TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 
        8.68         8.09        11.31        49.22        23.90         9.67 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI 
        8.94        39.39        17.98        34.92        47.21        30.08 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO 
       19.43        16.01        35.54        28.31        33.83        30.84 
TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 
        5.42         1.15        34.98        36.33         8.84        98.27 
TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG 
        2.70         6.18        47.51         9.53        29.46        44.25 
TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM 
        7.96        14.56        63.42       111.78       111.91        56.02 
TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MT TCGA-EE-A2MU 
       25.08        26.99        21.60        29.65        23.05         5.56 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG 
      122.73        25.84         3.68        30.15        13.81        15.95 
TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 
       12.72         3.22        22.92        21.60        21.60        16.14 
TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 
       22.22        27.35         0.46        13.94        33.60        18.61 
TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C 
       12.95        38.40         5.72        76.41        25.18         3.78 
TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L 
        3.52        11.90       114.15        34.88         4.21        13.45 
TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 
       42.84        34.68         9.57        36.07        17.72        78.44 
TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH 
       11.80         1.87         1.51        13.08        12.62        11.74 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A 
        9.04         6.58        22.49         1.71        18.41        85.74 
TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
        4.90        64.47         3.45        11.01        23.80        14.24 
TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZE 
       15.52         7.33         7.30         3.39        20.38        19.53 
TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM 
       11.08         7.17        30.87        12.92        12.89        47.38 
TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU 
       52.08         8.65         8.81        49.15        40.64         8.68 
TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 
       27.39         0.82         5.23        53.85         7.36        28.73 
TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 
       14.20        10.78         5.98         6.41         2.27         0.20 
TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
        0.99         0.13         0.16         0.43         9.90         7.23 
TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 
       12.85        24.85        31.33        84.72        10.13        16.24 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS 
       15.42        12.16        14.70         5.79 

  LRPPRC MUTATED LRPPRC WILD-TYPE 
            1.08             0.00 
  LRPPRC MUTATED LRPPRC WILD-TYPE 
          124.31           122.73 
  LRPPRC MUTATED LRPPRC WILD-TYPE 
           27.88            14.63 
[1] "1.1 - 124.3 (27.9)" "0.0 - 122.7 (14.6)"
[1] "hr=" "1.1"
D43V2, survival
                  sevent
clus2                0   1
  LRPPRC MUTATED     6   8
  LRPPRC WILD-TYPE 126 123
  LRPPRC MUTATED LRPPRC WILD-TYPE 
              14              249 
  LRPPRC MUTATED LRPPRC WILD-TYPE 
               8              123 
$`LRPPRC MUTATED`
TCGA-D3-A1Q6 TCGA-D3-A2JO TCGA-D3-A3CE TCGA-EE-A20H TCGA-EE-A29E TCGA-EE-A29L 
       71.80        66.08        60.23       168.26        39.62         2.60 
TCGA-EE-A2GC TCGA-EE-A2GS TCGA-EE-A2MS TCGA-EE-A3AA TCGA-ER-A193 TCGA-ER-A19F 
       67.43        55.59       136.47       124.31        31.40        26.37 
TCGA-ER-A19M TCGA-FS-A1ZD 
       61.05        53.52 

$`LRPPRC WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       16.57        16.67       112.04       112.57       133.25        28.08 
TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 
       31.59        90.90        95.74        43.43       103.10        65.49 
TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF 
       23.77       115.53       168.00        69.90        11.87        48.76 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JP 
      113.52        42.08        12.10       171.58        56.19        45.11 
TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC 
      130.72        58.06        46.98        46.32       166.52        86.93 
TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV 
       24.53        13.87         9.34       103.59        39.75        21.47 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N 
      161.85        43.69        40.14       131.90        18.38        10.03 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS 
       51.68        15.06       135.75       137.92       166.19         7.43 
TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 
      125.19       151.53        54.67         3.65         6.41        11.34 
TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1HW 
        3.25         9.90        25.18        66.25        48.89        36.03 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 
      117.21        20.38       194.83       176.55        35.93       107.34 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
       61.18        53.92        65.92        23.44        68.09        28.60 
TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG 
       10.49       215.44        15.68        13.87        10.16        45.11 
TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z 
       35.01         3.55        52.01        29.82        27.22         8.65 
TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 
       94.98        33.73        14.70        26.89        68.15         4.96 
TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B 
      109.64       151.27        78.87        13.55        63.35        80.61 
TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29N 
       47.84        13.97        72.07        32.19        44.35        18.61 
TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W 
       56.42        37.35        14.47        55.92        25.87       171.55 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 
       17.92        46.82       102.90        24.43        39.29        58.75 
TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ 
       47.54       314.56       135.95       208.04        48.72        89.33 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP 
       54.74        79.66        75.48        90.97       101.95        13.91 
TCGA-EE-A2GR TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 
       14.30        44.88        94.82        21.67       129.27        28.83 
TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH 
       19.76        61.51        47.28       103.27       103.20        16.96 
TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN 
      204.66        96.23       144.76       203.05       167.90        47.54 
TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AB 
      248.65        43.23       103.56        41.59        53.26       122.73 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH 
       25.84         3.68        54.51        13.81        23.47       138.81 
TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA 
      172.18       127.20        36.95        64.08        34.32        53.19 
TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 
       27.35        33.40       101.79       148.08        35.44        13.94 
TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D 
       50.76         9.17        77.75        98.40        48.89        12.59 
TCGA-ER-A19E TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19N 
       13.02       268.93       152.35         6.44       131.51        44.05 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
      162.08        50.89        37.25       148.18        79.99        43.82 
TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES 
       23.34        20.15        16.37        31.27        32.05       247.04 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
       80.32        46.98        33.21        92.98       174.21         4.90 
TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 
      216.92        48.59       228.59       202.65        20.91        28.08 
TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZE TCGA-FS-A1ZF 
        7.79        27.72        48.85       357.37        40.27        15.45 
TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP 
        9.70        32.75        47.38        23.93       101.26        74.73 
TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW 
      133.55        11.41       148.80        53.16        26.56        49.48 
TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 
       27.09        27.02        77.82        66.67        28.73       174.84 
TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 
       12.43        26.73        49.45        77.88         0.20        22.92 
TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 
       47.54         0.16         2.40         9.90         7.23        14.04 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 
      120.46       117.93        84.72        10.13        64.44        62.79 
TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS 
       32.48        39.58         6.67 

  LRPPRC MUTATED LRPPRC WILD-TYPE 
            2.60             0.16 
  LRPPRC MUTATED LRPPRC WILD-TYPE 
          168.26           357.37 
  LRPPRC MUTATED LRPPRC WILD-TYPE 
           60.64            47.54 
[1] "2.6 - 168.3 (60.6)" "0.2 - 357.4 (47.5)"
[1] "hr=" "1.1"
D43V3, continuous
                  vv
clus               DISTANT METASTASIS PRIMARY TUMOR
  LRPPRC MUTATED                    1             0
  LRPPRC WILD-TYPE                 34             4
                  vv
clus               REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  LRPPRC MUTATED                                           2
  LRPPRC WILD-TYPE                                        56
                  vv
clus               REGIONAL LYMPH NODE
  LRPPRC MUTATED                    11
  LRPPRC WILD-TYPE                 159
D43V4, multiclass
                                           clus
vv                                          LRPPRC MUTATED LRPPRC WILD-TYPE
  DISTANT METASTASIS                                     1               34
  PRIMARY TUMOR                                          0                4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE              2               56
  REGIONAL LYMPH NODE                                   11              159
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  LRPPRC MUTATED             0       0       1        0        2        1
  LRPPRC WILD-TYPE          10       6      21       10       22       16
                  vv
clus               STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  LRPPRC MUTATED           1         2         0         3          0
  LRPPRC WILD-TYPE         9        12         9        28         13
                  vv
clus               STAGE IIIB STAGE IIIC STAGE IV
  LRPPRC MUTATED            1          2        0
  LRPPRC WILD-TYPE         21         42       12
D43V5, multiclass
             clus
vv            LRPPRC MUTATED LRPPRC WILD-TYPE
  I OR II NOS              0               10
  STAGE 0                  0                6
  STAGE I                  1               21
  STAGE IA                 0               10
  STAGE IB                 2               22
  STAGE II                 1               16
  STAGE IIA                1                9
  STAGE IIB                2               12
  STAGE IIC                0                9
  STAGE III                3               28
  STAGE IIIA               0               13
  STAGE IIIB               1               21
  STAGE IIIC               2               42
  STAGE IV                 0               12
[1] 14  2
[1] 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
  LRPPRC MUTATED       2  4  4  2
  LRPPRC WILD-TYPE    49 54 49 53
D43V6, multiclass
       clus
vv      LRPPRC MUTATED LRPPRC WILD-TYPE
  T0+T1              2               49
  T2                 4               54
  T3                 4               49
  T4                 2               53
[1] 4 2
[1] TRUE
[1] "dimension 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
  LRPPRC MUTATED     8   4   0   2
  LRPPRC WILD-TYPE 130  44  32  31
D43V7, multiclass
    clus
vv   LRPPRC MUTATED LRPPRC WILD-TYPE
  N0              8              130
  N1              4               44
  N2              0               32
  N3              2               31
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                M0  M1 M1A M1B M1C
  LRPPRC MUTATED    14   0   0   0   0
  LRPPRC WILD-TYPE 226   4   2   2   5
D43V8, multiclass
     clus
vv    LRPPRC MUTATED LRPPRC WILD-TYPE
  M0              14              226
  M1               0                4
  M1A              0                2
  M1B              0                2
  M1C              0                5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V9, binary
                  cls
clus                0  1
  LRPPRC MUTATED    5  4
  LRPPRC WILD-TYPE 97 63
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LRPPRC MUTATED      5    4
  LRPPRC WILD-TYPE   97   63
     clus
vv    LRPPRC MUTATED LRPPRC WILD-TYPE
  NO               5               97
  YES              4               63
[1] 2 2
[1] FALSE
D43V10, binary
                  cls
clus                 0   1
  LRPPRC MUTATED     2  12
  LRPPRC WILD-TYPE  31 223
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LRPPRC MUTATED      2   12
  LRPPRC WILD-TYPE   31  223
     clus
vv    LRPPRC MUTATED LRPPRC WILD-TYPE
  NO               2               31
  YES             12              223
[1] 2 2
[1] FALSE
D43V11, continuous
D43V12, binary
                  cls
clus                 0   1
  LRPPRC MUTATED     3  11
  LRPPRC WILD-TYPE 100 154
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LRPPRC MUTATED      3   11
  LRPPRC WILD-TYPE  100  154
        clus
vv       LRPPRC MUTATED LRPPRC WILD-TYPE
  FEMALE              3              100
  MALE               11              154
[1] 2 2
[1] FALSE
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  LRPPRC MUTATED       0                         0    14
  LRPPRC WILD-TYPE     3                         1   250
D43V13, multiclass
                           clus
vv                          LRPPRC MUTATED LRPPRC WILD-TYPE
  ASIAN                                  0                3
  BLACK OR AFRICAN AMERICAN              0                1
  WHITE                                 14              250
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V14, binary
                  cls
clus                 0   1
  LRPPRC MUTATED     0  14
  LRPPRC WILD-TYPE   3 247
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LRPPRC MUTATED      0   14
  LRPPRC WILD-TYPE    3  247
                        clus
vv                       LRPPRC MUTATED LRPPRC WILD-TYPE
  HISPANIC OR LATINO                  0                3
  NOT HISPANIC OR LATINO             14              247
[1] 2 2
[1] FALSE

Clustering(44) Variable = BTK MUTATION ANALYSIS
D44V1, survival
               sevent
clus2             0   1
  BTK MUTATED    10   4
  BTK WILD-TYPE 118 126
  BTK MUTATED BTK WILD-TYPE 
           14           244 
  BTK MUTATED BTK WILD-TYPE 
            4           126 
$`BTK MUTATED`
TCGA-D3-A2JF TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A3MR TCGA-D3-A51T TCGA-DA-A1HV 
       30.87        56.19        64.44       103.59        13.94        48.79 
TCGA-DA-A1HY TCGA-EE-A181 TCGA-EE-A2GM TCGA-EE-A2MR TCGA-EE-A3AE TCGA-ER-A19H 
       51.12         1.12        28.31        29.65        30.15        34.88 
TCGA-ER-A1A1 TCGA-FS-A1Z3 
       78.44        14.24 

$`BTK WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.47         8.52       111.09        32.42        70.16       110.79 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       28.08        22.55        45.83        81.24        10.29        85.32 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
        8.38        21.14        88.50        68.22        69.90        11.41 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JP TCGA-D3-A3BZ 
        7.50        36.16         6.31        92.42        45.11       114.67 
TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE 
       15.25        46.98        46.32        82.29        61.38        13.32 
TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E 
       24.00         6.31         9.34        26.37         5.39        80.22 
TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R 
       42.71        15.09        41.10        17.72         8.84        20.48 
TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 
       52.01        47.87         1.55         6.97        23.11         4.01 
TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1HW TCGA-DA-A1I0 
        2.89         9.90        11.31        13.22        35.80        10.03 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 
       39.19        13.68         9.99        44.52        36.69        25.15 
TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 
        4.93        22.36         6.64        19.36         7.00        17.56 
TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN 
       14.83        13.15         0.20         0.00         0.00        13.22 
TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A182 TCGA-EE-A183 
       11.57        10.55         6.31         8.12         1.35        12.20 
TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H 
        5.13         4.31        36.07         4.34         5.13         9.21 
TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E 
        1.18         7.99         9.90        37.97        11.15        38.63 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P 
        8.55         4.41         1.08        27.12         9.50        12.03 
TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X 
        8.09         8.84         9.99         2.43         8.68         8.09 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB 
       11.31        49.22        23.90         9.67         8.94        39.39 
TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ 
       34.29        17.98        34.92        47.21        30.08        19.43 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR 
       16.01        35.54        33.83        30.84         5.42         1.15 
TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 
       13.02        34.98        36.33         8.84        98.27         2.70 
TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH 
        6.18        47.51         9.53        29.46        44.25         7.96 
TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN 
       14.56        63.42       111.78       111.91        56.02        25.08 
TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA 
       26.99        21.60        27.16        23.05         5.56       124.31 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH 
      122.73        25.84         3.68        13.81        15.95        12.72 
TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA 
        3.22        22.92        21.60        21.60        16.14        22.22 
TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 
       27.35         0.46        13.94        33.60        31.40        18.61 
TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C 
       12.95        38.40         5.72        76.41        25.18         3.78 
TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19J TCGA-ER-A19L 
        3.52        11.90        11.11       114.15         4.21        13.45 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W 
       28.60        42.84        34.68         9.57        36.07        17.72 
TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH 
       11.80         1.87         1.51        13.08        12.62        11.74 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A 
        9.04         6.58        22.49         1.71        18.41        85.74 
TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z4 
        4.90        64.47         3.45        11.01        23.80        15.52 
TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE 
        7.33         7.30         3.39        20.38         8.22        19.53 
TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM 
       11.08         7.17        30.87        12.92        12.89        47.38 
TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU 
       52.08         8.65         8.81        49.15        40.64         8.68 
TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 
       27.39         0.82         5.23        53.85         7.36        28.73 
TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 
       14.20        10.78         5.98         6.41         2.27         0.20 
TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
        0.99         0.13         0.16         0.43         9.90         7.23 
TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 
       12.85        24.85        31.33        84.72        10.13        16.24 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS 
       15.42        12.16        14.70         5.79 

  BTK MUTATED BTK WILD-TYPE 
         1.12          0.00 
  BTK MUTATED BTK WILD-TYPE 
       103.59        124.31 
  BTK MUTATED BTK WILD-TYPE 
       32.875        13.875 
[1] "1.1 - 103.6 (32.9)" "0.0 - 124.3 (13.9)"
[1] "hr=" "2.8"
D44V2, survival
               sevent
clus2             0   1
  BTK MUTATED    11   4
  BTK WILD-TYPE 121 127
  BTK MUTATED BTK WILD-TYPE 
           15           248 
  BTK MUTATED BTK WILD-TYPE 
            4           127 
$`BTK MUTATED`
TCGA-D3-A2JF TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A3MR TCGA-D3-A51T TCGA-D9-A149 
       48.76        56.19        66.08       103.59        15.06        54.67 
TCGA-DA-A1HV TCGA-DA-A1HY TCGA-EE-A181 TCGA-EE-A2GM TCGA-EE-A2MR TCGA-EE-A3AE 
       48.89       117.21        33.73        75.48       103.56        54.51 
TCGA-ER-A19H TCGA-ER-A1A1 TCGA-FS-A1Z3 
      152.35        79.99        20.91 

$`BTK WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.57        16.67       112.04       112.57        71.80       133.25 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       28.08        31.59        90.90        95.74        43.43       103.10 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
       65.49        23.77       115.53       168.00        69.90        11.87 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JP TCGA-D3-A3BZ 
      113.52        42.08        12.10       171.58        45.11       130.72 
TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE 
       58.06        46.98        46.32       166.52        86.93        60.23 
TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E 
       24.53        13.87         9.34        39.75        21.47       161.85 
TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R 
       43.69        40.14       131.90        18.38        10.03        51.68 
TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 
      135.75       137.92       166.19         7.43       125.19       151.53 
TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA 
        3.65         6.41        11.34         3.25         9.90        25.18 
TCGA-D9-A6EC TCGA-DA-A1HW TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 
       66.25        36.03        20.38       194.83       176.55        35.93 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC 
      107.34        61.18        53.92        65.92        23.44        68.09 
TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R 
       28.60        10.49       215.44        15.68        13.87        10.16 
TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y 
       45.11        35.01         3.55        52.01        29.82        27.22 
TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 
        8.65        94.98        14.70        26.89        68.15         4.96 
TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A 
      109.64       151.27        78.87       168.26        13.55        63.35 
TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H 
       80.61        47.84        13.97        39.62        72.07        32.19 
TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R 
        2.60        44.35        18.61        56.42        37.35        14.47 
TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 
       55.92        25.87       171.55        17.92        46.82       102.90 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD 
       24.43        39.29        58.75        47.54        67.43       314.56 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
      135.95       208.04        48.72        89.33        54.74        79.66 
TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT 
       90.97       101.95        13.91        14.30        55.59        44.88 
TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC 
       94.82        21.67       129.27        28.83        19.76        61.51 
TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ 
       47.28       103.27       103.20        16.96       204.66        96.23 
TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ 
      144.76       203.05       167.90        47.54       248.65        43.23 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC 
      136.47        41.59        53.26       124.31       122.73        25.84 
TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 
        3.68        13.81        23.47       138.81       172.18       127.20 
TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE 
       36.95        64.08        34.32        53.19        27.35        33.40 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 
      101.79       148.08        31.40        35.44        13.94        50.76 
TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E 
        9.17        77.75        98.40        48.89        12.59        13.02 
TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N 
       26.37       268.93         6.44       131.51        61.05        44.05 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A2NC TCGA-ER-A2ND 
      162.08        50.89        37.25       148.18        43.82        23.34 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET 
       20.15        16.37        31.27        32.05       247.04        80.32 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW 
       46.98        33.21        92.98       174.21         4.90       216.92 
TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA 
       48.59       228.59       202.65        28.08         7.79        27.72 
TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG 
       48.85       357.37        53.52        40.27        15.45         9.70 
TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ 
       32.75        47.38        23.93       101.26        74.73       133.55 
TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY 
       11.41       148.80        53.16        26.56        49.48        27.09 
TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 
       27.02        77.82        66.67        28.73       174.84        12.43 
TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU 
       26.73        49.45        77.88         0.20        22.92        47.54 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 
        0.16         2.40         9.90         7.23        14.04       120.46 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
      117.93        84.72        10.13        64.44        62.79        32.48 
TCGA-GN-A26D TCGA-QB-A6FS 
       39.58         6.67 

  BTK MUTATED BTK WILD-TYPE 
        15.06          0.16 
  BTK MUTATED BTK WILD-TYPE 
       152.35        357.37 
  BTK MUTATED BTK WILD-TYPE 
        56.19         47.46 
[1] "15.1 - 152.3 (56.2)" "0.2 - 357.4 (47.5)" 
[1] "hr=" "2"  
D44V3, continuous
               vv
clus            DISTANT METASTASIS PRIMARY TUMOR
  BTK MUTATED                    2             0
  BTK WILD-TYPE                 33             4
               vv
clus            REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  BTK MUTATED                                           5                   8
  BTK WILD-TYPE                                        53                 162
D44V4, multiclass
                                           clus
vv                                          BTK MUTATED BTK WILD-TYPE
  DISTANT METASTASIS                                  2            33
  PRIMARY TUMOR                                       0             4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE           5            53
  REGIONAL LYMPH NODE                                 8           162
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  BTK MUTATED             0       0       1        2        0        1
  BTK WILD-TYPE          10       6      21        8       24       16
               vv
clus            STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  BTK MUTATED           0         0         1         2          0          1
  BTK WILD-TYPE        10        14         8        29         13         21
               vv
clus            STAGE IIIC STAGE IV
  BTK MUTATED            4        1
  BTK WILD-TYPE         40       11
D44V5, multiclass
             clus
vv            BTK MUTATED BTK WILD-TYPE
  I OR II NOS           0            10
  STAGE 0               0             6
  STAGE I               1            21
  STAGE IA              2             8
  STAGE IB              0            24
  STAGE II              1            16
  STAGE IIA             0            10
  STAGE IIB             0            14
  STAGE IIC             1             8
  STAGE III             2            29
  STAGE IIIA            0            13
  STAGE IIIB            1            21
  STAGE IIIC            4            40
  STAGE IV              1            11
[1] 14  2
[1] 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
  BTK MUTATED       5  2  1  2
  BTK WILD-TYPE    46 56 52 53
D44V6, multiclass
       clus
vv      BTK MUTATED BTK WILD-TYPE
  T0+T1           5            46
  T2              2            56
  T3              1            52
  T4              2            53
[1] 4 2
[1] TRUE
[1] "dimension 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
  BTK MUTATED     7   4   1   3
  BTK WILD-TYPE 131  44  31  30
D44V7, multiclass
    clus
vv   BTK MUTATED BTK WILD-TYPE
  N0           7           131
  N1           4            44
  N2           1            31
  N3           3            30
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             M0  M1 M1A M1B M1C
  BTK MUTATED    14   1   0   0   0
  BTK WILD-TYPE 226   3   2   2   5
D44V8, multiclass
     clus
vv    BTK MUTATED BTK WILD-TYPE
  M0           14           226
  M1            1             3
  M1A           0             2
  M1B           0             2
  M1C           0             5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V9, binary
               cls
clus             0  1
  BTK MUTATED    4  4
  BTK WILD-TYPE 98 63
[1] "tbl2"
               cls
clus            [,1] [,2]
  BTK MUTATED      4    4
  BTK WILD-TYPE   98   63
     clus
vv    BTK MUTATED BTK WILD-TYPE
  NO            4            98
  YES           4            63
[1] 2 2
[1] FALSE
D44V10, binary
               cls
clus              0   1
  BTK MUTATED     5  10
  BTK WILD-TYPE  28 225
[1] "tbl2"
               cls
clus            [,1] [,2]
  BTK MUTATED      5   10
  BTK WILD-TYPE   28  225
     clus
vv    BTK MUTATED BTK WILD-TYPE
  NO            5            28
  YES          10           225
[1] 2 2
[1] FALSE
D44V11, continuous
D44V12, binary
               cls
clus              0   1
  BTK MUTATED     9   6
  BTK WILD-TYPE  94 159
[1] "tbl2"
               cls
clus            [,1] [,2]
  BTK MUTATED      9    6
  BTK WILD-TYPE   94  159
        clus
vv       BTK MUTATED BTK WILD-TYPE
  FEMALE           9            94
  MALE             6           159
[1] 2 2
[1] FALSE
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  BTK MUTATED       0                         0    15
  BTK WILD-TYPE     3                         1   249
D44V13, multiclass
                           clus
vv                          BTK MUTATED BTK WILD-TYPE
  ASIAN                               0             3
  BLACK OR AFRICAN AMERICAN           0             1
  WHITE                              15           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"
D44V14, binary
               cls
clus              0   1
  BTK MUTATED     0  15
  BTK WILD-TYPE   3 246
[1] "tbl2"
               cls
clus            [,1] [,2]
  BTK MUTATED      0   15
  BTK WILD-TYPE    3  246
                        clus
vv                       BTK MUTATED BTK WILD-TYPE
  HISPANIC OR LATINO               0             3
  NOT HISPANIC OR LATINO          15           246
[1] 2 2
[1] FALSE

Clustering(45) Variable = DSG3 MUTATION ANALYSIS
D45V1, survival
                sevent
clus2              0   1
  DSG3 MUTATED    23  22
  DSG3 WILD-TYPE 105 108
  DSG3 MUTATED DSG3 WILD-TYPE 
            45            213 
  DSG3 MUTATED DSG3 WILD-TYPE 
            22            108 
$`DSG3 MUTATED`
TCGA-D3-A2JA TCGA-D3-A3C7 TCGA-D9-A6E9 TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY 
       88.50        46.98         9.90        48.79        35.80        51.12 
TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IC TCGA-EB-A44Q 
       10.03        13.68        44.52        36.69         6.64        13.15 
TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A20H TCGA-EE-A29E TCGA-EE-A29L 
        1.12         1.35        12.20         9.21        38.63         1.08 
TCGA-EE-A29R TCGA-EE-A2A5 TCGA-EE-A2GC TCGA-EE-A2GJ TCGA-EE-A2GN TCGA-EE-A2GO 
        8.84         9.67        34.29        19.43        33.83        30.84 
TCGA-EE-A2GR TCGA-EE-A2M6 TCGA-EE-A2MC TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MR 
        1.15        98.27        47.51        14.56        63.42        29.65 
TCGA-EE-A3AF TCGA-EE-A3J5 TCGA-EE-A3JD TCGA-ER-A19G TCGA-ER-A19N TCGA-ER-A19P 
       13.81        21.60        27.35       114.15        42.84        34.68 
TCGA-ER-A19S TCGA-FS-A1Z3 TCGA-FS-A1ZK TCGA-FS-A1ZQ TCGA-FS-A1ZZ TCGA-FS-A4FC 
       36.07        14.24        12.89         8.65         5.23         6.41 
TCGA-FS-A4FD TCGA-FW-A3R5 TCGA-GN-A266 
        2.27         0.99        10.13 

$`DSG3 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.47         8.52       111.09        32.42        70.16       110.79 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       28.08        22.55        45.83        81.24        10.29        85.32 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF 
        8.38        21.14        68.22        69.90        11.41        30.87 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO 
        7.50        36.16         6.31        92.42        56.19        64.44 
TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC 
       45.11       114.67        15.25        46.32        82.29        61.38 
TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU 
       13.32        24.00         6.31         9.34       103.59        26.37 
TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K 
        5.39        80.22        42.71        15.09        41.10        17.72 
TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR 
        8.84        20.48        13.94        52.01        47.87         1.55 
TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6EA TCGA-D9-A6EC 
        6.97        23.11         4.01         2.89        11.31        13.22 
TCGA-DA-A1I1 TCGA-DA-A1I4 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A3F2 
       39.19         9.99        25.15         4.93        22.36        19.36 
TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH 
        7.00        17.56        14.83         0.20         0.00         0.00 
TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A184 
       13.22        11.57        10.55         6.31         8.12         5.13 
TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29A 
        4.31        36.07         4.34         5.13         1.18         7.99 
TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M 
        9.90        37.97        11.15         8.55         4.41        27.12 
TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W 
        9.50        12.03         8.09         9.99         2.43         8.68 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB 
        8.09        11.31        49.22        23.90         8.94        39.39 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GK TCGA-EE-A2GL 
       17.98        34.92        47.21        30.08        16.01        35.54 
TCGA-EE-A2GM TCGA-EE-A2GP TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 
       28.31         5.42        13.02        34.98        36.33         8.84 
TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH 
        2.70         6.18         9.53        29.46        44.25         7.96 
TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ 
      111.78       111.91        56.02        25.08        26.99        21.60 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC 
       27.16        23.05         5.56       124.31       122.73        25.84 
TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 
        3.68        30.15        15.95        12.72         3.22        22.92 
TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI 
       21.60        16.14        22.22         0.46        13.94        33.60 
TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A 
       31.40        18.61        12.95        38.40         5.72        76.41 
TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19H 
       25.18         3.78         3.52        11.90        11.11        34.88 
TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19Q TCGA-ER-A19W TCGA-ER-A1A1 
        4.21        13.45        28.60         9.57        17.72        78.44 
TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH 
       11.80         1.87         1.51        13.08        12.62        11.74 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A 
        9.04         6.58        22.49         1.71        18.41        85.74 
TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z4 
        4.90        64.47         3.45        11.01        23.80        15.52 
TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE 
        7.33         7.30         3.39        20.38         8.22        19.53 
TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZP 
       11.08         7.17        30.87        12.92        47.38        52.08 
TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY 
        8.81        49.15        40.64         8.68        27.39         0.82 
TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB 
       53.85         7.36        28.73        14.20        10.78         5.98 
TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
        0.20         0.13         0.16         0.43         9.90         7.23 
TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 
       12.85        24.85        31.33        84.72        16.24        15.42 
TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS 
       12.16        14.70         5.79 

  DSG3 MUTATED DSG3 WILD-TYPE 
          0.99           0.00 
  DSG3 MUTATED DSG3 WILD-TYPE 
        114.15         124.31 
  DSG3 MUTATED DSG3 WILD-TYPE 
         14.56          14.83 
[1] "1.0 - 114.2 (14.6)" "0.0 - 124.3 (14.8)"
[1] "hr=" "1.1"
D45V2, survival
                sevent
clus2              0   1
  DSG3 MUTATED    24  22
  DSG3 WILD-TYPE 108 109
  DSG3 MUTATED DSG3 WILD-TYPE 
            46            217 
  DSG3 MUTATED DSG3 WILD-TYPE 
            22            109 
$`DSG3 MUTATED`
TCGA-D3-A2JA TCGA-D3-A3C7 TCGA-D9-A6E9 TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY 
      115.53        46.98         9.90        48.89        36.03       117.21 
TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IC TCGA-EB-A44Q 
       20.38       176.55       107.34        61.18        68.09        13.87 
TCGA-EB-A5UL TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A20H TCGA-EE-A29E 
        3.55        33.73        14.70        26.89       168.26        39.62 
TCGA-EE-A29L TCGA-EE-A29R TCGA-EE-A2A5 TCGA-EE-A2GC TCGA-EE-A2GJ TCGA-EE-A2GN 
        2.60        14.47        39.29        67.43        89.33        90.97 
TCGA-EE-A2GO TCGA-EE-A2GR TCGA-EE-A2M6 TCGA-EE-A2MC TCGA-EE-A2MI TCGA-EE-A2MJ 
      101.95        14.30       129.27        61.51       204.66        96.23 
TCGA-EE-A2MR TCGA-EE-A3AF TCGA-EE-A3J5 TCGA-EE-A3JD TCGA-ER-A19G TCGA-ER-A19N 
      103.56        13.81        36.95        27.35       268.93        44.05 
TCGA-ER-A19P TCGA-ER-A19S TCGA-FS-A1Z3 TCGA-FS-A1ZK TCGA-FS-A1ZQ TCGA-FS-A1ZZ 
      162.08        37.25        20.91        23.93       133.55        27.02 
TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3R5 TCGA-GN-A266 
       49.45        77.88        22.92        10.13 

$`DSG3 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.57        16.67       112.04       112.57        71.80       133.25 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       28.08        31.59        90.90        95.74        43.43       103.10 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF 
       65.49        23.77       168.00        69.90        11.87        48.76 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO 
      113.52        42.08        12.10       171.58        56.19        66.08 
TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC 
       45.11       130.72        58.06        46.32       166.52        86.93 
TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU 
       60.23        24.53        13.87         9.34       103.59        39.75 
TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K 
       21.47       161.85        43.69        40.14       131.90        18.38 
TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR 
       10.03        51.68        15.06       135.75       137.92       166.19 
TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX 
        7.43       125.19       151.53        54.67         3.65         6.41 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1I1 TCGA-DA-A1I4 
       11.34         3.25        25.18        66.25       194.83        35.93 
TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 
       53.92        65.92        23.44        28.60        10.49       215.44 
TCGA-DA-A3F8 TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EE-A17X 
       15.68        10.16        45.11        35.01        52.01        29.82 
TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B 
       27.22         8.65        94.98        68.15         4.96       109.64 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C 
      151.27        78.87        13.55        63.35        80.61        47.84 
TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P 
       13.97        72.07        32.19        44.35        18.61        56.42 
TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 
       37.35        55.92        25.87       171.55        17.92        46.82 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE 
      102.90        24.43        58.75        47.54       314.56       135.95 
TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GP 
      208.04        48.72        54.74        79.66        75.48        13.91 
TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M7 TCGA-EE-A2M8 
       55.59        44.88        94.82        21.67        28.83        19.76 
TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MK TCGA-EE-A2ML 
       47.28       103.27       103.20        16.96       144.76       203.05 
TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MS TCGA-EE-A2MT 
      167.90        47.54       248.65        43.23       136.47        41.59 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE 
       53.26       124.31       122.73        25.84         3.68        54.51 
TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 
       23.47       138.81       172.18       127.20        64.08        34.32 
TCGA-EE-A3JA TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 
       53.19        33.40       101.79       148.08        31.40        35.44 
TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C 
       13.94        50.76         9.17        77.75        98.40        48.89 
TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L 
       12.59        13.02        26.37       152.35         6.44       131.51 
TCGA-ER-A19M TCGA-ER-A19Q TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
       61.05        50.89       148.18        79.99        43.82        23.34 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET 
       20.15        16.37        31.27        32.05       247.04        80.32 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW 
       46.98        33.21        92.98       174.21         4.90       216.92 
TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA 
       48.59       228.59       202.65        28.08         7.79        27.72 
TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG 
       48.85       357.37        53.52        40.27        15.45         9.70 
TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZR TCGA-FS-A1ZS 
       32.75        47.38       101.26        74.73        11.41       148.80 
TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A4F0 TCGA-FS-A4F4 
       53.16        26.56        49.48        27.09        77.82        66.67 
TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FW-A3I3 TCGA-FW-A3TU 
       28.73       174.84        12.43        26.73         0.20        47.54 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 
        0.16         2.40         9.90         7.23        14.04       120.46 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D 
      117.93        84.72        64.44        62.79        32.48        39.58 
TCGA-QB-A6FS 
        6.67 

  DSG3 MUTATED DSG3 WILD-TYPE 
          2.60           0.16 
  DSG3 MUTATED DSG3 WILD-TYPE 
        268.93         357.37 
  DSG3 MUTATED DSG3 WILD-TYPE 
        45.515         48.720 
[1] "2.6 - 268.9 (45.5)" "0.2 - 357.4 (48.7)"
[1] "hr=" "1"  
D45V3, continuous
                vv
clus             DISTANT METASTASIS PRIMARY TUMOR
  DSG3 MUTATED                    7             1
  DSG3 WILD-TYPE                 28             3
                vv
clus             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  DSG3 MUTATED                                          11                  27
  DSG3 WILD-TYPE                                        47                 143
D45V4, multiclass
                                           clus
vv                                          DSG3 MUTATED DSG3 WILD-TYPE
  DISTANT METASTASIS                                   7             28
  PRIMARY TUMOR                                        1              3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE           11             47
  REGIONAL LYMPH NODE                                 27            143
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  DSG3 MUTATED             1       1       4        1        1        4
  DSG3 WILD-TYPE           9       5      18        9       23       13
                vv
clus             STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DSG3 MUTATED           2         3         0         6          2          5
  DSG3 WILD-TYPE         8        11         9        25         11         17
                vv
clus             STAGE IIIC STAGE IV
  DSG3 MUTATED            8        3
  DSG3 WILD-TYPE         36        9
D45V5, multiclass
             clus
vv            DSG3 MUTATED DSG3 WILD-TYPE
  I OR II NOS            1              9
  STAGE 0                1              5
  STAGE I                4             18
  STAGE IA               1              9
  STAGE IB               1             23
  STAGE II               4             13
  STAGE IIA              2              8
  STAGE IIB              3             11
  STAGE IIC              0              9
  STAGE III              6             25
  STAGE IIIA             2             11
  STAGE IIIB             5             17
  STAGE IIIC             8             36
  STAGE IV               3              9
[1] 14  2
[1] 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
  DSG3 MUTATED       8  8  9  9
  DSG3 WILD-TYPE    43 50 44 46
D45V6, multiclass
       clus
vv      DSG3 MUTATED DSG3 WILD-TYPE
  T0+T1            8             43
  T2               8             50
  T3               9             44
  T4               9             46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  DSG3 MUTATED    22   9   6   6
  DSG3 WILD-TYPE 116  39  26  27
D45V7, multiclass
    clus
vv   DSG3 MUTATED DSG3 WILD-TYPE
  N0           22            116
  N1            9             39
  N2            6             26
  N3            6             27
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              M0  M1 M1A M1B M1C
  DSG3 MUTATED    40   1   1   0   1
  DSG3 WILD-TYPE 200   3   1   2   4
D45V8, multiclass
     clus
vv    DSG3 MUTATED DSG3 WILD-TYPE
  M0            40            200
  M1             1              3
  M1A            1              1
  M1B            0              2
  M1C            1              4
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V9, binary
                cls
clus              0  1
  DSG3 MUTATED   16 10
  DSG3 WILD-TYPE 86 57
[1] "tbl2"
                cls
clus             [,1] [,2]
  DSG3 MUTATED     16   10
  DSG3 WILD-TYPE   86   57
     clus
vv    DSG3 MUTATED DSG3 WILD-TYPE
  NO            16             86
  YES           10             57
[1] 2 2
[1] FALSE
D45V10, binary
                cls
clus               0   1
  DSG3 MUTATED     9  37
  DSG3 WILD-TYPE  24 198
[1] "tbl2"
                cls
clus             [,1] [,2]
  DSG3 MUTATED      9   37
  DSG3 WILD-TYPE   24  198
     clus
vv    DSG3 MUTATED DSG3 WILD-TYPE
  NO             9             24
  YES           37            198
[1] 2 2
[1] FALSE
D45V11, continuous
D45V12, binary
                cls
clus               0   1
  DSG3 MUTATED    17  29
  DSG3 WILD-TYPE  86 136
[1] "tbl2"
                cls
clus             [,1] [,2]
  DSG3 MUTATED     17   29
  DSG3 WILD-TYPE   86  136
        clus
vv       DSG3 MUTATED DSG3 WILD-TYPE
  FEMALE           17             86
  MALE             29            136
[1] 2 2
[1] FALSE
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DSG3 MUTATED       1                         0    45
  DSG3 WILD-TYPE     2                         1   219
D45V13, multiclass
                           clus
vv                          DSG3 MUTATED DSG3 WILD-TYPE
  ASIAN                                1              2
  BLACK OR AFRICAN AMERICAN            0              1
  WHITE                               45            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"
D45V14, binary
                cls
clus               0   1
  DSG3 MUTATED     1  45
  DSG3 WILD-TYPE   2 216
[1] "tbl2"
                cls
clus             [,1] [,2]
  DSG3 MUTATED      1   45
  DSG3 WILD-TYPE    2  216
                        clus
vv                       DSG3 MUTATED DSG3 WILD-TYPE
  HISPANIC OR LATINO                1              2
  NOT HISPANIC OR LATINO           45            216
[1] 2 2
[1] FALSE

Clustering(46) Variable = C1QTNF9 MUTATION ANALYSIS
D46V1, survival
                   sevent
clus2                 0   1
  C1QTNF9 MUTATED    10   6
  C1QTNF9 WILD-TYPE 118 124
  C1QTNF9 MUTATED C1QTNF9 WILD-TYPE 
               16               242 
  C1QTNF9 MUTATED C1QTNF9 WILD-TYPE 
                6               124 
$`C1QTNF9 MUTATED`
TCGA-D3-A1QB TCGA-D3-A2JF TCGA-D3-A51N TCGA-D9-A3Z1 TCGA-EE-A29A TCGA-EE-A29M 
       81.24        30.87         8.84         4.01         7.99        27.12 
TCGA-EE-A2A1 TCGA-EE-A2GM TCGA-EE-A2MD TCGA-EE-A2MI TCGA-EE-A2MR TCGA-EE-A2MU 
       49.22        28.31         9.53        14.56        29.65         5.56 
TCGA-EE-A3J3 TCGA-EE-A3J7 TCGA-EE-A3JA TCGA-FS-A4F9 
        3.22        21.60        22.22        10.78 

$`C1QTNF9 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.47         8.52       111.09        32.42        70.16       110.79 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 
       28.08        22.55        45.83        10.29        85.32         8.38 
TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JG 
       21.14        88.50        68.22        69.90        11.41         7.50 
TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP 
       36.16         6.31        92.42        56.19        64.44        45.11 
TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC 
      114.67        15.25        46.98        46.32        82.29        61.38 
TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU 
       13.32        24.00         6.31         9.34       103.59        26.37 
TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K 
        5.39        80.22        42.71        15.09        41.10        17.72 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS 
       20.48        13.94        52.01        47.87         1.55         6.97 
TCGA-D3-A5GU TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1HV 
       23.11         2.89         9.90        11.31        13.22        48.79 
TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 
       35.80        51.12        10.03        39.19        13.68         9.99 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC 
       44.52        36.69        25.15         4.93        22.36         6.64 
TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R 
       19.36         7.00        17.56        14.83        13.15         0.20 
TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z 
        0.00         0.00        13.22        11.57        10.55         6.31 
TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 
        8.12         1.12         1.35        12.20         5.13         4.31 
TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29B 
       36.07         4.34         5.13         9.21         1.18         9.90 
TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L 
       37.97        11.15        38.63         8.55         4.41         1.08 
TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V 
        9.50        12.03         8.09         8.84         9.99         2.43 
TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 
        8.68         8.09        11.31        23.90         9.67         8.94 
TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI 
       39.39        34.29        17.98        34.92        47.21        30.08 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP 
       19.43        16.01        35.54        33.83        30.84         5.42 
TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 
        1.15        13.02        34.98        36.33         8.84        98.27 
TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH 
        2.70         6.18        47.51        29.46        44.25         7.96 
TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP 
       63.42       111.78       111.91        56.02        25.08        26.99 
TCGA-EE-A2MQ TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC 
       21.60        27.16        23.05       124.31       122.73        25.84 
TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J4 
        3.68        30.15        13.81        15.95        12.72        22.92 
TCGA-EE-A3J5 TCGA-EE-A3J8 TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI 
       21.60        16.14        27.35         0.46        13.94        33.60 
TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A 
       31.40        18.61        12.95        38.40         5.72        76.41 
TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G 
       25.18         3.78         3.52        11.90        11.11       114.15 
TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P 
       34.88         4.21        13.45        28.60        42.84        34.68 
TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
        9.57        36.07        17.72        78.44        11.80         1.87 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET 
        1.51        13.08        12.62        11.74         9.04         6.58 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW 
       22.49         1.71        18.41        85.74         4.90        64.47 
TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 
        3.45        11.01        23.80        14.24        15.52         7.33 
TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF 
        7.30         3.39        20.38         8.22        19.53        11.08 
TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP 
        7.17        30.87        12.92        12.89        47.38        52.08 
TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW 
        8.65         8.81        49.15        40.64         8.68        27.39 
TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 
        0.82         5.23        53.85         7.36        28.73        14.20 
TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU 
        5.98         6.41         2.27         0.20         0.99         0.13 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 
        0.16         0.43         9.90         7.23        12.85        24.85 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
       31.33        84.72        10.13        16.24        15.42        12.16 
TCGA-GN-A26D TCGA-QB-A6FS 
       14.70         5.79 

  C1QTNF9 MUTATED C1QTNF9 WILD-TYPE 
             3.22              0.00 
  C1QTNF9 MUTATED C1QTNF9 WILD-TYPE 
            81.24            124.31 
  C1QTNF9 MUTATED C1QTNF9 WILD-TYPE 
           18.080            14.765 
[1] "3.2 - 81.2 (18.1)"  "0.0 - 124.3 (14.8)"
[1] "hr=" "1.3"
D46V2, survival
                   sevent
clus2                 0   1
  C1QTNF9 MUTATED    10   6
  C1QTNF9 WILD-TYPE 122 125
  C1QTNF9 MUTATED C1QTNF9 WILD-TYPE 
               16               247 
  C1QTNF9 MUTATED C1QTNF9 WILD-TYPE 
                6               125 
$`C1QTNF9 MUTATED`
TCGA-D3-A1QB TCGA-D3-A2JF TCGA-D3-A51N TCGA-D9-A3Z1 TCGA-EE-A29A TCGA-EE-A29M 
       95.74        48.76        10.03        11.34        63.35        44.35 
TCGA-EE-A2A1 TCGA-EE-A2GM TCGA-EE-A2MD TCGA-EE-A2MI TCGA-EE-A2MR TCGA-EE-A2MU 
      102.90        75.48        47.28       204.66       103.56        53.26 
TCGA-EE-A3J3 TCGA-EE-A3J7 TCGA-EE-A3JA TCGA-FS-A4F9 
      172.18        64.08        53.19        12.43 

$`C1QTNF9 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.57        16.67       112.04       112.57        71.80       133.25 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 
       28.08        31.59        90.90        43.43       103.10        65.49 
TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JG 
       23.77       115.53       168.00        69.90        11.87       113.52 
TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP 
       42.08        12.10       171.58        56.19        66.08        45.11 
TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC 
      130.72        58.06        46.98        46.32       166.52        86.93 
TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU 
       60.23        24.53        13.87         9.34       103.59        39.75 
TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K 
       21.47       161.85        43.69        40.14       131.90        18.38 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS 
       51.68        15.06       135.75       137.92       166.19         7.43 
TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z3 
      125.19       151.53        54.67         3.65         6.41         3.25 
TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY 
        9.90        25.18        66.25        48.89        36.03       117.21 
TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 
       20.38       194.83       176.55        35.93       107.34        61.18 
TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 
       53.92        65.92        23.44        68.09        28.60        10.49 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH 
      215.44        15.68        13.87        10.16        45.11        35.01 
TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 
        3.55        52.01        29.82        27.22         8.65        94.98 
TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B 
       33.73        14.70        26.89        68.15         4.96       109.64 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29B TCGA-EE-A29C 
      151.27        78.87       168.26        13.55        80.61        47.84 
TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29N 
       13.97        39.62        72.07        32.19         2.60        18.61 
TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W 
       56.42        37.35        14.47        55.92        25.87       171.55 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB 
       17.92        46.82        24.43        39.29        58.75        47.54 
TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ 
       67.43       314.56       135.95       208.04        48.72        89.33 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR 
       54.74        79.66        90.97       101.95        13.91        14.30 
TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 
       55.59        44.88        94.82        21.67       129.27        28.83 
TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MJ 
       19.76        61.51       103.27       103.20        16.96        96.23 
TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ 
      144.76       203.05       167.90        47.54       248.65        43.23 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD 
      136.47        41.59       124.31       122.73        25.84         3.68 
TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J4 TCGA-EE-A3J5 
       54.51        13.81        23.47       138.81       127.20        36.95 
TCGA-EE-A3J8 TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 
       34.32        27.35        33.40       101.79       148.08        31.40 
TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B 
       35.44        13.94        50.76         9.17        77.75        98.40 
TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H 
       48.89        12.59        13.02        26.37       268.93       152.35 
TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q 
        6.44       131.51        61.05        44.05       162.08        50.89 
TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE 
       37.25       148.18        79.99        43.82        23.34        20.15 
TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV 
       16.37        31.27        32.05       247.04        80.32        46.98 
TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX 
       33.21        92.98       174.21         4.90       216.92        48.59 
TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA 
      228.59       202.65        20.91        28.08         7.79        27.72 
TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG 
       48.85       357.37        53.52        40.27        15.45         9.70 
TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ 
       32.75        47.38        23.93       101.26        74.73       133.55 
TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY 
       11.41       148.80        53.16        26.56        49.48        27.09 
TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4FB 
       27.02        77.82        66.67        28.73       174.84        26.73 
TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV 
       49.45        77.88         0.20        22.92        47.54         0.16 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 
        2.40         9.90         7.23        14.04       120.46       117.93 
TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D 
       84.72        10.13        64.44        62.79        32.48        39.58 
TCGA-QB-A6FS 
        6.67 

  C1QTNF9 MUTATED C1QTNF9 WILD-TYPE 
            10.03              0.16 
  C1QTNF9 MUTATED C1QTNF9 WILD-TYPE 
           204.66            357.37 
  C1QTNF9 MUTATED C1QTNF9 WILD-TYPE 
           58.305            47.540 
[1] "10.0 - 204.7 (58.3)" "0.2 - 357.4 (47.5)" 
[1] "hr=" "1.5"
D46V3, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  C1QTNF9 MUTATED                    2             0
  C1QTNF9 WILD-TYPE                 33             4
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  C1QTNF9 MUTATED                                           4
  C1QTNF9 WILD-TYPE                                        54
                   vv
clus                REGIONAL LYMPH NODE
  C1QTNF9 MUTATED                    10
  C1QTNF9 WILD-TYPE                 160
D46V4, multiclass
                                           clus
vv                                          C1QTNF9 MUTATED C1QTNF9 WILD-TYPE
  DISTANT METASTASIS                                      2                33
  PRIMARY TUMOR                                           0                 4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE               4                54
  REGIONAL LYMPH NODE                                    10               160
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  C1QTNF9 MUTATED             0       0       2        2        4        1
  C1QTNF9 WILD-TYPE          10       6      20        8       20       16
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  C1QTNF9 MUTATED           0         1         1         1          1
  C1QTNF9 WILD-TYPE        10        13         8        30         12
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  C1QTNF9 MUTATED            0          2        1
  C1QTNF9 WILD-TYPE         22         42       11
D46V5, multiclass
             clus
vv            C1QTNF9 MUTATED C1QTNF9 WILD-TYPE
  I OR II NOS               0                10
  STAGE 0                   0                 6
  STAGE I                   2                20
  STAGE IA                  2                 8
  STAGE IB                  4                20
  STAGE II                  1                16
  STAGE IIA                 0                10
  STAGE IIB                 1                13
  STAGE IIC                 1                 8
  STAGE III                 1                30
  STAGE IIIA                1                12
  STAGE IIIB                0                22
  STAGE IIIC                2                42
  STAGE IV                  1                11
[1] 14  2
[1] 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
  C1QTNF9 MUTATED       4  7  2  3
  C1QTNF9 WILD-TYPE    47 51 51 52
D46V6, multiclass
       clus
vv      C1QTNF9 MUTATED C1QTNF9 WILD-TYPE
  T0+T1               4                47
  T2                  7                51
  T3                  2                51
  T4                  3                52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  C1QTNF9 MUTATED    11   1   1   3
  C1QTNF9 WILD-TYPE 127  47  31  30
D46V7, multiclass
    clus
vv   C1QTNF9 MUTATED C1QTNF9 WILD-TYPE
  N0              11               127
  N1               1                47
  N2               1                31
  N3               3                30
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1 M1A M1B M1C
  C1QTNF9 MUTATED    15   0   0   0   1
  C1QTNF9 WILD-TYPE 225   4   2   2   4
D46V8, multiclass
     clus
vv    C1QTNF9 MUTATED C1QTNF9 WILD-TYPE
  M0               15               225
  M1                0                 4
  M1A               0                 2
  M1B               0                 2
  M1C               1                 4
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V9, binary
                   cls
clus                 0  1
  C1QTNF9 MUTATED    7  4
  C1QTNF9 WILD-TYPE 95 63
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C1QTNF9 MUTATED      7    4
  C1QTNF9 WILD-TYPE   95   63
     clus
vv    C1QTNF9 MUTATED C1QTNF9 WILD-TYPE
  NO                7                95
  YES               4                63
[1] 2 2
[1] FALSE
D46V10, binary
                   cls
clus                  0   1
  C1QTNF9 MUTATED     2  14
  C1QTNF9 WILD-TYPE  31 221
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C1QTNF9 MUTATED      2   14
  C1QTNF9 WILD-TYPE   31  221
     clus
vv    C1QTNF9 MUTATED C1QTNF9 WILD-TYPE
  NO                2                31
  YES              14               221
[1] 2 2
[1] FALSE
D46V11, continuous
D46V12, binary
                   cls
clus                  0   1
  C1QTNF9 MUTATED     4  12
  C1QTNF9 WILD-TYPE  99 153
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C1QTNF9 MUTATED      4   12
  C1QTNF9 WILD-TYPE   99  153
        clus
vv       C1QTNF9 MUTATED C1QTNF9 WILD-TYPE
  FEMALE               4                99
  MALE                12               153
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  C1QTNF9 MUTATED       0                         0    16
  C1QTNF9 WILD-TYPE     3                         1   248
D46V13, multiclass
                           clus
vv                          C1QTNF9 MUTATED C1QTNF9 WILD-TYPE
  ASIAN                                   0                 3
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  16               248
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V14, binary
                   cls
clus                  0   1
  C1QTNF9 MUTATED     0  15
  C1QTNF9 WILD-TYPE   3 246
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C1QTNF9 MUTATED      0   15
  C1QTNF9 WILD-TYPE    3  246
                        clus
vv                       C1QTNF9 MUTATED C1QTNF9 WILD-TYPE
  HISPANIC OR LATINO                   0                 3
  NOT HISPANIC OR LATINO              15               246
[1] 2 2
[1] FALSE

Clustering(47) Variable = BLM MUTATION ANALYSIS
D47V1, survival
               sevent
clus2             0   1
  BLM MUTATED     9   6
  BLM WILD-TYPE 119 124
  BLM MUTATED BLM WILD-TYPE 
           15           243 
  BLM MUTATED BLM WILD-TYPE 
            6           124 
$`BLM MUTATED`
TCGA-D3-A1Q3 TCGA-D3-A1QA TCGA-D3-A2J6 TCGA-D3-A3C7 TCGA-D3-A3CE TCGA-DA-A1HW 
        8.52        45.83        10.29        46.98        13.32        35.80 
TCGA-EE-A29E TCGA-EE-A2GC TCGA-EE-A2MD TCGA-EE-A3AA TCGA-ER-A19F TCGA-ER-A3PL 
       38.63        34.29         9.53       124.31        11.11         1.71 
TCGA-FS-A4F9 TCGA-FW-A3R5 TCGA-GN-A262 
       10.78         0.99        24.85 

$`BLM WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       16.47       111.09        32.42        70.16       110.79        28.08 
TCGA-D3-A1Q9 TCGA-D3-A1QB TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA 
       22.55        81.24        85.32         8.38        21.14        88.50 
TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH 
       68.22        69.90        11.41        30.87         7.50        36.16 
TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ 
        6.31        92.42        56.19        64.44        45.11       114.67 
TCGA-D3-A3C6 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3ML 
       15.25        46.32        82.29        61.38        24.00         6.31 
TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F 
        9.34       103.59        26.37         5.39        80.22        42.71 
TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T 
       15.09        41.10        17.72         8.84        20.48        13.94 
TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 
       52.01        47.87         1.55         6.97        23.11         4.01 
TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1HY 
        2.89         9.90        11.31        13.22        48.79        51.12 
TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 
       10.03        39.19        13.68         9.99        44.52        36.69 
TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 
       25.15         4.93        22.36         6.64        19.36         7.00 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH 
       17.56        14.83        13.15         0.20         0.00         0.00 
TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 
       13.22        11.57        10.55         6.31         8.12         1.12 
TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C 
        1.35        12.20         5.13         4.31        36.07         4.34 
TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C 
        5.13         9.21         1.18         7.99         9.90        37.97 
TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N 
       11.15         8.55         4.41         1.08        27.12         9.50 
TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W 
       12.03         8.09         8.84         9.99         2.43         8.68 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 
        8.09        11.31        49.22        23.90         9.67         8.94 
TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ 
       39.39        17.98        34.92        47.21        30.08        19.43 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP 
       16.01        35.54        28.31        33.83        30.84         5.42 
TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 
        1.15        13.02        34.98        36.33         8.84        98.27 
TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH 
        2.70         6.18        47.51        29.46        44.25         7.96 
TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN 
       14.56        63.42       111.78       111.91        56.02        25.08 
TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU 
       26.99        21.60        29.65        27.16        23.05         5.56 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG 
      122.73        25.84         3.68        30.15        13.81        15.95 
TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 
       12.72         3.22        22.92        21.60        21.60        16.14 
TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 
       22.22        27.35         0.46        13.94        33.60        31.40 
TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B 
       18.61        12.95        38.40         5.72        76.41        25.18 
TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J 
        3.78         3.52        11.90       114.15        34.88         4.21 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S 
       13.45        28.60        42.84        34.68         9.57        36.07 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF 
       17.72        78.44        11.80         1.87         1.51        13.08 
TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-FR-A3YN 
       12.62        11.74         9.04         6.58        22.49        18.41 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 
       85.74         4.90        64.47         3.45        11.01        23.80 
TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC 
       14.24        15.52         7.33         7.30         3.39        20.38 
TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ 
        8.22        19.53        11.08         7.17        30.87        12.92 
TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS 
       12.89        47.38        52.08         8.65         8.81        49.15 
TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 
       40.64         8.68        27.39         0.82         5.23        53.85 
TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD 
        7.36        28.73        14.20         5.98         6.41         2.27 
TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
        0.20         0.13         0.16         0.43         9.90         7.23 
TCGA-GF-A6C8 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 
       12.85        31.33        84.72        10.13        16.24        15.42 
TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS 
       12.16        14.70         5.79 

  BLM MUTATED BLM WILD-TYPE 
         0.99          0.00 
  BLM MUTATED BLM WILD-TYPE 
       124.31        122.73 
  BLM MUTATED BLM WILD-TYPE 
        13.32         14.83 
[1] "1.0 - 124.3 (13.3)" "0.0 - 122.7 (14.8)"
[1] "hr=" "1.4"
D47V2, survival
               sevent
clus2             0   1
  BLM MUTATED     9   6
  BLM WILD-TYPE 123 125
  BLM MUTATED BLM WILD-TYPE 
           15           248 
  BLM MUTATED BLM WILD-TYPE 
            6           125 
$`BLM MUTATED`
TCGA-D3-A1Q3 TCGA-D3-A1QA TCGA-D3-A2J6 TCGA-D3-A3C7 TCGA-D3-A3CE TCGA-DA-A1HW 
       16.67        90.90        43.43        46.98        60.23        36.03 
TCGA-EE-A29E TCGA-EE-A2GC TCGA-EE-A2MD TCGA-EE-A3AA TCGA-ER-A19F TCGA-ER-A3PL 
       39.62        67.43        47.28       124.31        26.37        33.21 
TCGA-FS-A4F9 TCGA-FW-A3R5 TCGA-GN-A262 
       12.43        22.92       120.46 

$`BLM WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       16.57       112.04       112.57        71.80       133.25        28.08 
TCGA-D3-A1Q9 TCGA-D3-A1QB TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA 
       31.59        95.74       103.10        65.49        23.77       115.53 
TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH 
      168.00        69.90        11.87        48.76       113.52        42.08 
TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ 
       12.10       171.58        56.19        66.08        45.11       130.72 
TCGA-D3-A3C6 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3ML 
       58.06        46.32       166.52        86.93        24.53        13.87 
TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F 
        9.34       103.59        39.75        21.47       161.85        43.69 
TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T 
       40.14       131.90        18.38        10.03        51.68        15.06 
TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 
      135.75       137.92       166.19         7.43       125.19       151.53 
TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 
       54.67         3.65         6.41        11.34         3.25         9.90 
TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 
       25.18        66.25        48.89       117.21        20.38       194.83 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA 
      176.55        35.93       107.34        61.18        53.92        65.92 
TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 
       23.44        68.09        28.60        10.49       215.44        15.68 
TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN 
       13.87        10.16        45.11        35.01         3.55        52.01 
TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 
       29.82        27.22         8.65        94.98        33.73        14.70 
TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F 
       26.89        68.15         4.96       109.64       151.27        78.87 
TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D 
      168.26        13.55        63.35        80.61        47.84        13.97 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P 
       72.07        32.19         2.60        44.35        18.61        56.42 
TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X 
       37.35        14.47        55.92        25.87       171.55        17.92 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB 
       46.82       102.90        24.43        39.29        58.75        47.54 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK 
      314.56       135.95       208.04        48.72        89.33        54.74 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR 
       79.66        75.48        90.97       101.95        13.91        14.30 
TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 
       55.59        44.88        94.82        21.67       129.27        28.83 
TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI 
       19.76        61.51       103.27       103.20        16.96       204.66 
TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP 
       96.23       144.76       203.05       167.90        47.54       248.65 
TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AB 
       43.23       103.56       136.47        41.59        53.26       122.73 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH 
       25.84         3.68        54.51        13.81        23.47       138.81 
TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA 
      172.18       127.20        36.95        64.08        34.32        53.19 
TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 
       27.35        33.40       101.79       148.08        31.40        35.44 
TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C 
       13.94        50.76         9.17        77.75        98.40        48.89 
TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L 
       12.59        13.02       268.93       152.35         6.44       131.51 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W 
       61.05        44.05       162.08        50.89        37.25       148.18 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG 
       79.99        43.82        23.34        20.15        16.37        31.27 
TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-FR-A3YN TCGA-FR-A44A 
       32.05       247.04        80.32        46.98        92.98       174.21 
TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
        4.90       216.92        48.59       228.59       202.65        20.91 
TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD 
       28.08         7.79        27.72        48.85       357.37        53.52 
TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK 
       40.27        15.45         9.70        32.75        47.38        23.93 
TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT 
      101.26        74.73       133.55        11.41       148.80        53.16 
TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 
       26.56        49.48        27.09        27.02        77.82        66.67 
TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 
       28.73       174.84        26.73        49.45        77.88         0.20 
TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 
       47.54         0.16         2.40         9.90         7.23        14.04 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
      117.93        84.72        10.13        64.44        62.79        32.48 
TCGA-GN-A26D TCGA-QB-A6FS 
       39.58         6.67 

  BLM MUTATED BLM WILD-TYPE 
        12.43          0.16 
  BLM MUTATED BLM WILD-TYPE 
       124.31        357.37 
  BLM MUTATED BLM WILD-TYPE 
       43.430        48.805 
[1] "12.4 - 124.3 (43.4)" "0.2 - 357.4 (48.8)" 
[1] "hr=" "1"  
D47V3, continuous
               vv
clus            DISTANT METASTASIS PRIMARY TUMOR
  BLM MUTATED                    0             0
  BLM WILD-TYPE                 35             4
               vv
clus            REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  BLM MUTATED                                           2                  13
  BLM WILD-TYPE                                        56                 157
D47V4, multiclass
                                           clus
vv                                          BLM MUTATED BLM WILD-TYPE
  DISTANT METASTASIS                                  0            35
  PRIMARY TUMOR                                       0             4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE           2            56
  REGIONAL LYMPH NODE                                13           157
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  BLM MUTATED             0       0       0        0        1        1
  BLM WILD-TYPE          10       6      22       10       23       16
               vv
clus            STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  BLM MUTATED           0         2         1         4          0          2
  BLM WILD-TYPE        10        12         8        27         13         20
               vv
clus            STAGE IIIC STAGE IV
  BLM MUTATED            1        1
  BLM WILD-TYPE         43       11
D47V5, multiclass
             clus
vv            BLM MUTATED BLM WILD-TYPE
  I OR II NOS           0            10
  STAGE 0               0             6
  STAGE I               0            22
  STAGE IA              0            10
  STAGE IB              1            23
  STAGE II              1            16
  STAGE IIA             0            10
  STAGE IIB             2            12
  STAGE IIC             1             8
  STAGE III             4            27
  STAGE IIIA            0            13
  STAGE IIIB            2            20
  STAGE IIIC            1            43
  STAGE IV              1            11
[1] 14  2
[1] 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
  BLM MUTATED       4  1  5  2
  BLM WILD-TYPE    47 57 48 53
D47V6, multiclass
       clus
vv      BLM MUTATED BLM WILD-TYPE
  T0+T1           4            47
  T2              1            57
  T3              5            48
  T4              2            53
[1] 4 2
[1] TRUE
[1] "dimension 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
  BLM MUTATED     7   5   1   1
  BLM WILD-TYPE 131  43  31  32
D47V7, multiclass
    clus
vv   BLM MUTATED BLM WILD-TYPE
  N0           7           131
  N1           5            43
  N2           1            31
  N3           1            32
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             M0  M1 M1A M1B M1C
  BLM MUTATED    13   0   1   0   0
  BLM WILD-TYPE 227   4   1   2   5
D47V8, multiclass
     clus
vv    BLM MUTATED BLM WILD-TYPE
  M0           13           227
  M1            0             4
  M1A           1             1
  M1B           0             2
  M1C           0             5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V9, binary
               cls
clus             0  1
  BLM MUTATED    3  6
  BLM WILD-TYPE 99 61
[1] "tbl2"
               cls
clus            [,1] [,2]
  BLM MUTATED      3    6
  BLM WILD-TYPE   99   61
     clus
vv    BLM MUTATED BLM WILD-TYPE
  NO            3            99
  YES           6            61
[1] 2 2
[1] FALSE
D47V10, binary
               cls
clus              0   1
  BLM MUTATED     3  12
  BLM WILD-TYPE  30 223
[1] "tbl2"
               cls
clus            [,1] [,2]
  BLM MUTATED      3   12
  BLM WILD-TYPE   30  223
     clus
vv    BLM MUTATED BLM WILD-TYPE
  NO            3            30
  YES          12           223
[1] 2 2
[1] FALSE
D47V11, continuous
D47V12, binary
               cls
clus              0   1
  BLM MUTATED     4  11
  BLM WILD-TYPE  99 154
[1] "tbl2"
               cls
clus            [,1] [,2]
  BLM MUTATED      4   11
  BLM WILD-TYPE   99  154
        clus
vv       BLM MUTATED BLM WILD-TYPE
  FEMALE           4            99
  MALE            11           154
[1] 2 2
[1] FALSE
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  BLM MUTATED       0                         0    15
  BLM WILD-TYPE     3                         1   249
D47V13, multiclass
                           clus
vv                          BLM MUTATED BLM WILD-TYPE
  ASIAN                               0             3
  BLACK OR AFRICAN AMERICAN           0             1
  WHITE                              15           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"
D47V14, binary
               cls
clus              0   1
  BLM MUTATED     0  15
  BLM WILD-TYPE   3 246
[1] "tbl2"
               cls
clus            [,1] [,2]
  BLM MUTATED      0   15
  BLM WILD-TYPE    3  246
                        clus
vv                       BLM MUTATED BLM WILD-TYPE
  HISPANIC OR LATINO               0             3
  NOT HISPANIC OR LATINO          15           246
[1] 2 2
[1] FALSE

Clustering(48) Variable = ACSM2B MUTATION ANALYSIS
D48V1, survival
                  sevent
clus2                0   1
  ACSM2B MUTATED    18  22
  ACSM2B WILD-TYPE 110 108
  ACSM2B MUTATED ACSM2B WILD-TYPE 
              40              218 
  ACSM2B MUTATED ACSM2B WILD-TYPE 
              22              108 
$`ACSM2B MUTATED`
TCGA-D3-A2JF TCGA-D3-A2JP TCGA-D3-A3ML TCGA-D3-A3MR TCGA-D9-A6EA TCGA-D9-A6EC 
       30.87        45.11         6.31       103.59        11.31        13.22 
TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A20C TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29C 
        1.35        12.20         4.34         9.21         7.99        37.97 
TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29V TCGA-EE-A2GC 
       11.15        38.63         1.08        27.12         2.43        34.29 
TCGA-EE-A2GI TCGA-EE-A2GM TCGA-EE-A2GT TCGA-EE-A2M5 TCGA-EE-A2MG TCGA-EE-A2MI 
       30.08        28.31        34.98         8.84        44.25        14.56 
TCGA-EE-A2MJ TCGA-EE-A2MM TCGA-EE-A3AD TCGA-EE-A3AG TCGA-EE-A3JD TCGA-ER-A19M 
       63.42        56.02         3.68        15.95        27.35        28.60 
TCGA-ER-A19P TCGA-ER-A1A1 TCGA-FR-A3YN TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A4F9 
       34.68        78.44        18.41         8.65         8.81        10.78 
TCGA-FW-A3R5 TCGA-GN-A265 TCGA-GN-A267 TCGA-QB-A6FS 
        0.99        84.72        16.24         5.79 

$`ACSM2B WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.47         8.52       111.09        32.42        70.16       110.79 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       28.08        22.55        45.83        81.24        10.29        85.32 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
        8.38        21.14        88.50        68.22        69.90        11.41 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO 
        7.50        36.16         6.31        92.42        56.19        64.44 
TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC 
      114.67        15.25        46.98        46.32        82.29        61.38 
TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E 
       13.32        24.00         9.34        26.37         5.39        80.22 
TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R 
       42.71        15.09        41.10        17.72         8.84        20.48 
TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU 
       13.94        52.01        47.87         1.55         6.97        23.11 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY 
        4.01         2.89         9.90        48.79        35.80        51.12 
TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 
       10.03        39.19        13.68         9.99        44.52        36.69 
TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 
       25.15         4.93        22.36         6.64        19.36         7.00 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH 
       17.56        14.83        13.15         0.20         0.00         0.00 
TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 
       13.22        11.57        10.55         6.31         8.12         1.12 
TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29B 
        5.13         4.31        36.07         5.13         1.18         9.90 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R 
        8.55         4.41         9.50        12.03         8.09         8.84 
TCGA-EE-A29S TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 
        9.99         8.68         8.09        11.31        49.22        23.90 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH 
        9.67         8.94        39.39        17.98        34.92        47.21 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP 
       19.43        16.01        35.54        33.83        30.84         5.42 
TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 
        1.15        13.02        36.33        98.27         2.70         6.18 
TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MH TCGA-EE-A2MK TCGA-EE-A2ML 
       47.51         9.53        29.46         7.96       111.78       111.91 
TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT 
       25.08        26.99        21.60        29.65        27.16        23.05 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AE TCGA-EE-A3AF 
        5.56       124.31       122.73        25.84        30.15        13.81 
TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 
       12.72         3.22        22.92        21.60        21.60        16.14 
TCGA-EE-A3JA TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 
       22.22         0.46        13.94        33.60        31.40        18.61 
TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C 
       12.95        38.40         5.72        76.41        25.18         3.78 
TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J 
        3.52        11.90        11.11       114.15        34.88         4.21 
TCGA-ER-A19L TCGA-ER-A19N TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A2NC 
       13.45        42.84         9.57        36.07        17.72        11.80 
TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES 
        1.87         1.51        13.08        12.62        11.74         9.04 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW 
        6.58        22.49         1.71        85.74         4.90        64.47 
TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 
        3.45        11.01        23.80        14.24        15.52         7.33 
TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF 
        7.30         3.39        20.38         8.22        19.53        11.08 
TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP 
        7.17        30.87        12.92        12.89        47.38        52.08 
TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ 
       49.15        40.64         8.68        27.39         0.82         5.23 
TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4FB TCGA-FS-A4FC 
       53.85         7.36        28.73        14.20         5.98         6.41 
TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
        2.27         0.20         0.13         0.16         0.43         9.90 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A266 TCGA-GN-A268 
        7.23        12.85        24.85        31.33        10.13        15.42 
TCGA-GN-A26A TCGA-GN-A26D 
       12.16        14.70 

  ACSM2B MUTATED ACSM2B WILD-TYPE 
            0.99             0.00 
  ACSM2B MUTATED ACSM2B WILD-TYPE 
          103.59           124.31 
  ACSM2B MUTATED ACSM2B WILD-TYPE 
          16.095           14.470 
[1] "1.0 - 103.6 (16.1)" "0.0 - 124.3 (14.5)"
[1] "hr=" "1.1"
D48V2, survival
                  sevent
clus2                0   1
  ACSM2B MUTATED    20  22
  ACSM2B WILD-TYPE 112 109
  ACSM2B MUTATED ACSM2B WILD-TYPE 
              42              221 
  ACSM2B MUTATED ACSM2B WILD-TYPE 
              22              109 
$`ACSM2B MUTATED`
TCGA-D3-A2JF TCGA-D3-A2JP TCGA-D3-A3ML TCGA-D3-A3MR TCGA-D9-A1JW TCGA-D9-A6EA 
       48.76        45.11        13.87       103.59         3.65        25.18 
TCGA-D9-A6EC TCGA-EB-A5UL TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A20C TCGA-EE-A20H 
       66.25         3.55        14.70        26.89       151.27       168.26 
TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29L TCGA-EE-A29M 
       63.35        47.84        13.97        39.62         2.60        44.35 
TCGA-EE-A29V TCGA-EE-A2GC TCGA-EE-A2GI TCGA-EE-A2GM TCGA-EE-A2GT TCGA-EE-A2M5 
       25.87        67.43        48.72        75.48        44.88        21.67 
TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MM TCGA-EE-A3AD TCGA-EE-A3AG 
      103.20       204.66        96.23       167.90         3.68        23.47 
TCGA-EE-A3JD TCGA-ER-A19M TCGA-ER-A19P TCGA-ER-A1A1 TCGA-FR-A3YN TCGA-FS-A1ZQ 
       27.35        61.05       162.08        79.99        92.98       133.55 
TCGA-FS-A1ZR TCGA-FS-A4F9 TCGA-FW-A3R5 TCGA-GN-A265 TCGA-GN-A267 TCGA-QB-A6FS 
       11.41        12.43        22.92        84.72        64.44         6.67 

$`ACSM2B WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.57        16.67       112.04       112.57        71.80       133.25 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       28.08        31.59        90.90        95.74        43.43       103.10 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
       65.49        23.77       115.53       168.00        69.90        11.87 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO 
      113.52        42.08        12.10       171.58        56.19        66.08 
TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC 
      130.72        58.06        46.98        46.32       166.52        86.93 
TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E 
       60.23        24.53         9.34        39.75        21.47       161.85 
TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R 
       43.69        40.14       131.90        18.38        10.03        51.68 
TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU 
       15.06       135.75       137.92       166.19         7.43       125.19 
TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 
      151.53        54.67         6.41        11.34         3.25         9.90 
TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 
       48.89        36.03       117.21        20.38       194.83       176.55 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB 
       35.93       107.34        61.18        53.92        65.92        23.44 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q 
       68.09        28.60        10.49       215.44        15.68        13.87 
TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y 
       10.16        45.11        35.01        52.01        29.82        27.22 
TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B 
        8.65        94.98        33.73        68.15         4.96       109.64 
TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29B TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29N 
       78.87        13.55        80.61        72.07        32.19        18.61 
TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29W TCGA-EE-A29X 
       56.42        37.35        14.47        55.92       171.55        17.92 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB 
       46.82       102.90        24.43        39.29        58.75        47.54 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
      314.56       135.95       208.04        89.33        54.74        79.66 
TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU 
       90.97       101.95        13.91        14.30        55.59        94.82 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME 
      129.27        28.83        19.76        61.51        47.28       103.27 
TCGA-EE-A2MH TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ 
       16.96       144.76       203.05        47.54       248.65        43.23 
TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB 
      103.56       136.47        41.59        53.26       124.31       122.73 
TCGA-EE-A3AC TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 
       25.84        54.51        13.81       138.81       172.18       127.20 
TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JE TCGA-EE-A3JH 
       36.95        64.08        34.32        53.19        33.40       101.79 
TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 
      148.08        31.40        35.44        13.94        50.76         9.17 
TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F 
       77.75        98.40        48.89        12.59        13.02        26.37 
TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19N TCGA-ER-A19Q 
      268.93       152.35         6.44       131.51        44.05        50.89 
TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF 
       37.25       148.18        43.82        23.34        20.15        16.37 
TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL 
       31.27        32.05       247.04        80.32        46.98        33.21 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 
      174.21         4.90       216.92        48.59       228.59       202.65 
TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC 
       20.91        28.08         7.79        27.72        48.85       357.37 
TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ 
       53.52        40.27        15.45         9.70        32.75        47.38 
TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU 
       23.93       101.26        74.73       148.80        53.16        26.56 
TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 
       49.48        27.09        27.02        77.82        66.67        28.73 
TCGA-FS-A4F8 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU 
      174.84        26.73        49.45        77.88         0.20        47.54 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 
        0.16         2.40         9.90         7.23        14.04       120.46 
TCGA-GN-A264 TCGA-GN-A266 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D 
      117.93        10.13        62.79        32.48        39.58 

  ACSM2B MUTATED ACSM2B WILD-TYPE 
            2.60             0.16 
  ACSM2B MUTATED ACSM2B WILD-TYPE 
          204.66           357.37 
  ACSM2B MUTATED ACSM2B WILD-TYPE 
          46.475           48.850 
[1] "2.6 - 204.7 (46.5)" "0.2 - 357.4 (48.9)"
[1] "hr=" "1.2"
D48V3, continuous
                  vv
clus               DISTANT METASTASIS PRIMARY TUMOR
  ACSM2B MUTATED                    7             2
  ACSM2B WILD-TYPE                 28             2
                  vv
clus               REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  ACSM2B MUTATED                                           4
  ACSM2B WILD-TYPE                                        54
                  vv
clus               REGIONAL LYMPH NODE
  ACSM2B MUTATED                    29
  ACSM2B WILD-TYPE                 141
D48V4, multiclass
                                           clus
vv                                          ACSM2B MUTATED ACSM2B WILD-TYPE
  DISTANT METASTASIS                                     7               28
  PRIMARY TUMOR                                          2                2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE              4               54
  REGIONAL LYMPH NODE                                   29              141
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  ACSM2B MUTATED             1       2       4        2        4        1
  ACSM2B WILD-TYPE           9       4      18        8       20       16
                  vv
clus               STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  ACSM2B MUTATED           1         2         1         7          4
  ACSM2B WILD-TYPE         9        12         8        24          9
                  vv
clus               STAGE IIIB STAGE IIIC STAGE IV
  ACSM2B MUTATED            1          9        0
  ACSM2B WILD-TYPE         21         35       12
D48V5, multiclass
             clus
vv            ACSM2B MUTATED ACSM2B WILD-TYPE
  I OR II NOS              1                9
  STAGE 0                  2                4
  STAGE I                  4               18
  STAGE IA                 2                8
  STAGE IB                 4               20
  STAGE II                 1               16
  STAGE IIA                1                9
  STAGE IIB                2               12
  STAGE IIC                1                8
  STAGE III                7               24
  STAGE IIIA               4                9
  STAGE IIIB               1               21
  STAGE IIIC               9               35
  STAGE IV                 0               12
[1] 14  2
[1] 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
  ACSM2B MUTATED       8  9  8  8
  ACSM2B WILD-TYPE    43 49 45 47
D48V6, multiclass
       clus
vv      ACSM2B MUTATED ACSM2B WILD-TYPE
  T0+T1              8               43
  T2                 9               49
  T3                 8               45
  T4                 8               47
[1] 4 2
[1] TRUE
[1] "dimension 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
  ACSM2B MUTATED    20  10   5   6
  ACSM2B WILD-TYPE 118  38  27  27
D48V7, multiclass
    clus
vv   ACSM2B MUTATED ACSM2B WILD-TYPE
  N0             20              118
  N1             10               38
  N2              5               27
  N3              6               27
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                M0  M1 M1A M1B M1C
  ACSM2B MUTATED    41   0   0   0   0
  ACSM2B WILD-TYPE 199   4   2   2   5
D48V8, multiclass
     clus
vv    ACSM2B MUTATED ACSM2B WILD-TYPE
  M0              41              199
  M1               0                4
  M1A              0                2
  M1B              0                2
  M1C              0                5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V9, binary
                  cls
clus                0  1
  ACSM2B MUTATED   16  7
  ACSM2B WILD-TYPE 86 60
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ACSM2B MUTATED     16    7
  ACSM2B WILD-TYPE   86   60
     clus
vv    ACSM2B MUTATED ACSM2B WILD-TYPE
  NO              16               86
  YES              7               60
[1] 2 2
[1] FALSE
D48V10, binary
                  cls
clus                 0   1
  ACSM2B MUTATED     8  34
  ACSM2B WILD-TYPE  25 201
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ACSM2B MUTATED      8   34
  ACSM2B WILD-TYPE   25  201
     clus
vv    ACSM2B MUTATED ACSM2B WILD-TYPE
  NO               8               25
  YES             34              201
[1] 2 2
[1] FALSE
D48V11, continuous
D48V12, binary
                  cls
clus                 0   1
  ACSM2B MUTATED     6  36
  ACSM2B WILD-TYPE  97 129
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ACSM2B MUTATED      6   36
  ACSM2B WILD-TYPE   97  129
        clus
vv       ACSM2B MUTATED ACSM2B WILD-TYPE
  FEMALE              6               97
  MALE               36              129
[1] 2 2
[1] FALSE
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ACSM2B MUTATED       0                         0    42
  ACSM2B WILD-TYPE     3                         1   222
D48V13, multiclass
                           clus
vv                          ACSM2B MUTATED ACSM2B WILD-TYPE
  ASIAN                                  0                3
  BLACK OR AFRICAN AMERICAN              0                1
  WHITE                                 42              222
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V14, binary
                  cls
clus                 0   1
  ACSM2B MUTATED     0  41
  ACSM2B WILD-TYPE   3 220
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ACSM2B MUTATED      0   41
  ACSM2B WILD-TYPE    3  220
                        clus
vv                       ACSM2B MUTATED ACSM2B WILD-TYPE
  HISPANIC OR LATINO                  0                3
  NOT HISPANIC OR LATINO             41              220
[1] 2 2
[1] FALSE

Clustering(49) Variable = PARM1 MUTATION ANALYSIS
D49V1, survival
                 sevent
clus2               0   1
  PARM1 MUTATED     6  12
  PARM1 WILD-TYPE 122 118
  PARM1 MUTATED PARM1 WILD-TYPE 
             18             240 
  PARM1 MUTATED PARM1 WILD-TYPE 
             12             118 
$`PARM1 MUTATED`
TCGA-D3-A1Q6 TCGA-D3-A2J8 TCGA-D3-A3C8 TCGA-EE-A182 TCGA-EE-A185 TCGA-EE-A29D 
       70.16         8.38        46.32         1.35         4.31        11.15 
TCGA-EE-A29P TCGA-EE-A29V TCGA-EE-A2GI TCGA-EE-A3JD TCGA-EE-A3JI TCGA-ER-A2NC 
       12.03         2.43        30.08        27.35        33.60        11.80 
TCGA-FS-A1ZA TCGA-FS-A1ZC TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FW-A3R5 TCGA-GN-A266 
        7.30        20.38        47.38        52.08         0.99        10.13 

$`PARM1 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       16.47         8.52       111.09        32.42       110.79        28.08 
TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J9 
       22.55        45.83        81.24        10.29        85.32        21.14 
TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JG 
       88.50        68.22        69.90        11.41        30.87         7.50 
TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP 
       36.16         6.31        92.42        56.19        64.44        45.11 
TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE 
      114.67        15.25        46.98        82.29        61.38        13.32 
TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV 
       24.00         6.31         9.34       103.59        26.37         5.39 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N 
       80.22        42.71        15.09        41.10        17.72         8.84 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS 
       20.48        13.94        52.01        47.87         1.55         6.97 
TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC 
       23.11         4.01         2.89         9.90        11.31        13.22 
TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 
       48.79        35.80        51.12        10.03        39.19        13.68 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB 
        9.99        44.52        36.69        25.15         4.93        22.36 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q 
        6.64        19.36         7.00        17.56        14.83        13.15 
TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y 
        0.20         0.00         0.00        13.22        11.57        10.55 
TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A20B 
        6.31         8.12         1.12        12.20         5.13        36.07 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B 
        4.34         5.13         9.21         1.18         7.99         9.90 
TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M 
       37.97        38.63         8.55         4.41         1.08        27.12 
TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29W TCGA-EE-A29X 
        9.50         8.09         8.84         9.99         8.68         8.09 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB 
       11.31        49.22        23.90         9.67         8.94        39.39 
TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK 
       34.29        17.98        34.92        47.21        19.43        16.01 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR 
       35.54        28.31        33.83        30.84         5.42         1.15 
TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 
       13.02        34.98        36.33         8.84        98.27         2.70 
TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH 
        6.18        47.51         9.53        29.46        44.25         7.96 
TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN 
       14.56        63.42       111.78       111.91        56.02        25.08 
TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU 
       26.99        21.60        29.65        27.16        23.05         5.56 
TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF 
      124.31       122.73        25.84         3.68        30.15        13.81 
TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 
       15.95        12.72         3.22        22.92        21.60        21.60 
TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A195 
       16.14        22.22         0.46        13.94        31.40        18.61 
TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C 
       12.95        38.40         5.72        76.41        25.18         3.78 
TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J 
        3.52        11.90        11.11       114.15        34.88         4.21 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S 
       13.45        28.60        42.84        34.68         9.57        36.07 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG 
       17.72        78.44         1.87         1.51        13.08        12.62 
TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN 
       11.74         9.04         6.58        22.49         1.71        18.41 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 
       85.74         4.90        64.47         3.45        11.01        23.80 
TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZB TCGA-FS-A1ZD TCGA-FS-A1ZE 
       14.24        15.52         7.33         3.39         8.22        19.53 
TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZQ 
       11.08         7.17        30.87        12.92        12.89         8.65 
TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY 
        8.81        49.15        40.64         8.68        27.39         0.82 
TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 
        5.23        53.85         7.36        28.73        14.20        10.78 
TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV 
        5.98         6.41         2.27         0.20         0.13         0.16 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 
        0.43         9.90         7.23        12.85        24.85        31.33 
TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS 
       84.72        16.24        15.42        12.16        14.70         5.79 

  PARM1 MUTATED PARM1 WILD-TYPE 
           0.99            0.00 
  PARM1 MUTATED PARM1 WILD-TYPE 
          70.16          124.31 
  PARM1 MUTATED PARM1 WILD-TYPE 
         11.915          14.960 
[1] "1.0 - 70.2 (11.9)"  "0.0 - 124.3 (15.0)"
[1] "hr=" "1.5"
D49V2, survival
                 sevent
clus2               0   1
  PARM1 MUTATED     6  12
  PARM1 WILD-TYPE 126 119
  PARM1 MUTATED PARM1 WILD-TYPE 
             18             245 
  PARM1 MUTATED PARM1 WILD-TYPE 
             12             119 
$`PARM1 MUTATED`
TCGA-D3-A1Q6 TCGA-D3-A2J8 TCGA-D3-A3C8 TCGA-EE-A182 TCGA-EE-A185 TCGA-EE-A29D 
       71.80        65.49        46.32        14.70         4.96        13.97 
TCGA-EE-A29P TCGA-EE-A29V TCGA-EE-A2GI TCGA-EE-A3JD TCGA-EE-A3JI TCGA-ER-A2NC 
       56.42        25.87        48.72        27.35       148.08        43.82 
TCGA-FS-A1ZA TCGA-FS-A1ZC TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FW-A3R5 TCGA-GN-A266 
       27.72       357.37       101.26        74.73        22.92        10.13 

$`PARM1 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       16.57        16.67       112.04       112.57       133.25        28.08 
TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J9 
       31.59        90.90        95.74        43.43       103.10        23.77 
TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JG 
      115.53       168.00        69.90        11.87        48.76       113.52 
TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP 
       42.08        12.10       171.58        56.19        66.08        45.11 
TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE 
      130.72        58.06        46.98       166.52        86.93        60.23 
TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV 
       24.53        13.87         9.34       103.59        39.75        21.47 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N 
      161.85        43.69        40.14       131.90        18.38        10.03 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS 
       51.68        15.06       135.75       137.92       166.19         7.43 
TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 
      125.19       151.53        54.67         3.65         6.41        11.34 
TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1HW 
        3.25         9.90        25.18        66.25        48.89        36.03 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 
      117.21        20.38       194.83       176.55        35.93       107.34 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
       61.18        53.92        65.92        23.44        68.09        28.60 
TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG 
       10.49       215.44        15.68        13.87        10.16        45.11 
TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z 
       35.01         3.55        52.01        29.82        27.22         8.65 
TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A20B TCGA-EE-A20C 
       94.98        33.73        26.89        68.15       109.64       151.27 
TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C 
       78.87       168.26        13.55        63.35        80.61        47.84 
TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N 
       39.62        72.07        32.19         2.60        44.35        18.61 
TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 
       37.35        14.47        55.92       171.55        17.92        46.82 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC 
      102.90        24.43        39.29        58.75        47.54        67.43 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
      314.56       135.95       208.04        89.33        54.74        79.66 
TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS 
       75.48        90.97       101.95        13.91        14.30        55.59 
TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 
       44.88        94.82        21.67       129.27        28.83        19.76 
TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI 
       61.51        47.28       103.27       103.20        16.96       204.66 
TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP 
       96.23       144.76       203.05       167.90        47.54       248.65 
TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA 
       43.23       103.56       136.47        41.59        53.26       124.31 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG 
      122.73        25.84         3.68        54.51        13.81        23.47 
TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 
      138.81       172.18       127.20        36.95        64.08        34.32 
TCGA-EE-A3JA TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 
       53.19        33.40       101.79        31.40        35.44        13.94 
TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D 
       50.76         9.17        77.75        98.40        48.89        12.59 
TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L 
       13.02        26.37       268.93       152.35         6.44       131.51 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W 
       61.05        44.05       162.08        50.89        37.25       148.18 
TCGA-ER-A1A1 TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH 
       79.99        23.34        20.15        16.37        31.27        32.05 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A 
      247.04        80.32        46.98        33.21        92.98       174.21 
TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
        4.90       216.92        48.59       228.59       202.65        20.91 
TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZB TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF 
       28.08         7.79        48.85        53.52        40.27        15.45 
TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZQ TCGA-FS-A1ZR 
        9.70        32.75        47.38        23.93       133.55        11.41 
TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ 
      148.80        53.16        26.56        49.48        27.09        27.02 
TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB 
       77.82        66.67        28.73       174.84        12.43        26.73 
TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY 
       49.45        77.88         0.20        47.54         0.16         2.40 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        9.90         7.23        14.04       120.46       117.93        84.72 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS 
       64.44        62.79        32.48        39.58         6.67 

  PARM1 MUTATED PARM1 WILD-TYPE 
           4.96            0.16 
  PARM1 MUTATED PARM1 WILD-TYPE 
         357.37          314.56 
  PARM1 MUTATED PARM1 WILD-TYPE 
          45.07           48.76 
[1] "5.0 - 357.4 (45.1)" "0.2 - 314.6 (48.8)"
[1] "hr=" "1.4"
D49V3, continuous
                 vv
clus              DISTANT METASTASIS PRIMARY TUMOR
  PARM1 MUTATED                    5             0
  PARM1 WILD-TYPE                 30             4
                 vv
clus              REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  PARM1 MUTATED                                           4                   9
  PARM1 WILD-TYPE                                        54                 161
D49V4, multiclass
                                           clus
vv                                          PARM1 MUTATED PARM1 WILD-TYPE
  DISTANT METASTASIS                                    5              30
  PRIMARY TUMOR                                         0               4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE             4              54
  REGIONAL LYMPH NODE                                   9             161
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  PARM1 MUTATED             1       0       1        1        2        1
  PARM1 WILD-TYPE           9       6      21        9       22       16
                 vv
clus              STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  PARM1 MUTATED           0         0         1         4          0          1
  PARM1 WILD-TYPE        10        14         8        27         13         21
                 vv
clus              STAGE IIIC STAGE IV
  PARM1 MUTATED            5        0
  PARM1 WILD-TYPE         39       12
D49V5, multiclass
             clus
vv            PARM1 MUTATED PARM1 WILD-TYPE
  I OR II NOS             1               9
  STAGE 0                 0               6
  STAGE I                 1              21
  STAGE IA                1               9
  STAGE IB                2              22
  STAGE II                1              16
  STAGE IIA               0              10
  STAGE IIB               0              14
  STAGE IIC               1               8
  STAGE III               4              27
  STAGE IIIA              0              13
  STAGE IIIB              1              21
  STAGE IIIC              5              39
  STAGE IV                0              12
[1] 14  2
[1] 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
  PARM1 MUTATED       1  4  3  5
  PARM1 WILD-TYPE    50 54 50 50
D49V6, multiclass
       clus
vv      PARM1 MUTATED PARM1 WILD-TYPE
  T0+T1             1              50
  T2                4              54
  T3                3              50
  T4                5              50
[1] 4 2
[1] TRUE
[1] "dimension 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
  PARM1 MUTATED     7   4   4   2
  PARM1 WILD-TYPE 131  44  28  31
D49V7, multiclass
    clus
vv   PARM1 MUTATED PARM1 WILD-TYPE
  N0             7             131
  N1             4              44
  N2             4              28
  N3             2              31
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               M0  M1 M1A M1B M1C
  PARM1 MUTATED    17   0   0   0   0
  PARM1 WILD-TYPE 223   4   2   2   5
D49V8, multiclass
     clus
vv    PARM1 MUTATED PARM1 WILD-TYPE
  M0             17             223
  M1              0               4
  M1A             0               2
  M1B             0               2
  M1C             0               5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V9, binary
                 cls
clus               0  1
  PARM1 MUTATED    4  6
  PARM1 WILD-TYPE 98 61
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PARM1 MUTATED      4    6
  PARM1 WILD-TYPE   98   61
     clus
vv    PARM1 MUTATED PARM1 WILD-TYPE
  NO              4              98
  YES             6              61
[1] 2 2
[1] FALSE
D49V10, binary
                 cls
clus                0   1
  PARM1 MUTATED     2  16
  PARM1 WILD-TYPE  31 219
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PARM1 MUTATED      2   16
  PARM1 WILD-TYPE   31  219
     clus
vv    PARM1 MUTATED PARM1 WILD-TYPE
  NO              2              31
  YES            16             219
[1] 2 2
[1] FALSE
D49V11, continuous
D49V12, binary
                 cls
clus                0   1
  PARM1 MUTATED     5  13
  PARM1 WILD-TYPE  98 152
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PARM1 MUTATED      5   13
  PARM1 WILD-TYPE   98  152
        clus
vv       PARM1 MUTATED PARM1 WILD-TYPE
  FEMALE             5              98
  MALE              13             152
[1] 2 2
[1] FALSE
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PARM1 MUTATED       0                         0    18
  PARM1 WILD-TYPE     3                         1   246
D49V13, multiclass
                           clus
vv                          PARM1 MUTATED PARM1 WILD-TYPE
  ASIAN                                 0               3
  BLACK OR AFRICAN AMERICAN             0               1
  WHITE                                18             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"
D49V14, binary
                 cls
clus                0   1
  PARM1 MUTATED     0  18
  PARM1 WILD-TYPE   3 243
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PARM1 MUTATED      0   18
  PARM1 WILD-TYPE    3  243
                        clus
vv                       PARM1 MUTATED PARM1 WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO            18             243
[1] 2 2
[1] FALSE

Clustering(50) Variable = TP63 MUTATION ANALYSIS
D50V1, survival
                sevent
clus2              0   1
  TP63 MUTATED    25  20
  TP63 WILD-TYPE 103 110
  TP63 MUTATED TP63 WILD-TYPE 
            45            213 
  TP63 MUTATED TP63 WILD-TYPE 
            20            110 
$`TP63 MUTATED`
TCGA-D3-A2JK TCGA-D3-A3C7 TCGA-D3-A3ML TCGA-D3-A3MU TCGA-D3-A51R TCGA-D3-A51T 
        6.31        46.98         6.31        26.37        20.48        13.94 
TCGA-D3-A5GO TCGA-D9-A3Z3 TCGA-D9-A6EC TCGA-DA-A1HV TCGA-EE-A181 TCGA-EE-A29C 
       47.87         2.89        13.22        48.79         1.12        37.97 
TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29R TCGA-EE-A2GB 
       38.63         4.41        27.12         9.50         8.84        39.39 
TCGA-EE-A2GC TCGA-EE-A2GR TCGA-EE-A2M5 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2MI 
       34.29         1.15         8.84        47.51         9.53        14.56 
TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MR TCGA-EE-A3AF TCGA-EE-A3J8 
       63.42       111.78       111.91        29.65        13.81        16.14 
TCGA-EE-A3JD TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A19F TCGA-FR-A3YN TCGA-FS-A1Z7 
       27.35        33.60        31.40        11.11        18.41         7.33 
TCGA-FS-A1ZA TCGA-FS-A1ZE TCGA-FS-A1ZZ TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-GF-A4EO 
        7.30        19.53         5.23         0.99         0.13         7.23 
TCGA-GF-A6C8 TCGA-GN-A266 TCGA-GN-A267 
       12.85        10.13        16.24 

$`TP63 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.47         8.52       111.09        32.42        70.16       110.79 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       28.08        22.55        45.83        81.24        10.29        85.32 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
        8.38        21.14        88.50        68.22        69.90        11.41 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO 
       30.87         7.50        36.16        92.42        56.19        64.44 
TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC 
       45.11       114.67        15.25        46.32        82.29        61.38 
TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MV TCGA-D3-A51E 
       13.32        24.00         9.34       103.59         5.39        80.22 
TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A5GN 
       42.71        15.09        41.10        17.72         8.84        52.01 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A6E9 TCGA-D9-A6EA 
        1.55         6.97        23.11         4.01         9.90        11.31 
TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 
       35.80        51.12        10.03        39.19        13.68         9.99 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC 
       44.52        36.69        25.15         4.93        22.36         6.64 
TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R 
       19.36         7.00        17.56        14.83        13.15         0.20 
TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z 
        0.00         0.00        13.22        11.57        10.55         6.31 
TCGA-EE-A180 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B 
        8.12         1.35        12.20         5.13         4.31        36.07 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B 
        4.34         5.13         9.21         1.18         7.99         9.90 
TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29L TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29S 
       11.15         8.55         1.08        12.03         8.09         9.99 
TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 
        2.43         8.68         8.09        11.31        49.22        23.90 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI 
        9.67         8.94        17.98        34.92        47.21        30.08 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO 
       19.43        16.01        35.54        28.31        33.83        30.84 
TCGA-EE-A2GP TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 
        5.42        13.02        34.98        36.33        98.27         2.70 
TCGA-EE-A2M8 TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MM TCGA-EE-A2MN 
        6.18        29.46        44.25         7.96        56.02        25.08 
TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA 
       26.99        21.60        27.16        23.05         5.56       124.31 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AG TCGA-EE-A3AH 
      122.73        25.84         3.68        30.15        15.95        12.72 
TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3JA TCGA-EE-A3JE 
        3.22        22.92        21.60        21.60        22.22         0.46 
TCGA-EE-A3JH TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A 
       13.94        18.61        12.95        38.40         5.72        76.41 
TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19G TCGA-ER-A19H 
       25.18         3.78         3.52        11.90       114.15        34.88 
TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q 
        4.21        13.45        28.60        42.84        34.68         9.57 
TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE 
       36.07        17.72        78.44        11.80         1.87         1.51 
TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV 
       13.08        12.62        11.74         9.04         6.58        22.49 
TCGA-ER-A3PL TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY 
        1.71        85.74         4.90        64.47         3.45        11.01 
TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD 
       23.80        14.24        15.52         3.39        20.38         8.22 
TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM 
       11.08         7.17        30.87        12.92        12.89        47.38 
TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU 
       52.08         8.65         8.81        49.15        40.64         8.68 
TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 
       27.39         0.82        53.85         7.36        28.73        14.20 
TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TV 
       10.78         5.98         6.41         2.27         0.20         0.16 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A268 
        0.43         9.90        24.85        31.33        84.72        15.42 
TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS 
       12.16        14.70         5.79 

  TP63 MUTATED TP63 WILD-TYPE 
          0.13           0.00 
  TP63 MUTATED TP63 WILD-TYPE 
        111.91         124.31 
  TP63 MUTATED TP63 WILD-TYPE 
         14.56          14.83 
[1] "0.1 - 111.9 (14.6)" "0.0 - 124.3 (14.8)"
[1] "hr=" "1.1"
D50V2, survival
                sevent
clus2              0   1
  TP63 MUTATED    25  20
  TP63 WILD-TYPE 107 111
  TP63 MUTATED TP63 WILD-TYPE 
            45            218 
  TP63 MUTATED TP63 WILD-TYPE 
            20            111 
$`TP63 MUTATED`
TCGA-D3-A2JK TCGA-D3-A3C7 TCGA-D3-A3ML TCGA-D3-A3MU TCGA-D3-A51R TCGA-D3-A51T 
       12.10        46.98        13.87        39.75        51.68        15.06 
TCGA-D3-A5GO TCGA-D9-A3Z3 TCGA-D9-A6EC TCGA-DA-A1HV TCGA-EE-A181 TCGA-EE-A29C 
      137.92         3.25        66.25        48.89        33.73        47.84 
TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29R TCGA-EE-A2GB 
       39.62        32.19        44.35        18.61        14.47        47.54 
TCGA-EE-A2GC TCGA-EE-A2GR TCGA-EE-A2M5 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2MI 
       67.43        14.30        21.67        61.51        47.28       204.66 
TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MR TCGA-EE-A3AF TCGA-EE-A3J8 
       96.23       144.76       203.05       103.56        13.81        34.32 
TCGA-EE-A3JD TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A19F TCGA-FR-A3YN TCGA-FS-A1Z7 
       27.35       148.08        31.40        26.37        92.98         7.79 
TCGA-FS-A1ZA TCGA-FS-A1ZE TCGA-FS-A1ZZ TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-GF-A4EO 
       27.72        40.27        27.02        22.92        47.54         7.23 
TCGA-GF-A6C8 TCGA-GN-A266 TCGA-GN-A267 
       14.04        10.13        64.44 

$`TP63 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.57        16.67       112.04       112.57        71.80       133.25 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       28.08        31.59        90.90        95.74        43.43       103.10 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
       65.49        23.77       115.53       168.00        69.90        11.87 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO 
       48.76       113.52        42.08       171.58        56.19        66.08 
TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC 
       45.11       130.72        58.06        46.32       166.52        86.93 
TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MV TCGA-D3-A51E 
       60.23        24.53         9.34       103.59        21.47       161.85 
TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A5GN 
       43.69        40.14       131.90        18.38        10.03       135.75 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW 
      166.19         7.43       125.19       151.53        54.67         3.65 
TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-DA-A1HW TCGA-DA-A1HY 
        6.41        11.34         9.90        25.18        36.03       117.21 
TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 
       20.38       194.83       176.55        35.93       107.34        61.18 
TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 
       53.92        65.92        23.44        68.09        28.60        10.49 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH 
      215.44        15.68        13.87        10.16        45.11        35.01 
TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 
        3.55        52.01        29.82        27.22         8.65        94.98 
TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C 
       14.70        26.89        68.15         4.96       109.64       151.27 
TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29D 
       78.87       168.26        13.55        63.35        80.61        13.97 
TCGA-EE-A29G TCGA-EE-A29L TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29V 
       72.07         2.60        56.42        37.35        55.92        25.87 
TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 
      171.55        17.92        46.82       102.90        24.43        39.29 
TCGA-EE-A2A6 TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ 
       58.75       314.56       135.95       208.04        48.72        89.33 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP 
       54.74        79.66        75.48        90.97       101.95        13.91 
TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 
       55.59        44.88        94.82       129.27        28.83        19.76 
TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP 
      103.27       103.20        16.96       167.90        47.54       248.65 
TCGA-EE-A2MQ TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB 
       43.23       136.47        41.59        53.26       124.31       122.73 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 
       25.84         3.68        54.51        23.47       138.81       172.18 
TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3JA TCGA-EE-A3JE TCGA-EE-A3JH 
      127.20        36.95        64.08        53.19        33.40       101.79 
TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B 
       35.44        13.94        50.76         9.17        77.75        98.40 
TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J 
       48.89        12.59        13.02       268.93       152.35         6.44 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S 
      131.51        61.05        44.05       162.08        50.89        37.25 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF 
      148.18        79.99        43.82        23.34        20.15        16.37 
TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL 
       31.27        32.05       247.04        80.32        46.98        33.21 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 
      174.21         4.90       216.92        48.59       228.59       202.65 
TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZF 
       20.91        28.08        48.85       357.37        53.52        15.45 
TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP 
        9.70        32.75        47.38        23.93       101.26        74.73 
TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW 
      133.55        11.41       148.80        53.16        26.56        49.48 
TCGA-FS-A1ZY TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 
       27.09        77.82        66.67        28.73       174.84        12.43 
TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TV TCGA-FW-A5DY 
       26.73        49.45        77.88         0.20         0.16         2.40 
TCGA-GF-A3OT TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A268 TCGA-GN-A26A 
        9.90       120.46       117.93        84.72        62.79        32.48 
TCGA-GN-A26D TCGA-QB-A6FS 
       39.58         6.67 

  TP63 MUTATED TP63 WILD-TYPE 
          3.25           0.16 
  TP63 MUTATED TP63 WILD-TYPE 
        204.66         357.37 
  TP63 MUTATED TP63 WILD-TYPE 
         39.62          51.45 
[1] "3.2 - 204.7 (39.6)" "0.2 - 357.4 (51.5)"
[1] "hr=" "1.2"
D50V3, continuous
                vv
clus             DISTANT METASTASIS PRIMARY TUMOR
  TP63 MUTATED                    5             1
  TP63 WILD-TYPE                 30             3
                vv
clus             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  TP63 MUTATED                                           4                  36
  TP63 WILD-TYPE                                        54                 134
D50V4, multiclass
                                           clus
vv                                          TP63 MUTATED TP63 WILD-TYPE
  DISTANT METASTASIS                                   5             30
  PRIMARY TUMOR                                        1              3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE            4             54
  REGIONAL LYMPH NODE                                 36            134
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  TP63 MUTATED             1       1       4        1        3        5
  TP63 WILD-TYPE           9       5      18        9       21       12
                vv
clus             STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  TP63 MUTATED           1         5         1         5          5          5
  TP63 WILD-TYPE         9         9         8        26          8         17
                vv
clus             STAGE IIIC STAGE IV
  TP63 MUTATED            5        0
  TP63 WILD-TYPE         39       12
D50V5, multiclass
             clus
vv            TP63 MUTATED TP63 WILD-TYPE
  I OR II NOS            1              9
  STAGE 0                1              5
  STAGE I                4             18
  STAGE IA               1              9
  STAGE IB               3             21
  STAGE II               5             12
  STAGE IIA              1              9
  STAGE IIB              5              9
  STAGE IIC              1              8
  STAGE III              5             26
  STAGE IIIA             5              8
  STAGE IIIB             5             17
  STAGE IIIC             5             39
  STAGE IV               0             12
[1] 14  2
[1] 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
  TP63 MUTATED       4  8 14 12
  TP63 WILD-TYPE    47 50 39 43
D50V6, multiclass
       clus
vv      TP63 MUTATED TP63 WILD-TYPE
  T0+T1            4             47
  T2               8             50
  T3              14             39
  T4              12             43
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  TP63 MUTATED    24  10   7   1
  TP63 WILD-TYPE 114  38  25  32
D50V7, multiclass
    clus
vv   TP63 MUTATED TP63 WILD-TYPE
  N0           24            114
  N1           10             38
  N2            7             25
  N3            1             32
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              M0  M1 M1A M1B M1C
  TP63 MUTATED    43   0   0   0   0
  TP63 WILD-TYPE 197   4   2   2   5
D50V8, multiclass
     clus
vv    TP63 MUTATED TP63 WILD-TYPE
  M0            43            197
  M1             0              4
  M1A            0              2
  M1B            0              2
  M1C            0              5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V9, binary
                cls
clus              0  1
  TP63 MUTATED   20 11
  TP63 WILD-TYPE 82 56
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP63 MUTATED     20   11
  TP63 WILD-TYPE   82   56
     clus
vv    TP63 MUTATED TP63 WILD-TYPE
  NO            20             82
  YES           11             56
[1] 2 2
[1] FALSE
D50V10, binary
                cls
clus               0   1
  TP63 MUTATED     6  40
  TP63 WILD-TYPE  27 195
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP63 MUTATED      6   40
  TP63 WILD-TYPE   27  195
     clus
vv    TP63 MUTATED TP63 WILD-TYPE
  NO             6             27
  YES           40            195
[1] 2 2
[1] FALSE
D50V11, continuous
D50V12, binary
                cls
clus               0   1
  TP63 MUTATED    16  30
  TP63 WILD-TYPE  87 135
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP63 MUTATED     16   30
  TP63 WILD-TYPE   87  135
        clus
vv       TP63 MUTATED TP63 WILD-TYPE
  FEMALE           16             87
  MALE             30            135
[1] 2 2
[1] FALSE
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TP63 MUTATED       0                         0    46
  TP63 WILD-TYPE     3                         1   218
D50V13, multiclass
                           clus
vv                          TP63 MUTATED TP63 WILD-TYPE
  ASIAN                                0              3
  BLACK OR AFRICAN AMERICAN            0              1
  WHITE                               46            218
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V14, binary
                cls
clus               0   1
  TP63 MUTATED     1  45
  TP63 WILD-TYPE   2 216
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP63 MUTATED      1   45
  TP63 WILD-TYPE    2  216
                        clus
vv                       TP63 MUTATED TP63 WILD-TYPE
  HISPANIC OR LATINO                1              2
  NOT HISPANIC OR LATINO           45            216
[1] 2 2
[1] FALSE

Clustering(51) Variable = NGF MUTATION ANALYSIS
D51V1, survival
               sevent
clus2             0   1
  NGF MUTATED     6   3
  NGF WILD-TYPE 122 127
  NGF MUTATED NGF WILD-TYPE 
            9           249 
  NGF MUTATED NGF WILD-TYPE 
            3           127 
$`NGF MUTATED`
TCGA-D3-A1Q7 TCGA-D3-A5GN TCGA-D3-A5GO TCGA-DA-A3F3 TCGA-EB-A5UN TCGA-EE-A29S 
      110.79        52.01        47.87         7.00        13.22         9.99 
TCGA-EE-A2MS TCGA-FS-A1ZZ TCGA-GN-A266 
       27.16         5.23        10.13 

$`NGF WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q8 
       16.47         8.52       111.09        32.42        70.16        28.08 
TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 
       22.55        45.83        81.24        10.29        85.32         8.38 
TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF 
       21.14        88.50        68.22        69.90        11.41        30.87 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO 
        7.50        36.16         6.31        92.42        56.19        64.44 
TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB 
       45.11       114.67        15.25        46.98        46.32        82.29 
TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR 
       61.38        13.32        24.00         6.31         9.34       103.59 
TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J 
       26.37         5.39        80.22        42.71        15.09        41.10 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GR TCGA-D3-A5GS 
       17.72         8.84        20.48        13.94         1.55         6.97 
TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC 
       23.11         4.01         2.89         9.90        11.31        13.22 
TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 
       48.79        35.80        51.12        10.03        39.19        13.68 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB 
        9.99        44.52        36.69        25.15         4.93        22.36 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R 
        6.64        19.36        17.56        14.83        13.15         0.20 
TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 
        0.00         0.00        11.57        10.55         6.31         8.12 
TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B 
        1.12         1.35        12.20         5.13         4.31        36.07 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B 
        4.34         5.13         9.21         1.18         7.99         9.90 
TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L 
       37.97        11.15        38.63         8.55         4.41         1.08 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29V 
       27.12         9.50        12.03         8.09         8.84         2.43 
TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 
        8.68         8.09        11.31        49.22        23.90         9.67 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH 
        8.94        39.39        34.29        17.98        34.92        47.21 
TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN 
       30.08        19.43        16.01        35.54        28.31        33.83 
TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU 
       30.84         5.42         1.15        13.02        34.98        36.33 
TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD 
        8.84        98.27         2.70         6.18        47.51         9.53 
TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK 
       29.46        44.25         7.96        14.56        63.42       111.78 
TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR 
      111.91        56.02        25.08        26.99        21.60        29.65 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD 
       23.05         5.56       124.31       122.73        25.84         3.68 
TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 
       30.15        13.81        15.95        12.72         3.22        22.92 
TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE 
       21.60        21.60        16.14        22.22        27.35         0.46 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 
       13.94        33.60        31.40        18.61        12.95        38.40 
TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E 
        5.72        76.41        25.18         3.78         3.52        11.90 
TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M 
       11.11       114.15        34.88         4.21        13.45        28.60 
TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 
       42.84        34.68         9.57        36.07        17.72        78.44 
TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH 
       11.80         1.87         1.51        13.08        12.62        11.74 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A 
        9.04         6.58        22.49         1.71        18.41        85.74 
TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
        4.90        64.47         3.45        11.01        23.80        14.24 
TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD 
       15.52         7.33         7.30         3.39        20.38         8.22 
TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK 
       19.53        11.08         7.17        30.87        12.92        12.89 
TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT 
       47.38        52.08         8.65         8.81        49.15        40.64 
TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 
        8.68        27.39         0.82        53.85         7.36        28.73 
TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 
       14.20        10.78         5.98         6.41         2.27         0.20 
TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
        0.99         0.13         0.16         0.43         9.90         7.23 
TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 
       12.85        24.85        31.33        84.72        16.24        15.42 
TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS 
       12.16        14.70         5.79 

  NGF MUTATED NGF WILD-TYPE 
         5.23          0.00 
  NGF MUTATED NGF WILD-TYPE 
       110.79        124.31 
  NGF MUTATED NGF WILD-TYPE 
        13.22         14.83 
[1] "5.2 - 110.8 (13.2)" "0.0 - 124.3 (14.8)"
[1] "hr=" "1.6"
D51V2, survival
               sevent
clus2             0   1
  NGF MUTATED     6   3
  NGF WILD-TYPE 126 128
  NGF MUTATED NGF WILD-TYPE 
            9           254 
  NGF MUTATED NGF WILD-TYPE 
            3           128 
$`NGF MUTATED`
TCGA-D3-A1Q7 TCGA-D3-A5GN TCGA-D3-A5GO TCGA-DA-A3F3 TCGA-EB-A5UN TCGA-EE-A29S 
      133.25       135.75       137.92        10.49        52.01        55.92 
TCGA-EE-A2MS TCGA-FS-A1ZZ TCGA-GN-A266 
      136.47        27.02        10.13 

$`NGF WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q8 
       16.57        16.67       112.04       112.57        71.80        28.08 
TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 
       31.59        90.90        95.74        43.43       103.10        65.49 
TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF 
       23.77       115.53       168.00        69.90        11.87        48.76 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO 
      113.52        42.08        12.10       171.58        56.19        66.08 
TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB 
       45.11       130.72        58.06        46.98        46.32       166.52 
TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR 
       86.93        60.23        24.53        13.87         9.34       103.59 
TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J 
       39.75        21.47       161.85        43.69        40.14       131.90 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GR TCGA-D3-A5GS 
       18.38        10.03        51.68        15.06       166.19         7.43 
TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 
      125.19       151.53        54.67         3.65         6.41        11.34 
TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1HW 
        3.25         9.90        25.18        66.25        48.89        36.03 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 
      117.21        20.38       194.83       176.55        35.93       107.34 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
       61.18        53.92        65.92        23.44        68.09        28.60 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH 
      215.44        15.68        13.87        10.16        45.11        35.01 
TCGA-EB-A5UL TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 
        3.55        29.82        27.22         8.65        94.98        33.73 
TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C 
       14.70        26.89        68.15         4.96       109.64       151.27 
TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C 
       78.87       168.26        13.55        63.35        80.61        47.84 
TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M 
       13.97        39.62        72.07        32.19         2.60        44.35 
TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29V TCGA-EE-A29W 
       18.61        56.42        37.35        14.47        25.87       171.55 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 
       17.92        46.82       102.90        24.43        39.29        58.75 
TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI 
       47.54        67.43       314.56       135.95       208.04        48.72 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO 
       89.33        54.74        79.66        75.48        90.97       101.95 
TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 
       13.91        14.30        55.59        44.88        94.82        21.67 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME 
      129.27        28.83        19.76        61.51        47.28       103.27 
TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML 
      103.20        16.96       204.66        96.23       144.76       203.05 
TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MT 
      167.90        47.54       248.65        43.23       103.56        41.59 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE 
       53.26       124.31       122.73        25.84         3.68        54.51 
TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 
       13.81        23.47       138.81       172.18       127.20        36.95 
TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH 
       64.08        34.32        53.19        27.35        33.40       101.79 
TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 
      148.08        31.40        35.44        13.94        50.76         9.17 
TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F 
       77.75        98.40        48.89        12.59        13.02        26.37 
TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N 
      268.93       152.35         6.44       131.51        61.05        44.05 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
      162.08        50.89        37.25       148.18        79.99        43.82 
TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES 
       23.34        20.15        16.37        31.27        32.05       247.04 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
       80.32        46.98        33.21        92.98       174.21         4.90 
TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 
      216.92        48.59       228.59       202.65        20.91        28.08 
TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE 
        7.79        27.72        48.85       357.37        53.52        40.27 
TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM 
       15.45         9.70        32.75        47.38        23.93       101.26 
TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU 
       74.73       133.55        11.41       148.80        53.16        26.56 
TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 
       49.48        27.09        77.82        66.67        28.73       174.84 
TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 
       12.43        26.73        49.45        77.88         0.20        22.92 
TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 
       47.54         0.16         2.40         9.90         7.23        14.04 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
      120.46       117.93        84.72        64.44        62.79        32.48 
TCGA-GN-A26D TCGA-QB-A6FS 
       39.58         6.67 

  NGF MUTATED NGF WILD-TYPE 
        10.13          0.16 
  NGF MUTATED NGF WILD-TYPE 
       137.92        357.37 
  NGF MUTATED NGF WILD-TYPE 
        55.92         47.69 
[1] "10.1 - 137.9 (55.9)" "0.2 - 357.4 (47.7)" 
[1] "hr=" "1.5"
D51V3, continuous
               vv
clus            DISTANT METASTASIS PRIMARY TUMOR
  NGF MUTATED                    3             0
  NGF WILD-TYPE                 32             4
               vv
clus            REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  NGF MUTATED                                           1                   5
  NGF WILD-TYPE                                        57                 165
D51V4, multiclass
                                           clus
vv                                          NGF MUTATED NGF WILD-TYPE
  DISTANT METASTASIS                                  3            32
  PRIMARY TUMOR                                       0             4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE           1            57
  REGIONAL LYMPH NODE                                 5           165
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  NGF MUTATED             0       0       1        0        1        2
  NGF WILD-TYPE          10       6      21       10       23       15
               vv
clus            STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  NGF MUTATED           1         1         1         0          0          1
  NGF WILD-TYPE         9        13         8        31         13         21
               vv
clus            STAGE IIIC STAGE IV
  NGF MUTATED            0        0
  NGF WILD-TYPE         44       12
D51V5, multiclass
             clus
vv            NGF MUTATED NGF WILD-TYPE
  I OR II NOS           0            10
  STAGE 0               0             6
  STAGE I               1            21
  STAGE IA              0            10
  STAGE IB              1            23
  STAGE II              2            15
  STAGE IIA             1             9
  STAGE IIB             1            13
  STAGE IIC             1             8
  STAGE III             0            31
  STAGE IIIA            0            13
  STAGE IIIB            1            21
  STAGE IIIC            0            44
  STAGE IV              0            12
[1] 14  2
[1] 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
  NGF MUTATED       3  0  3  2
  NGF WILD-TYPE    48 58 50 53
D51V6, multiclass
       clus
vv      NGF MUTATED NGF WILD-TYPE
  T0+T1           3            48
  T2              0            58
  T3              3            50
  T4              2            53
[1] 4 2
[1] TRUE
[1] "dimension 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
  NGF MUTATED     6   0   1   0
  NGF WILD-TYPE 132  48  31  33
D51V7, multiclass
    clus
vv   NGF MUTATED NGF WILD-TYPE
  N0           6           132
  N1           0            48
  N2           1            31
  N3           0            33
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             M0  M1 M1A M1B M1C
  NGF MUTATED     8   0   0   0   0
  NGF WILD-TYPE 232   4   2   2   5
D51V8, multiclass
     clus
vv    NGF MUTATED NGF WILD-TYPE
  M0            8           232
  M1            0             4
  M1A           0             2
  M1B           0             2
  M1C           0             5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V9, binary
               cls
clus             0  1
  NGF MUTATED    3  2
  NGF WILD-TYPE 99 65
[1] "tbl2"
               cls
clus            [,1] [,2]
  NGF MUTATED      3    2
  NGF WILD-TYPE   99   65
     clus
vv    NGF MUTATED NGF WILD-TYPE
  NO            3            99
  YES           2            65
[1] 2 2
[1] FALSE
D51V10, binary
               cls
clus              0   1
  NGF MUTATED     2   7
  NGF WILD-TYPE  31 228
[1] "tbl2"
               cls
clus            [,1] [,2]
  NGF MUTATED      2    7
  NGF WILD-TYPE   31  228
     clus
vv    NGF MUTATED NGF WILD-TYPE
  NO            2            31
  YES           7           228
[1] 2 2
[1] FALSE
D51V11, continuous
D51V12, binary
               cls
clus              0   1
  NGF MUTATED     3   6
  NGF WILD-TYPE 100 159
[1] "tbl2"
               cls
clus            [,1] [,2]
  NGF MUTATED      3    6
  NGF WILD-TYPE  100  159
        clus
vv       NGF MUTATED NGF WILD-TYPE
  FEMALE           3           100
  MALE             6           159
[1] 2 2
[1] FALSE
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  NGF MUTATED       0                         0     9
  NGF WILD-TYPE     3                         1   255
D51V13, multiclass
                           clus
vv                          NGF MUTATED NGF WILD-TYPE
  ASIAN                               0             3
  BLACK OR AFRICAN AMERICAN           0             1
  WHITE                               9           255
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V14, binary
               cls
clus              0   1
  NGF MUTATED     1   8
  NGF WILD-TYPE   2 253
[1] "tbl2"
               cls
clus            [,1] [,2]
  NGF MUTATED      1    8
  NGF WILD-TYPE    2  253
                        clus
vv                       NGF MUTATED NGF WILD-TYPE
  HISPANIC OR LATINO               1             2
  NOT HISPANIC OR LATINO           8           253
[1] 2 2
[1] FALSE

Clustering(52) Variable = ANO4 MUTATION ANALYSIS
D52V1, survival
                sevent
clus2              0   1
  ANO4 MUTATED    19  21
  ANO4 WILD-TYPE 109 109
  ANO4 MUTATED ANO4 WILD-TYPE 
            40            218 
  ANO4 MUTATED ANO4 WILD-TYPE 
            21            109 
$`ANO4 MUTATED`
TCGA-D3-A1Q4 TCGA-D3-A2J7 TCGA-D3-A2JF TCGA-D3-A3ML TCGA-D3-A3MR TCGA-D3-A51R 
      111.09        85.32        30.87         6.31       103.59        20.48 
TCGA-DA-A1HY TCGA-DA-A1I8 TCGA-DA-A1IC TCGA-DA-A3F5 TCGA-EE-A17X TCGA-EE-A181 
       51.12        25.15         6.64        17.56        11.57         1.12 
TCGA-EE-A20C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N 
        4.34        11.15        38.63         1.08        27.12         9.50 
TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GR TCGA-EE-A2M5 
        8.09         9.99        47.21        30.08         1.15         8.84 
TCGA-EE-A2MH TCGA-EE-A2ML TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A3AC TCGA-EE-A3AE 
        7.96       111.91        29.65        27.16        25.84        30.15 
TCGA-EE-A3AG TCGA-EE-A3J5 TCGA-EE-A3JD TCGA-ER-A195 TCGA-FS-A1ZD TCGA-FS-A1ZZ 
       15.95        21.60        27.35        18.61         8.22         5.23 
TCGA-FS-A4FB TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-QB-A6FS 
        5.98         0.99         0.13         5.79 

$`ANO4 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       16.47         8.52        32.42        70.16       110.79        28.08 
TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J8 TCGA-D3-A2J9 
       22.55        45.83        81.24        10.29         8.38        21.14 
TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JH 
       88.50        68.22        69.90        11.41         7.50        36.16 
TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ 
        6.31        92.42        56.19        64.44        45.11       114.67 
TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE 
       15.25        46.98        46.32        82.29        61.38        13.32 
TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F 
       24.00         9.34        26.37         5.39        80.22        42.71 
TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51T TCGA-D3-A5GN 
       15.09        41.10        17.72         8.84        13.94        52.01 
TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 
       47.87         1.55         6.97        23.11         4.01         2.89 
TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1I0 
        9.90        11.31        13.22        48.79        35.80        10.03 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA 
       39.19        13.68         9.99        44.52        36.69         4.93 
TCGA-DA-A1IB TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R 
       22.36        19.36         7.00        14.83        13.15         0.20 
TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 
        0.00         0.00        13.22        10.55         6.31         8.12 
TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20F 
        1.35        12.20         5.13         4.31        36.07         5.13 
TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29G 
        9.21         1.18         7.99         9.90        37.97         8.55 
TCGA-EE-A29H TCGA-EE-A29P TCGA-EE-A29R TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X 
        4.41        12.03         8.84         2.43         8.68         8.09 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB 
       11.31        49.22        23.90         9.67         8.94        39.39 
TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
       34.29        17.98        34.92        19.43        16.01        35.54 
TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GS TCGA-EE-A2GT 
       28.31        33.83        30.84         5.42        13.02        34.98 
TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD 
       36.33        98.27         2.70         6.18        47.51         9.53 
TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2MM 
       29.46        44.25        14.56        63.42       111.78        56.02 
TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA 
       25.08        26.99        21.60        23.05         5.56       124.31 
TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 
      122.73         3.68        13.81        12.72         3.22        22.92 
TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI 
       21.60        16.14        22.22         0.46        13.94        33.60 
TCGA-ER-A193 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B 
       31.40        12.95        38.40         5.72        76.41        25.18 
TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H 
        3.78         3.52        11.90        11.11       114.15        34.88 
TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q 
        4.21        13.45        28.60        42.84        34.68         9.57 
TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE 
       36.07        17.72        78.44        11.80         1.87         1.51 
TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV 
       13.08        12.62        11.74         9.04         6.58        22.49 
TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX 
        1.71        18.41        85.74         4.90        64.47         3.45 
TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA 
       11.01        23.80        14.24        15.52         7.33         7.30 
TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH 
        3.39        20.38        19.53        11.08         7.17        30.87 
TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR 
       12.92        12.89        47.38        52.08         8.65         8.81 
TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A4F0 
       49.15        40.64         8.68        27.39         0.82        53.85 
TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FS-A4FD 
        7.36        28.73        14.20        10.78         6.41         2.27 
TCGA-FW-A3I3 TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 
        0.20         0.16         0.43         9.90         7.23        12.85 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 
       24.85        31.33        84.72        10.13        16.24        15.42 
TCGA-GN-A26A TCGA-GN-A26D 
       12.16        14.70 

  ANO4 MUTATED ANO4 WILD-TYPE 
          0.13           0.00 
  ANO4 MUTATED ANO4 WILD-TYPE 
        111.91         124.31 
  ANO4 MUTATED ANO4 WILD-TYPE 
        16.755         14.630 
[1] "0.1 - 111.9 (16.8)" "0.0 - 124.3 (14.6)"
[1] "hr=" "1.1"
D52V2, survival
                sevent
clus2              0   1
  ANO4 MUTATED    19  21
  ANO4 WILD-TYPE 113 110
  ANO4 MUTATED ANO4 WILD-TYPE 
            40            223 
  ANO4 MUTATED ANO4 WILD-TYPE 
            21            110 
$`ANO4 MUTATED`
TCGA-D3-A1Q4 TCGA-D3-A2J7 TCGA-D3-A2JF TCGA-D3-A3ML TCGA-D3-A3MR TCGA-D3-A51R 
      112.04       103.10        48.76        13.87       103.59        51.68 
TCGA-DA-A1HY TCGA-DA-A1I8 TCGA-DA-A1IC TCGA-DA-A3F5 TCGA-EE-A17X TCGA-EE-A181 
      117.21        53.92        68.09       215.44        29.82        33.73 
TCGA-EE-A20C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N 
      151.27        13.97        39.62         2.60        44.35        18.61 
TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GR TCGA-EE-A2M5 
       37.35        55.92       208.04        48.72        14.30        21.67 
TCGA-EE-A2MH TCGA-EE-A2ML TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A3AC TCGA-EE-A3AE 
       16.96       203.05       103.56       136.47        25.84        54.51 
TCGA-EE-A3AG TCGA-EE-A3J5 TCGA-EE-A3JD TCGA-ER-A195 TCGA-FS-A1ZD TCGA-FS-A1ZZ 
       23.47        36.95        27.35        35.44        53.52        27.02 
TCGA-FS-A4FB TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-QB-A6FS 
       26.73        22.92        47.54         6.67 

$`ANO4 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       16.57        16.67       112.57        71.80       133.25        28.08 
TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J8 TCGA-D3-A2J9 
       31.59        90.90        95.74        43.43        65.49        23.77 
TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JH 
      115.53       168.00        69.90        11.87       113.52        42.08 
TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ 
       12.10       171.58        56.19        66.08        45.11       130.72 
TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE 
       58.06        46.98        46.32       166.52        86.93        60.23 
TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F 
       24.53         9.34        39.75        21.47       161.85        43.69 
TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51T TCGA-D3-A5GN 
       40.14       131.90        18.38        10.03        15.06       135.75 
TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 
      137.92       166.19         7.43       125.19       151.53        54.67 
TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA 
        3.65         6.41        11.34         3.25         9.90        25.18 
TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 
       66.25        48.89        36.03        20.38       194.83       176.55 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A3F2 
       35.93       107.34        61.18        65.92        23.44        28.60 
TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH 
       10.49        15.68        13.87        10.16        45.11        35.01 
TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A182 
        3.55        52.01        27.22         8.65        94.98        14.70 
TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H 
       26.89        68.15         4.96       109.64        78.87       168.26 
TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29G TCGA-EE-A29H 
       13.55        63.35        80.61        47.84        72.07        32.19 
TCGA-EE-A29P TCGA-EE-A29R TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 
       56.42        14.47        25.87       171.55        17.92        46.82 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC 
      102.90        24.43        39.29        58.75        47.54        67.43 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM 
      314.56       135.95        89.33        54.74        79.66        75.48 
TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU 
       90.97       101.95        13.91        55.59        44.88        94.82 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME 
      129.27        28.83        19.76        61.51        47.28       103.27 
TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2MM TCGA-EE-A2MN 
      103.20       204.66        96.23       144.76       167.90        47.54 
TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB 
      248.65        43.23        41.59        53.26       124.31       122.73 
TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 
        3.68        13.81       138.81       172.18       127.20        64.08 
TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 
       34.32        53.19        33.40       101.79       148.08        31.40 
TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C 
       13.94        50.76         9.17        77.75        98.40        48.89 
TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J 
       12.59        13.02        26.37       268.93       152.35         6.44 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S 
      131.51        61.05        44.05       162.08        50.89        37.25 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF 
      148.18        79.99        43.82        23.34        20.15        16.37 
TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL 
       31.27        32.05       247.04        80.32        46.98        33.21 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY 
       92.98       174.21         4.90       216.92        48.59       228.59 
TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB 
      202.65        20.91        28.08         7.79        27.72        48.85 
TCGA-FS-A1ZC TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ 
      357.37        40.27        15.45         9.70        32.75        47.38 
TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS 
       23.93       101.26        74.73       133.55        11.41       148.80 
TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A4F0 TCGA-FS-A4F4 
       53.16        26.56        49.48        27.09        77.82        66.67 
TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 
       28.73       174.84        12.43        49.45        77.88         0.20 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 
        0.16         2.40         9.90         7.23        14.04       120.46 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
      117.93        84.72        10.13        64.44        62.79        32.48 
TCGA-GN-A26D 
       39.58 

  ANO4 MUTATED ANO4 WILD-TYPE 
          2.60           0.16 
  ANO4 MUTATED ANO4 WILD-TYPE 
        215.44         357.37 
  ANO4 MUTATED ANO4 WILD-TYPE 
        41.985         48.890 
[1] "2.6 - 215.4 (42.0)" "0.2 - 357.4 (48.9)"
[1] "hr=" "1.2"
D52V3, continuous
                vv
clus             DISTANT METASTASIS PRIMARY TUMOR
  ANO4 MUTATED                    5             0
  ANO4 WILD-TYPE                 30             4
                vv
clus             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  ANO4 MUTATED                                           7                  29
  ANO4 WILD-TYPE                                        51                 141
D52V4, multiclass
                                           clus
vv                                          ANO4 MUTATED ANO4 WILD-TYPE
  DISTANT METASTASIS                                   5             30
  PRIMARY TUMOR                                        0              4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE            7             51
  REGIONAL LYMPH NODE                                 29            141
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  ANO4 MUTATED             2       1       3        4        1        4
  ANO4 WILD-TYPE           8       5      19        6       23       13
                vv
clus             STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  ANO4 MUTATED           3         2         0         8          1          2
  ANO4 WILD-TYPE         7        12         9        23         12         20
                vv
clus             STAGE IIIC STAGE IV
  ANO4 MUTATED            8        0
  ANO4 WILD-TYPE         36       12
D52V5, multiclass
             clus
vv            ANO4 MUTATED ANO4 WILD-TYPE
  I OR II NOS            2              8
  STAGE 0                1              5
  STAGE I                3             19
  STAGE IA               4              6
  STAGE IB               1             23
  STAGE II               4             13
  STAGE IIA              3              7
  STAGE IIB              2             12
  STAGE IIC              0              9
  STAGE III              8             23
  STAGE IIIA             1             12
  STAGE IIIB             2             20
  STAGE IIIC             8             36
  STAGE IV               0             12
[1] 14  2
[1] 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
  ANO4 MUTATED       9  9 12  5
  ANO4 WILD-TYPE    42 49 41 50
D52V6, multiclass
       clus
vv      ANO4 MUTATED ANO4 WILD-TYPE
  T0+T1            9             42
  T2               9             49
  T3              12             41
  T4               5             50
[1] 4 2
[1] TRUE
[1] "dimension 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
  ANO4 MUTATED    22   7   6   5
  ANO4 WILD-TYPE 116  41  26  28
D52V7, multiclass
    clus
vv   ANO4 MUTATED ANO4 WILD-TYPE
  N0           22            116
  N1            7             41
  N2            6             26
  N3            5             28
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              M0  M1 M1A M1B M1C
  ANO4 MUTATED    40   0   0   0   0
  ANO4 WILD-TYPE 200   4   2   2   5
D52V8, multiclass
     clus
vv    ANO4 MUTATED ANO4 WILD-TYPE
  M0            40            200
  M1             0              4
  M1A            0              2
  M1B            0              2
  M1C            0              5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V9, binary
                cls
clus              0  1
  ANO4 MUTATED   16  9
  ANO4 WILD-TYPE 86 58
[1] "tbl2"
                cls
clus             [,1] [,2]
  ANO4 MUTATED     16    9
  ANO4 WILD-TYPE   86   58
     clus
vv    ANO4 MUTATED ANO4 WILD-TYPE
  NO            16             86
  YES            9             58
[1] 2 2
[1] FALSE
D52V10, binary
                cls
clus               0   1
  ANO4 MUTATED     5  36
  ANO4 WILD-TYPE  28 199
[1] "tbl2"
                cls
clus             [,1] [,2]
  ANO4 MUTATED      5   36
  ANO4 WILD-TYPE   28  199
     clus
vv    ANO4 MUTATED ANO4 WILD-TYPE
  NO             5             28
  YES           36            199
[1] 2 2
[1] FALSE
D52V11, continuous
D52V12, binary
                cls
clus               0   1
  ANO4 MUTATED    10  31
  ANO4 WILD-TYPE  93 134
[1] "tbl2"
                cls
clus             [,1] [,2]
  ANO4 MUTATED     10   31
  ANO4 WILD-TYPE   93  134
        clus
vv       ANO4 MUTATED ANO4 WILD-TYPE
  FEMALE           10             93
  MALE             31            134
[1] 2 2
[1] FALSE
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ANO4 MUTATED       0                         0    41
  ANO4 WILD-TYPE     3                         1   223
D52V13, multiclass
                           clus
vv                          ANO4 MUTATED ANO4 WILD-TYPE
  ASIAN                                0              3
  BLACK OR AFRICAN AMERICAN            0              1
  WHITE                               41            223
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V14, binary
                cls
clus               0   1
  ANO4 MUTATED     1  39
  ANO4 WILD-TYPE   2 222
[1] "tbl2"
                cls
clus             [,1] [,2]
  ANO4 MUTATED      1   39
  ANO4 WILD-TYPE    2  222
                        clus
vv                       ANO4 MUTATED ANO4 WILD-TYPE
  HISPANIC OR LATINO                1              2
  NOT HISPANIC OR LATINO           39            222
[1] 2 2
[1] FALSE

Clustering(53) Variable = PCDH18 MUTATION ANALYSIS
D53V1, survival
                  sevent
clus2                0   1
  PCDH18 MUTATED    25  21
  PCDH18 WILD-TYPE 103 109
  PCDH18 MUTATED PCDH18 WILD-TYPE 
              46              212 
  PCDH18 MUTATED PCDH18 WILD-TYPE 
              21              109 
$`PCDH18 MUTATED`
TCGA-D3-A1QB TCGA-D3-A2JF TCGA-D3-A2JH TCGA-D3-A3CB TCGA-D3-A51F TCGA-D9-A6EC 
       81.24        30.87        36.16        82.29        42.71        13.22 
TCGA-DA-A1HY TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A20C TCGA-EE-A20H TCGA-EE-A29B 
       51.12         1.12         1.35         4.34         9.21         9.90 
TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29S TCGA-EE-A2A1 
       11.15         8.55         1.08        27.12         9.99        49.22 
TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2M5 TCGA-EE-A2MI 
       39.39        34.29         1.15        13.02         8.84        14.56 
TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3JA TCGA-EE-A3JD 
       63.42       111.91       124.31       122.73        22.22        27.35 
TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A19A TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19N 
       33.60        31.40        76.41         3.52        11.90        42.84 
TCGA-ER-A2NH TCGA-ER-A3PL TCGA-FS-A1Z0 TCGA-FS-A1ZK TCGA-FS-A1ZW TCGA-FS-A1ZZ 
       11.74         1.71        23.80        12.89        27.39         5.23 
TCGA-FW-A3R5 TCGA-GN-A266 TCGA-GN-A268 TCGA-QB-A6FS 
        0.99        10.13        15.42         5.79 

$`PCDH18 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.47         8.52       111.09        32.42        70.16       110.79 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 
       28.08        22.55        45.83        10.29        85.32         8.38 
TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JG 
       21.14        88.50        68.22        69.90        11.41         7.50 
TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ 
        6.31        92.42        56.19        64.44        45.11       114.67 
TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF 
       15.25        46.98        46.32        61.38        13.32        24.00 
TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E 
        6.31         9.34       103.59        26.37         5.39        80.22 
TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T 
       15.09        41.10        17.72         8.84        20.48        13.94 
TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 
       52.01        47.87         1.55         6.97        23.11         4.01 
TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1I0 
        2.89         9.90        11.31        48.79        35.80        10.03 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 
       39.19        13.68         9.99        44.52        36.69        25.15 
TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 
        4.93        22.36         6.64        19.36         7.00        17.56 
TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN 
       14.83        13.15         0.20         0.00         0.00        13.22 
TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A183 TCGA-EE-A184 
       11.57        10.55         6.31         8.12        12.20         5.13 
TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29C 
        4.31        36.07         5.13         1.18         7.99        37.97 
TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R 
       38.63         4.41         9.50        12.03         8.09         8.84 
TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A2 TCGA-EE-A2A5 
        2.43         8.68         8.09        11.31        23.90         9.67 
TCGA-EE-A2A6 TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ 
        8.94        17.98        34.92        47.21        30.08        19.43 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP 
       16.01        35.54        28.31        33.83        30.84         5.42 
TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC 
       34.98        36.33        98.27         2.70         6.18        47.51 
TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MK TCGA-EE-A2MM 
        9.53        29.46        44.25         7.96       111.78        56.02 
TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT 
       25.08        26.99        21.60        29.65        27.16        23.05 
TCGA-EE-A2MU TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG 
        5.56        25.84         3.68        30.15        13.81        15.95 
TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 
       12.72         3.22        22.92        21.60        21.60        16.14 
TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 
        0.46        13.94        18.61        12.95        38.40         5.72 
TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J 
       25.18         3.78        11.11       114.15        34.88         4.21 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W 
       13.45        28.60        34.68         9.57        36.07        17.72 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG 
       78.44        11.80         1.87         1.51        13.08        12.62 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
        9.04         6.58        22.49        18.41        85.74         4.90 
TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 
       64.47         3.45        11.01        14.24        15.52         7.33 
TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF 
        7.30         3.39        20.38         8.22        19.53        11.08 
TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ 
        7.17        30.87        12.92        47.38        52.08         8.65 
TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZY TCGA-FS-A4F0 
        8.81        49.15        40.64         8.68         0.82        53.85 
TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC 
        7.36        28.73        14.20        10.78         5.98         6.41 
TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
        2.27         0.20         0.13         0.16         0.43         9.90 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 
        7.23        12.85        24.85        31.33        84.72        16.24 
TCGA-GN-A26A TCGA-GN-A26D 
       12.16        14.70 

  PCDH18 MUTATED PCDH18 WILD-TYPE 
            0.99             0.00 
  PCDH18 MUTATED PCDH18 WILD-TYPE 
          124.31           114.67 
  PCDH18 MUTATED PCDH18 WILD-TYPE 
          14.990           14.765 
[1] "1.0 - 124.3 (15.0)" "0.0 - 114.7 (14.8)"
[1] "hr=" "1.3"
D53V2, survival
                  sevent
clus2                0   1
  PCDH18 MUTATED    25  21
  PCDH18 WILD-TYPE 107 110
  PCDH18 MUTATED PCDH18 WILD-TYPE 
              46              217 
  PCDH18 MUTATED PCDH18 WILD-TYPE 
              21              110 
$`PCDH18 MUTATED`
TCGA-D3-A1QB TCGA-D3-A2JF TCGA-D3-A2JH TCGA-D3-A3CB TCGA-D3-A51F TCGA-D9-A6EC 
       95.74        48.76        42.08       166.52        43.69        66.25 
TCGA-DA-A1HY TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A20C TCGA-EE-A20H TCGA-EE-A29B 
      117.21        33.73        14.70       151.27       168.26        80.61 
TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29S TCGA-EE-A2A1 
       13.97        72.07         2.60        44.35        55.92       102.90 
TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2M5 TCGA-EE-A2MI 
       47.54        67.43        14.30        55.59        21.67       204.66 
TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3JA TCGA-EE-A3JD 
       96.23       203.05       124.31       122.73        53.19        27.35 
TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A19A TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19N 
      148.08        31.40        77.75        12.59        13.02        44.05 
TCGA-ER-A2NH TCGA-ER-A3PL TCGA-FS-A1Z0 TCGA-FS-A1ZK TCGA-FS-A1ZW TCGA-FS-A1ZZ 
       32.05        33.21       202.65        23.93        49.48        27.02 
TCGA-FW-A3R5 TCGA-GN-A266 TCGA-GN-A268 TCGA-QB-A6FS 
       22.92        10.13        62.79         6.67 

$`PCDH18 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.57        16.67       112.04       112.57        71.80       133.25 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 
       28.08        31.59        90.90        43.43       103.10        65.49 
TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JG 
       23.77       115.53       168.00        69.90        11.87       113.52 
TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ 
       12.10       171.58        56.19        66.08        45.11       130.72 
TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF 
       58.06        46.98        46.32        86.93        60.23        24.53 
TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E 
       13.87         9.34       103.59        39.75        21.47       161.85 
TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T 
       40.14       131.90        18.38        10.03        51.68        15.06 
TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 
      135.75       137.92       166.19         7.43       125.19       151.53 
TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 
       54.67         3.65         6.41        11.34         3.25         9.90 
TCGA-D9-A6EA TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 
       25.18        48.89        36.03        20.38       194.83       176.55 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB 
       35.93       107.34        61.18        53.92        65.92        23.44 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q 
       68.09        28.60        10.49       215.44        15.68        13.87 
TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X 
       10.16        45.11        35.01         3.55        52.01        29.82 
TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 
       27.22         8.65        94.98        26.89        68.15         4.96 
TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29E 
      109.64        78.87        13.55        63.35        47.84        39.62 
TCGA-EE-A29H TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29V 
       32.19        18.61        56.42        37.35        14.47        25.87 
TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 
      171.55        17.92        46.82        24.43        39.29        58.75 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK 
      314.56       135.95       208.04        48.72        89.33        54.74 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GT 
       79.66        75.48        90.97       101.95        13.91        44.88 
TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD 
       94.82       129.27        28.83        19.76        61.51        47.28 
TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MK TCGA-EE-A2MM TCGA-EE-A2MN 
      103.27       103.20        16.96       144.76       167.90        47.54 
TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU 
      248.65        43.23       103.56       136.47        41.59        53.26 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH 
       25.84         3.68        54.51        13.81        23.47       138.81 
TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JE 
      172.18       127.20        36.95        64.08        34.32        33.40 
TCGA-EE-A3JH TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19B 
      101.79        35.44        13.94        50.76         9.17        98.40 
TCGA-ER-A19C TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L 
       48.89        26.37       268.93       152.35         6.44       131.51 
TCGA-ER-A19M TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 
       61.05       162.08        50.89        37.25       148.18        79.99 
TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES 
       43.82        23.34        20.15        16.37        31.27       247.04 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW 
       80.32        46.98        92.98       174.21         4.90       216.92 
TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA 
       48.59       228.59        20.91        28.08         7.79        27.72 
TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG 
       48.85       357.37        53.52        40.27        15.45         9.70 
TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR 
       32.75        47.38       101.26        74.73       133.55        11.41 
TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZY TCGA-FS-A4F0 TCGA-FS-A4F4 
      148.80        53.16        26.56        27.09        77.82        66.67 
TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD 
       28.73       174.84        12.43        26.73        49.45        77.88 
TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
        0.20        47.54         0.16         2.40         9.90         7.23 
TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A26A 
       14.04       120.46       117.93        84.72        64.44        32.48 
TCGA-GN-A26D 
       39.58 

  PCDH18 MUTATED PCDH18 WILD-TYPE 
            2.60             0.16 
  PCDH18 MUTATED PCDH18 WILD-TYPE 
          204.66           357.37 
  PCDH18 MUTATED PCDH18 WILD-TYPE 
           49.12            47.84 
[1] "2.6 - 204.7 (49.1)" "0.2 - 357.4 (47.8)"
[1] "hr=" "1.1"
D53V3, continuous
                  vv
clus               DISTANT METASTASIS PRIMARY TUMOR
  PCDH18 MUTATED                    8             1
  PCDH18 WILD-TYPE                 27             3
                  vv
clus               REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  PCDH18 MUTATED                                           8
  PCDH18 WILD-TYPE                                        50
                  vv
clus               REGIONAL LYMPH NODE
  PCDH18 MUTATED                    30
  PCDH18 WILD-TYPE                 140
D53V4, multiclass
                                           clus
vv                                          PCDH18 MUTATED PCDH18 WILD-TYPE
  DISTANT METASTASIS                                     8               27
  PRIMARY TUMOR                                          1                3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE              8               50
  REGIONAL LYMPH NODE                                   30              140
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  PCDH18 MUTATED             1       2       3        2        7        4
  PCDH18 WILD-TYPE           9       4      19        8       17       13
                  vv
clus               STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  PCDH18 MUTATED           1         6         0         6          2
  PCDH18 WILD-TYPE         9         8         9        25         11
                  vv
clus               STAGE IIIB STAGE IIIC STAGE IV
  PCDH18 MUTATED            2          7        2
  PCDH18 WILD-TYPE         20         37       10
D53V5, multiclass
             clus
vv            PCDH18 MUTATED PCDH18 WILD-TYPE
  I OR II NOS              1                9
  STAGE 0                  2                4
  STAGE I                  3               19
  STAGE IA                 2                8
  STAGE IB                 7               17
  STAGE II                 4               13
  STAGE IIA                1                9
  STAGE IIB                6                8
  STAGE IIC                0                9
  STAGE III                6               25
  STAGE IIIA               2               11
  STAGE IIIB               2               20
  STAGE IIIC               7               37
  STAGE IV                 2               10
[1] 14  2
[1] 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
  PCDH18 MUTATED       7 13 10 10
  PCDH18 WILD-TYPE    44 45 43 45
D53V6, multiclass
       clus
vv      PCDH18 MUTATED PCDH18 WILD-TYPE
  T0+T1              7               44
  T2                13               45
  T3                10               43
  T4                10               45
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  PCDH18 MUTATED    29   7   5   4
  PCDH18 WILD-TYPE 109  41  27  29
D53V7, multiclass
    clus
vv   PCDH18 MUTATED PCDH18 WILD-TYPE
  N0             29              109
  N1              7               41
  N2              5               27
  N3              4               29
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                M0  M1 M1A M1B M1C
  PCDH18 MUTATED    43   1   1   0   0
  PCDH18 WILD-TYPE 197   3   1   2   5
D53V8, multiclass
     clus
vv    PCDH18 MUTATED PCDH18 WILD-TYPE
  M0              43              197
  M1               1                3
  M1A              1                1
  M1B              0                2
  M1C              0                5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V9, binary
                  cls
clus                0  1
  PCDH18 MUTATED   19 11
  PCDH18 WILD-TYPE 83 56
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PCDH18 MUTATED     19   11
  PCDH18 WILD-TYPE   83   56
     clus
vv    PCDH18 MUTATED PCDH18 WILD-TYPE
  NO              19               83
  YES             11               56
[1] 2 2
[1] FALSE
D53V10, binary
                  cls
clus                 0   1
  PCDH18 MUTATED     8  39
  PCDH18 WILD-TYPE  25 196
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PCDH18 MUTATED      8   39
  PCDH18 WILD-TYPE   25  196
     clus
vv    PCDH18 MUTATED PCDH18 WILD-TYPE
  NO               8               25
  YES             39              196
[1] 2 2
[1] FALSE
D53V11, continuous
D53V12, binary
                  cls
clus                 0   1
  PCDH18 MUTATED    11  36
  PCDH18 WILD-TYPE  92 129
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PCDH18 MUTATED     11   36
  PCDH18 WILD-TYPE   92  129
        clus
vv       PCDH18 MUTATED PCDH18 WILD-TYPE
  FEMALE             11               92
  MALE               36              129
[1] 2 2
[1] FALSE
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PCDH18 MUTATED       0                         0    47
  PCDH18 WILD-TYPE     3                         1   217
D53V13, multiclass
                           clus
vv                          PCDH18 MUTATED PCDH18 WILD-TYPE
  ASIAN                                  0                3
  BLACK OR AFRICAN AMERICAN              0                1
  WHITE                                 47              217
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V14, binary
                  cls
clus                 0   1
  PCDH18 MUTATED     1  46
  PCDH18 WILD-TYPE   2 215
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PCDH18 MUTATED      1   46
  PCDH18 WILD-TYPE    2  215
                        clus
vv                       PCDH18 MUTATED PCDH18 WILD-TYPE
  HISPANIC OR LATINO                  1                2
  NOT HISPANIC OR LATINO             46              215
[1] 2 2
[1] FALSE

Clustering(54) Variable = NMS MUTATION ANALYSIS
D54V1, survival
               sevent
clus2             0   1
  NMS MUTATED     9   4
  NMS WILD-TYPE 119 126
  NMS MUTATED NMS WILD-TYPE 
           13           245 
  NMS MUTATED NMS WILD-TYPE 
            4           126 
$`NMS MUTATED`
TCGA-D3-A2JF TCGA-D3-A2JO TCGA-D3-A3C8 TCGA-EE-A181 TCGA-EE-A29S TCGA-EE-A29V 
       30.87        64.44        46.32         1.12         9.99         2.43 
TCGA-EE-A2GI TCGA-EE-A2GM TCGA-EE-A3AA TCGA-EE-A3AE TCGA-EE-A3JD TCGA-FS-A1Z3 
       30.08        28.31       124.31        30.15        27.35        14.24 
TCGA-GF-A3OT 
        9.90 

$`NMS WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.47         8.52       111.09        32.42        70.16       110.79 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       28.08        22.55        45.83        81.24        10.29        85.32 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
        8.38        21.14        88.50        68.22        69.90        11.41 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JP 
        7.50        36.16         6.31        92.42        56.19        45.11 
TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE 
      114.67        15.25        46.98        82.29        61.38        13.32 
TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV 
       24.00         6.31         9.34       103.59        26.37         5.39 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N 
       80.22        42.71        15.09        41.10        17.72         8.84 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS 
       20.48        13.94        52.01        47.87         1.55         6.97 
TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC 
       23.11         4.01         2.89         9.90        11.31        13.22 
TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 
       48.79        35.80        51.12        10.03        39.19        13.68 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB 
        9.99        44.52        36.69        25.15         4.93        22.36 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q 
        6.64        19.36         7.00        17.56        14.83        13.15 
TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y 
        0.20         0.00         0.00        13.22        11.57        10.55 
TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 
        6.31         8.12         1.35        12.20         5.13         4.31 
TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A 
       36.07         4.34         5.13         9.21         1.18         7.99 
TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H 
        9.90        37.97        11.15        38.63         8.55         4.41 
TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R 
        1.08        27.12         9.50        12.03         8.09         8.84 
TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 
        8.68         8.09        11.31        49.22        23.90         9.67 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH 
        8.94        39.39        34.29        17.98        34.92        47.21 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP 
       19.43        16.01        35.54        33.83        30.84         5.42 
TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 
        1.15        13.02        34.98        36.33         8.84        98.27 
TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG 
        2.70         6.18        47.51         9.53        29.46        44.25 
TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM 
        7.96        14.56        63.42       111.78       111.91        56.02 
TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT 
       25.08        26.99        21.60        29.65        27.16        23.05 
TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AG 
        5.56       122.73        25.84         3.68        13.81        15.95 
TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 
       12.72         3.22        22.92        21.60        21.60        16.14 
TCGA-EE-A3JA TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 
       22.22         0.46        13.94        33.60        31.40        18.61 
TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C 
       12.95        38.40         5.72        76.41        25.18         3.78 
TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J 
        3.52        11.90        11.11       114.15        34.88         4.21 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S 
       13.45        28.60        42.84        34.68         9.57        36.07 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF 
       17.72        78.44        11.80         1.87         1.51        13.08 
TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL 
       12.62        11.74         9.04         6.58        22.49         1.71 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY 
       18.41        85.74         4.90        64.47         3.45        11.01 
TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC 
       23.80        15.52         7.33         7.30         3.39        20.38 
TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ 
        8.22        19.53        11.08         7.17        30.87        12.92 
TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS 
       12.89        47.38        52.08         8.65         8.81        49.15 
TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 
       40.64         8.68        27.39         0.82         5.23        53.85 
TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC 
        7.36        28.73        14.20        10.78         5.98         6.41 
TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY 
        2.27         0.20         0.99         0.13         0.16         0.43 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 
        7.23        12.85        24.85        31.33        84.72        10.13 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS 
       16.24        15.42        12.16        14.70         5.79 

  NMS MUTATED NMS WILD-TYPE 
         1.12          0.00 
  NMS MUTATED NMS WILD-TYPE 
       124.31        122.73 
  NMS MUTATED NMS WILD-TYPE 
        28.31         14.56 
[1] "1.1 - 124.3 (28.3)" "0.0 - 122.7 (14.6)"
[1] "hr=" "2"  
D54V2, survival
               sevent
clus2             0   1
  NMS MUTATED     9   4
  NMS WILD-TYPE 123 127
  NMS MUTATED NMS WILD-TYPE 
           13           250 
  NMS MUTATED NMS WILD-TYPE 
            4           127 
$`NMS MUTATED`
TCGA-D3-A2JF TCGA-D3-A2JO TCGA-D3-A3C8 TCGA-EE-A181 TCGA-EE-A29S TCGA-EE-A29V 
       48.76        66.08        46.32        33.73        55.92        25.87 
TCGA-EE-A2GI TCGA-EE-A2GM TCGA-EE-A3AA TCGA-EE-A3AE TCGA-EE-A3JD TCGA-FS-A1Z3 
       48.72        75.48       124.31        54.51        27.35        20.91 
TCGA-GF-A3OT 
        9.90 

$`NMS WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.57        16.67       112.04       112.57        71.80       133.25 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       28.08        31.59        90.90        95.74        43.43       103.10 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
       65.49        23.77       115.53       168.00        69.90        11.87 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JP 
      113.52        42.08        12.10       171.58        56.19        45.11 
TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE 
      130.72        58.06        46.98       166.52        86.93        60.23 
TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV 
       24.53        13.87         9.34       103.59        39.75        21.47 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N 
      161.85        43.69        40.14       131.90        18.38        10.03 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS 
       51.68        15.06       135.75       137.92       166.19         7.43 
TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 
      125.19       151.53        54.67         3.65         6.41        11.34 
TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1HW 
        3.25         9.90        25.18        66.25        48.89        36.03 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 
      117.21        20.38       194.83       176.55        35.93       107.34 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
       61.18        53.92        65.92        23.44        68.09        28.60 
TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG 
       10.49       215.44        15.68        13.87        10.16        45.11 
TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z 
       35.01         3.55        52.01        29.82        27.22         8.65 
TCGA-EE-A180 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B 
       94.98        14.70        26.89        68.15         4.96       109.64 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B 
      151.27        78.87       168.26        13.55        63.35        80.61 
TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L 
       47.84        13.97        39.62        72.07        32.19         2.60 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29W 
       44.35        18.61        56.42        37.35        14.47       171.55 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 
       17.92        46.82       102.90        24.43        39.29        58.75 
TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ 
       47.54        67.43       314.56       135.95       208.04        89.33 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR 
       54.74        79.66        90.97       101.95        13.91        14.30 
TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 
       55.59        44.88        94.82        21.67       129.27        28.83 
TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH 
       19.76        61.51        47.28       103.27       103.20        16.96 
TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN 
      204.66        96.23       144.76       203.05       167.90        47.54 
TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU 
      248.65        43.23       103.56       136.47        41.59        53.26 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH 
      122.73        25.84         3.68        13.81        23.47       138.81 
TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA 
      172.18       127.20        36.95        64.08        34.32        53.19 
TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 
       33.40       101.79       148.08        31.40        35.44        13.94 
TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D 
       50.76         9.17        77.75        98.40        48.89        12.59 
TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L 
       13.02        26.37       268.93       152.35         6.44       131.51 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W 
       61.05        44.05       162.08        50.89        37.25       148.18 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG 
       79.99        43.82        23.34        20.15        16.37        31.27 
TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN 
       32.05       247.04        80.32        46.98        33.21        92.98 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 
      174.21         4.90       216.92        48.59       228.59       202.65 
TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD 
       28.08         7.79        27.72        48.85       357.37        53.52 
TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK 
       40.27        15.45         9.70        32.75        47.38        23.93 
TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT 
      101.26        74.73       133.55        11.41       148.80        53.16 
TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 
       26.56        49.48        27.09        27.02        77.82        66.67 
TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD 
       28.73       174.84        12.43        26.73        49.45        77.88 
TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A4EO 
        0.20        22.92        47.54         0.16         2.40         7.23 
TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 
       14.04       120.46       117.93        84.72        10.13        64.44 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS 
       62.79        32.48        39.58         6.67 

  NMS MUTATED NMS WILD-TYPE 
         9.90          0.16 
  NMS MUTATED NMS WILD-TYPE 
       124.31        357.37 
  NMS MUTATED NMS WILD-TYPE 
       48.720        48.215 
[1] "9.9 - 124.3 (48.7)" "0.2 - 357.4 (48.2)"
[1] "hr=" "1.3"
D54V3, continuous
               vv
clus            DISTANT METASTASIS PRIMARY TUMOR
  NMS MUTATED                    3             0
  NMS WILD-TYPE                 32             4
               vv
clus            REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  NMS MUTATED                                           3                   7
  NMS WILD-TYPE                                        55                 163
D54V4, multiclass
                                           clus
vv                                          NMS MUTATED NMS WILD-TYPE
  DISTANT METASTASIS                                  3            32
  PRIMARY TUMOR                                       0             4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE           3            55
  REGIONAL LYMPH NODE                                 7           163
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  NMS MUTATED             0       0       0        3        0        1
  NMS WILD-TYPE          10       6      22        7       24       16
               vv
clus            STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  NMS MUTATED           1         0         1         2          0          0
  NMS WILD-TYPE         9        14         8        29         13         22
               vv
clus            STAGE IIIC STAGE IV
  NMS MUTATED            4        1
  NMS WILD-TYPE         40       11
D54V5, multiclass
             clus
vv            NMS MUTATED NMS WILD-TYPE
  I OR II NOS           0            10
  STAGE 0               0             6
  STAGE I               0            22
  STAGE IA              3             7
  STAGE IB              0            24
  STAGE II              1            16
  STAGE IIA             1             9
  STAGE IIB             0            14
  STAGE IIC             1             8
  STAGE III             2            29
  STAGE IIIA            0            13
  STAGE IIIB            0            22
  STAGE IIIC            4            40
  STAGE IV              1            11
[1] 14  2
[1] 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
  NMS MUTATED       4  0  4  1
  NMS WILD-TYPE    47 58 49 54
D54V6, multiclass
       clus
vv      NMS MUTATED NMS WILD-TYPE
  T0+T1           4            47
  T2              0            58
  T3              4            49
  T4              1            54
[1] 4 2
[1] TRUE
[1] "dimension 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
  NMS MUTATED     7   2   1   3
  NMS WILD-TYPE 131  46  31  30
D54V7, multiclass
    clus
vv   NMS MUTATED NMS WILD-TYPE
  N0           7           131
  N1           2            46
  N2           1            31
  N3           3            30
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             M0  M1 M1A M1B M1C
  NMS MUTATED    12   1   0   0   0
  NMS WILD-TYPE 228   3   2   2   5
D54V8, multiclass
     clus
vv    NMS MUTATED NMS WILD-TYPE
  M0           12           228
  M1            1             3
  M1A           0             2
  M1B           0             2
  M1C           0             5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V9, binary
               cls
clus             0  1
  NMS MUTATED    4  3
  NMS WILD-TYPE 98 64
[1] "tbl2"
               cls
clus            [,1] [,2]
  NMS MUTATED      4    3
  NMS WILD-TYPE   98   64
     clus
vv    NMS MUTATED NMS WILD-TYPE
  NO            4            98
  YES           3            64
[1] 2 2
[1] FALSE
D54V10, binary
               cls
clus              0   1
  NMS MUTATED     3  10
  NMS WILD-TYPE  30 225
[1] "tbl2"
               cls
clus            [,1] [,2]
  NMS MUTATED      3   10
  NMS WILD-TYPE   30  225
     clus
vv    NMS MUTATED NMS WILD-TYPE
  NO            3            30
  YES          10           225
[1] 2 2
[1] FALSE
D54V11, continuous
D54V12, binary
               cls
clus              0   1
  NMS MUTATED     7   6
  NMS WILD-TYPE  96 159
[1] "tbl2"
               cls
clus            [,1] [,2]
  NMS MUTATED      7    6
  NMS WILD-TYPE   96  159
        clus
vv       NMS MUTATED NMS WILD-TYPE
  FEMALE           7            96
  MALE             6           159
[1] 2 2
[1] FALSE
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  NMS MUTATED       0                         0    13
  NMS WILD-TYPE     3                         1   251
D54V13, multiclass
                           clus
vv                          NMS MUTATED NMS WILD-TYPE
  ASIAN                               0             3
  BLACK OR AFRICAN AMERICAN           0             1
  WHITE                              13           251
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V14, binary
               cls
clus              0   1
  NMS MUTATED     0  13
  NMS WILD-TYPE   3 248
[1] "tbl2"
               cls
clus            [,1] [,2]
  NMS MUTATED      0   13
  NMS WILD-TYPE    3  248
                        clus
vv                       NMS MUTATED NMS WILD-TYPE
  HISPANIC OR LATINO               0             3
  NOT HISPANIC OR LATINO          13           248
[1] 2 2
[1] FALSE

Clustering(55) Variable = C12ORF43 MUTATION ANALYSIS
D55V1, survival
                    sevent
clus2                  0   1
  C12ORF43 MUTATED     2   3
  C12ORF43 WILD-TYPE 126 127
  C12ORF43 MUTATED C12ORF43 WILD-TYPE 
                 5                253 
  C12ORF43 MUTATED C12ORF43 WILD-TYPE 
                 3                127 
$`C12ORF43 MUTATED`
TCGA-D3-A1Q6 TCGA-D3-A2JF TCGA-D3-A2JO TCGA-EE-A184 TCGA-ER-A195 
       70.16        30.87        64.44         5.13        18.61 

$`C12ORF43 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       16.47         8.52       111.09        32.42       110.79        28.08 
TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 
       22.55        45.83        81.24        10.29        85.32         8.38 
TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JG 
       21.14        88.50        68.22        69.90        11.41         7.50 
TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3BZ 
       36.16         6.31        92.42        56.19        45.11       114.67 
TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE 
       15.25        46.98        46.32        82.29        61.38        13.32 
TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV 
       24.00         6.31         9.34       103.59        26.37         5.39 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N 
       80.22        42.71        15.09        41.10        17.72         8.84 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS 
       20.48        13.94        52.01        47.87         1.55         6.97 
TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC 
       23.11         4.01         2.89         9.90        11.31        13.22 
TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 
       48.79        35.80        51.12        10.03        39.19        13.68 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB 
        9.99        44.52        36.69        25.15         4.93        22.36 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q 
        6.64        19.36         7.00        17.56        14.83        13.15 
TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y 
        0.20         0.00         0.00        13.22        11.57        10.55 
TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A185 
        6.31         8.12         1.12         1.35        12.20         4.31 
TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A 
       36.07         4.34         5.13         9.21         1.18         7.99 
TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H 
        9.90        37.97        11.15        38.63         8.55         4.41 
TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R 
        1.08        27.12         9.50        12.03         8.09         8.84 
TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 
        9.99         2.43         8.68         8.09        11.31        49.22 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD 
       23.90         9.67         8.94        39.39        34.29        17.98 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
       34.92        47.21        30.08        19.43        16.01        35.54 
TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS 
       28.31        33.83        30.84         5.42         1.15        13.02 
TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 
       34.98        36.33         8.84        98.27         2.70         6.18 
TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI 
       47.51         9.53        29.46        44.25         7.96        14.56 
TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP 
       63.42       111.78       111.91        56.02        25.08        26.99 
TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA 
       21.60        29.65        27.16        23.05         5.56       124.31 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG 
      122.73        25.84         3.68        30.15        13.81        15.95 
TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 
       12.72         3.22        22.92        21.60        21.60        16.14 
TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 
       22.22        27.35         0.46        13.94        33.60        31.40 
TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C 
       12.95        38.40         5.72        76.41        25.18         3.78 
TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J 
        3.52        11.90        11.11       114.15        34.88         4.21 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S 
       13.45        28.60        42.84        34.68         9.57        36.07 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF 
       17.72        78.44        11.80         1.87         1.51        13.08 
TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL 
       12.62        11.74         9.04         6.58        22.49         1.71 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY 
       18.41        85.74         4.90        64.47         3.45        11.01 
TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB 
       23.80        14.24        15.52         7.33         7.30         3.39 
TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH 
       20.38         8.22        19.53        11.08         7.17        30.87 
TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR 
       12.92        12.89        47.38        52.08         8.65         8.81 
TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ 
       49.15        40.64         8.68        27.39         0.82         5.23 
TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB 
       53.85         7.36        28.73        14.20        10.78         5.98 
TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV 
        6.41         2.27         0.20         0.99         0.13         0.16 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 
        0.43         9.90         7.23        12.85        24.85        31.33 
TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D 
       84.72        10.13        16.24        15.42        12.16        14.70 
TCGA-QB-A6FS 
        5.79 

  C12ORF43 MUTATED C12ORF43 WILD-TYPE 
              5.13               0.00 
  C12ORF43 MUTATED C12ORF43 WILD-TYPE 
             70.16             124.31 
  C12ORF43 MUTATED C12ORF43 WILD-TYPE 
             30.87              14.56 
[1] "5.1 - 70.2 (30.9)"  "0.0 - 124.3 (14.6)"
[1] "hr=" "1.2"
D55V2, survival
                    sevent
clus2                  0   1
  C12ORF43 MUTATED     2   3
  C12ORF43 WILD-TYPE 130 128
  C12ORF43 MUTATED C12ORF43 WILD-TYPE 
                 5                258 
  C12ORF43 MUTATED C12ORF43 WILD-TYPE 
                 3                128 
$`C12ORF43 MUTATED`
TCGA-D3-A1Q6 TCGA-D3-A2JF TCGA-D3-A2JO TCGA-EE-A184 TCGA-ER-A195 
       71.80        48.76        66.08        68.15        35.44 

$`C12ORF43 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       16.57        16.67       112.04       112.57       133.25        28.08 
TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 
       31.59        90.90        95.74        43.43       103.10        65.49 
TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JG 
       23.77       115.53       168.00        69.90        11.87       113.52 
TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3BZ 
       42.08        12.10       171.58        56.19        45.11       130.72 
TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE 
       58.06        46.98        46.32       166.52        86.93        60.23 
TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV 
       24.53        13.87         9.34       103.59        39.75        21.47 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N 
      161.85        43.69        40.14       131.90        18.38        10.03 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS 
       51.68        15.06       135.75       137.92       166.19         7.43 
TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 
      125.19       151.53        54.67         3.65         6.41        11.34 
TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1HW 
        3.25         9.90        25.18        66.25        48.89        36.03 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 
      117.21        20.38       194.83       176.55        35.93       107.34 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
       61.18        53.92        65.92        23.44        68.09        28.60 
TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG 
       10.49       215.44        15.68        13.87        10.16        45.11 
TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z 
       35.01         3.55        52.01        29.82        27.22         8.65 
TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B 
       94.98        33.73        14.70        26.89         4.96       109.64 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B 
      151.27        78.87       168.26        13.55        63.35        80.61 
TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L 
       47.84        13.97        39.62        72.07        32.19         2.60 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S 
       44.35        18.61        56.42        37.35        14.47        55.92 
TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 
       25.87       171.55        17.92        46.82       102.90        24.43 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE 
       39.29        58.75        47.54        67.43       314.56       135.95 
TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM 
      208.04        48.72        89.33        54.74        79.66        75.48 
TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT 
       90.97       101.95        13.91        14.30        55.59        44.88 
TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC 
       94.82        21.67       129.27        28.83        19.76        61.51 
TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ 
       47.28       103.27       103.20        16.96       204.66        96.23 
TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ 
      144.76       203.05       167.90        47.54       248.65        43.23 
TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB 
      103.56       136.47        41.59        53.26       124.31       122.73 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH 
       25.84         3.68        54.51        13.81        23.47       138.81 
TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA 
      172.18       127.20        36.95        64.08        34.32        53.19 
TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A197 
       27.35        33.40       101.79       148.08        31.40        13.94 
TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D 
       50.76         9.17        77.75        98.40        48.89        12.59 
TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L 
       13.02        26.37       268.93       152.35         6.44       131.51 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W 
       61.05        44.05       162.08        50.89        37.25       148.18 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG 
       79.99        43.82        23.34        20.15        16.37        31.27 
TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN 
       32.05       247.04        80.32        46.98        33.21        92.98 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 
      174.21         4.90       216.92        48.59       228.59       202.65 
TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC 
       20.91        28.08         7.79        27.72        48.85       357.37 
TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ 
       53.52        40.27        15.45         9.70        32.75        47.38 
TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS 
       23.93       101.26        74.73       133.55        11.41       148.80 
TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 
       53.16        26.56        49.48        27.09        27.02        77.82 
TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC 
       66.67        28.73       174.84        12.43        26.73        49.45 
TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY 
       77.88         0.20        22.92        47.54         0.16         2.40 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        9.90         7.23        14.04       120.46       117.93        84.72 
TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS 
       10.13        64.44        62.79        32.48        39.58         6.67 

  C12ORF43 MUTATED C12ORF43 WILD-TYPE 
             35.44               0.16 
  C12ORF43 MUTATED C12ORF43 WILD-TYPE 
             71.80             357.37 
  C12ORF43 MUTATED C12ORF43 WILD-TYPE 
             66.08              47.69 
[1] "35.4 - 71.8 (66.1)" "0.2 - 357.4 (47.7)"
[1] "hr=" "1.2"
D55V3, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  C12ORF43 MUTATED                    2             0
  C12ORF43 WILD-TYPE                 33             4
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  C12ORF43 MUTATED                                           2
  C12ORF43 WILD-TYPE                                        56
                    vv
clus                 REGIONAL LYMPH NODE
  C12ORF43 MUTATED                     1
  C12ORF43 WILD-TYPE                 169
D55V4, multiclass
                                           clus
vv                                          C12ORF43 MUTATED C12ORF43 WILD-TYPE
  DISTANT METASTASIS                                       2                 33
  PRIMARY TUMOR                                            0                  4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                2                 56
  REGIONAL LYMPH NODE                                      1                169
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  C12ORF43 MUTATED             0       0       0        1        1        0
  C12ORF43 WILD-TYPE          10       6      22        9       23       17
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  C12ORF43 MUTATED           0         0         0         1          0
  C12ORF43 WILD-TYPE        10        14         9        30         13
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  C12ORF43 MUTATED            0          1        0
  C12ORF43 WILD-TYPE         22         43       12
D55V5, multiclass
             clus
vv            C12ORF43 MUTATED C12ORF43 WILD-TYPE
  I OR II NOS                0                 10
  STAGE 0                    0                  6
  STAGE I                    0                 22
  STAGE IA                   1                  9
  STAGE IB                   1                 23
  STAGE II                   0                 17
  STAGE IIA                  0                 10
  STAGE IIB                  0                 14
  STAGE IIC                  0                  9
  STAGE III                  1                 30
  STAGE IIIA                 0                 13
  STAGE IIIB                 0                 22
  STAGE IIIC                 1                 43
  STAGE IV                   0                 12
[1] 14  2
[1] 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  1  0  1
  C12ORF43 WILD-TYPE    50 57 53 54
D55V6, multiclass
       clus
vv      C12ORF43 MUTATED C12ORF43 WILD-TYPE
  T0+T1                1                 50
  T2                   1                 57
  T3                   0                 53
  T4                   1                 54
[1] 4 2
[1] TRUE
[1] "dimension 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     3   1   0   1
  C12ORF43 WILD-TYPE 135  47  32  32
D55V7, multiclass
    clus
vv   C12ORF43 MUTATED C12ORF43 WILD-TYPE
  N0                3                135
  N1                1                 47
  N2                0                 32
  N3                1                 32
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1 M1A M1B M1C
  C12ORF43 MUTATED     5   0   0   0   0
  C12ORF43 WILD-TYPE 235   4   2   2   5
D55V8, multiclass
     clus
vv    C12ORF43 MUTATED C12ORF43 WILD-TYPE
  M0                 5                235
  M1                 0                  4
  M1A                0                  2
  M1B                0                  2
  M1C                0                  5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V9, binary
                    cls
clus                   0   1
  C12ORF43 MUTATED     2   1
  C12ORF43 WILD-TYPE 100  66
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C12ORF43 MUTATED      2    1
  C12ORF43 WILD-TYPE  100   66
     clus
vv    C12ORF43 MUTATED C12ORF43 WILD-TYPE
  NO                 2                100
  YES                1                 66
[1] 2 2
[1] FALSE
D55V10, binary
                    cls
clus                   0   1
  C12ORF43 MUTATED     0   5
  C12ORF43 WILD-TYPE  33 230
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C12ORF43 MUTATED      0    5
  C12ORF43 WILD-TYPE   33  230
     clus
vv    C12ORF43 MUTATED C12ORF43 WILD-TYPE
  NO                 0                 33
  YES                5                230
[1] 2 2
[1] FALSE
D55V11, continuous
D55V12, binary
                    cls
clus                   0   1
  C12ORF43 MUTATED     1   4
  C12ORF43 WILD-TYPE 102 161
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C12ORF43 MUTATED      1    4
  C12ORF43 WILD-TYPE  102  161
        clus
vv       C12ORF43 MUTATED C12ORF43 WILD-TYPE
  FEMALE                1                102
  MALE                  4                161
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  C12ORF43 MUTATED       0                         0     5
  C12ORF43 WILD-TYPE     3                         1   259
D55V13, multiclass
                           clus
vv                          C12ORF43 MUTATED C12ORF43 WILD-TYPE
  ASIAN                                    0                  3
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                    5                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"
D55V14, binary
                    cls
clus                   0   1
  C12ORF43 MUTATED     0   5
  C12ORF43 WILD-TYPE   3 256
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C12ORF43 MUTATED      0    5
  C12ORF43 WILD-TYPE    3  256
                        clus
vv                       C12ORF43 MUTATED C12ORF43 WILD-TYPE
  HISPANIC OR LATINO                    0                  3
  NOT HISPANIC OR LATINO                5                256
[1] 2 2
[1] FALSE

Clustering(56) Variable = XIRP2 MUTATION ANALYSIS
D56V1, survival
                 sevent
clus2              0  1
  XIRP2 MUTATED   47 38
  XIRP2 WILD-TYPE 81 92
  XIRP2 MUTATED XIRP2 WILD-TYPE 
             85             173 
  XIRP2 MUTATED XIRP2 WILD-TYPE 
             38              92 
$`XIRP2 MUTATED`
TCGA-D3-A1QB TCGA-D3-A2JD TCGA-D3-A2JH TCGA-D3-A2JO TCGA-D3-A3C6 TCGA-D3-A3C7 
       81.24        11.41        36.16        64.44        15.25        46.98 
TCGA-D3-A3MR TCGA-D3-A3MV TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO 
      103.59         5.39        20.48        13.94        52.01        47.87 
TCGA-D3-A5GS TCGA-D9-A3Z1 TCGA-D9-A6E9 TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1HY 
        6.97         4.01         9.90        13.22        48.79        51.12 
TCGA-DA-A1I0 TCGA-DA-A1I5 TCGA-DA-A1IA TCGA-DA-A3F8 TCGA-EB-A5UN TCGA-EE-A17X 
       10.03        44.52         4.93        14.83        13.22        11.57 
TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A20C TCGA-EE-A20H TCGA-EE-A29D 
        8.12         1.12         1.35         4.34         9.21        11.15 
TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29R 
       38.63         4.41         1.08        27.12        12.03         8.84 
TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A2A0 TCGA-EE-A2A2 TCGA-EE-A2GC TCGA-EE-A2GD 
        9.99         2.43        11.31        23.90        34.29        17.98 
TCGA-EE-A2GI TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GR TCGA-EE-A2GT TCGA-EE-A2GU 
       30.08        33.83        30.84         1.15        34.98        36.33 
TCGA-EE-A2M5 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2MG TCGA-EE-A2MR TCGA-EE-A2MS 
        8.84        47.51         9.53        44.25        29.65        27.16 
TCGA-EE-A2MT TCGA-EE-A3AC TCGA-EE-A3AE TCGA-EE-A3AG TCGA-EE-A3J4 TCGA-EE-A3J5 
       23.05        25.84        30.15        15.95        22.92        21.60 
TCGA-EE-A3JD TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A198 TCGA-ER-A19D TCGA-ER-A19E 
       27.35        31.40        18.61        38.40         3.52        11.90 
TCGA-ER-A2NC TCGA-ER-A2NG TCGA-ER-A2NH TCGA-FS-A1Z3 TCGA-FS-A1ZA TCGA-FS-A1ZB 
       11.80        12.62        11.74        14.24         7.30         3.39 
TCGA-FS-A1ZK TCGA-FS-A1ZQ TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F5 TCGA-FS-A4F9 
       12.89         8.65         5.23        53.85        28.73        10.78 
TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-GN-A266 
        6.41         2.27         0.99         0.13         0.16        10.13 
TCGA-GN-A268 
       15.42 

$`XIRP2 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.47         8.52       111.09        32.42        70.16       110.79 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 
       28.08        22.55        45.83        10.29        85.32         8.38 
TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JF TCGA-D3-A2JG 
       21.14        88.50        68.22        69.90        30.87         7.50 
TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C8 
        6.31        92.42        56.19        45.11       114.67        46.32 
TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO 
       82.29        61.38        13.32        24.00         6.31         9.34 
TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K 
       26.37        80.22        42.71        15.09        41.10        17.72 
TCGA-D3-A51N TCGA-D3-A5GR TCGA-D3-A5GU TCGA-D9-A3Z3 TCGA-D9-A6EA TCGA-DA-A1HW 
        8.84         1.55        23.11         2.89        11.31        35.80 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IB 
       39.19        13.68         9.99        36.69        25.15        22.36 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-EB-A44Q TCGA-EB-A44R 
        6.64        19.36         7.00        17.56        13.15         0.20 
TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A183 TCGA-EE-A184 
        0.00         0.00        10.55         6.31        12.20         5.13 
TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B 
        4.31        36.07         5.13         1.18         7.99         9.90 
TCGA-EE-A29C TCGA-EE-A29G TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A29W TCGA-EE-A29X 
       37.97         8.55         9.50         8.09         8.68         8.09 
TCGA-EE-A2A1 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH 
       49.22         9.67         8.94        39.39        34.92        47.21 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GP TCGA-EE-A2GS 
       19.43        16.01        35.54        28.31         5.42        13.02 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2ME TCGA-EE-A2MH TCGA-EE-A2MI 
       98.27         2.70         6.18        29.46         7.96        14.56 
TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP 
       63.42       111.78       111.91        56.02        25.08        26.99 
TCGA-EE-A2MQ TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AF 
       21.60         5.56       124.31       122.73         3.68        13.81 
TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JE 
       12.72         3.22        21.60        16.14        22.22         0.46 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B 
       13.94        33.60        12.95         5.72        76.41        25.18 
TCGA-ER-A19C TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L 
        3.78        11.11       114.15        34.88         4.21        13.45 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W 
       28.60        42.84        34.68         9.57        36.07        17.72 
TCGA-ER-A1A1 TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A3ES TCGA-ER-A3ET 
       78.44         1.87         1.51        13.08         9.04         6.58 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW 
       22.49         1.71        18.41        85.74         4.90        64.47 
TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZC 
        3.45        11.01        23.80        15.52         7.33        20.38 
TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ 
        8.22        19.53        11.08         7.17        30.87        12.92 
TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU 
       47.38        52.08         8.81        49.15        40.64         8.68 
TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4FB TCGA-FW-A3I3 
       27.39         0.82         7.36        14.20         5.98         0.20 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 
        0.43         9.90         7.23        12.85        24.85        31.33 
TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS 
       84.72        16.24        12.16        14.70         5.79 

  XIRP2 MUTATED XIRP2 WILD-TYPE 
           0.13            0.00 
  XIRP2 MUTATED XIRP2 WILD-TYPE 
         103.59          124.31 
  XIRP2 MUTATED XIRP2 WILD-TYPE 
          13.22           16.01 
[1] "0.1 - 103.6 (13.2)" "0.0 - 124.3 (16.0)"
[1] "hr=" "1"  
D56V2, survival
                 sevent
clus2              0  1
  XIRP2 MUTATED   49 38
  XIRP2 WILD-TYPE 83 93
  XIRP2 MUTATED XIRP2 WILD-TYPE 
             87             176 
  XIRP2 MUTATED XIRP2 WILD-TYPE 
             38              93 
$`XIRP2 MUTATED`
TCGA-D3-A1QB TCGA-D3-A2JD TCGA-D3-A2JH TCGA-D3-A2JO TCGA-D3-A3C6 TCGA-D3-A3C7 
       95.74        11.87        42.08        66.08        58.06        46.98 
TCGA-D3-A3MR TCGA-D3-A3MV TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO 
      103.59        21.47        51.68        15.06       135.75       137.92 
TCGA-D3-A5GS TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A3Z1 TCGA-D9-A6E9 TCGA-D9-A6EC 
        7.43        54.67         3.65        11.34         9.90        66.25 
TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I5 TCGA-DA-A1IA TCGA-DA-A3F8 
       48.89       117.21        20.38       107.34        65.92        15.68 
TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A20C 
       52.01        29.82        94.98        33.73        14.70       151.27 
TCGA-EE-A20H TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M 
      168.26        13.97        39.62        32.19         2.60        44.35 
TCGA-EE-A29P TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A2A0 TCGA-EE-A2A2 
       56.42        14.47        55.92        25.87        46.82        24.43 
TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GI TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GR 
       67.43       314.56        48.72        90.97       101.95        14.30 
TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2MG 
       44.88        94.82        21.67        61.51        47.28       103.20 
TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AC TCGA-EE-A3AE TCGA-EE-A3AG 
      103.56       136.47        41.59        25.84        54.51        23.47 
TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3JD TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A198 
      127.20        36.95        27.35        31.40        35.44        50.76 
TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A2NC TCGA-ER-A2NG TCGA-ER-A2NH TCGA-FS-A1Z3 
       12.59        13.02        43.82        31.27        32.05        20.91 
TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZK TCGA-FS-A1ZQ TCGA-FS-A1ZZ TCGA-FS-A4F0 
       27.72        48.85        23.93       133.55        27.02        77.82 
TCGA-FS-A4F5 TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3R5 TCGA-FW-A3TU 
       28.73        12.43        49.45        77.88        22.92        47.54 
TCGA-FW-A3TV TCGA-GN-A266 TCGA-GN-A268 
        0.16        10.13        62.79 

$`XIRP2 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.57        16.67       112.04       112.57        71.80       133.25 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 
       28.08        31.59        90.90        43.43       103.10        65.49 
TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JF TCGA-D3-A2JG 
       23.77       115.53       168.00        69.90        48.76       113.52 
TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C8 
       12.10       171.58        56.19        45.11       130.72        46.32 
TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO 
      166.52        86.93        60.23        24.53        13.87         9.34 
TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K 
       39.75       161.85        43.69        40.14       131.90        18.38 
TCGA-D3-A51N TCGA-D3-A5GR TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A1JX TCGA-D9-A3Z3 
       10.03       166.19       125.19       151.53         6.41         3.25 
TCGA-D9-A6EA TCGA-DA-A1HW TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I7 
       25.18        36.03       194.83       176.55        35.93        61.18 
TCGA-DA-A1I8 TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 
       53.92        23.44        68.09        28.60        10.49       215.44 
TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EE-A17Y 
       13.87        10.16        45.11        35.01         3.55        27.22 
TCGA-EE-A17Z TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20F 
        8.65        26.89        68.15         4.96       109.64        78.87 
TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29G TCGA-EE-A29N 
       13.55        63.35        80.61        47.84        72.07        18.61 
TCGA-EE-A29Q TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A1 TCGA-EE-A2A5 TCGA-EE-A2A6 
       37.35       171.55        17.92       102.90        39.29        58.75 
TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
       47.54       135.95       208.04        89.33        54.74        79.66 
TCGA-EE-A2GM TCGA-EE-A2GP TCGA-EE-A2GS TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 
       75.48        13.91        55.59       129.27        28.83        19.76 
TCGA-EE-A2ME TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML 
      103.27        16.96       204.66        96.23       144.76       203.05 
TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MU TCGA-EE-A3AA 
      167.90        47.54       248.65        43.23        53.26       124.31 
TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J7 
      122.73         3.68        13.81       138.81       172.18        64.08 
TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A197 
       34.32        53.19        33.40       101.79       148.08        13.94 
TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19F TCGA-ER-A19G 
        9.17        77.75        98.40        48.89        26.37       268.93 
TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P 
      152.35         6.44       131.51        61.05        44.05       162.08 
TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2ND TCGA-ER-A2NE 
       50.89        37.25       148.18        79.99        23.34        20.15 
TCGA-ER-A2NF TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN 
       16.37       247.04        80.32        46.98        33.21        92.98 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 
      174.21         4.90       216.92        48.59       228.59       202.65 
TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF 
       28.08         7.79       357.37        53.52        40.27        15.45 
TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZR 
        9.70        32.75        47.38       101.26        74.73        11.41 
TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A4F4 
      148.80        53.16        26.56        49.48        27.09        66.67 
TCGA-FS-A4F8 TCGA-FS-A4FB TCGA-FW-A3I3 TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
      174.84        26.73         0.20         2.40         9.90         7.23 
TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A26A 
       14.04       120.46       117.93        84.72        64.44        32.48 
TCGA-GN-A26D TCGA-QB-A6FS 
       39.58         6.67 

  XIRP2 MUTATED XIRP2 WILD-TYPE 
           0.16            0.20 
  XIRP2 MUTATED XIRP2 WILD-TYPE 
         314.56          357.37 
  XIRP2 MUTATED XIRP2 WILD-TYPE 
         44.350          53.175 
[1] "0.2 - 314.6 (44.4)" "0.2 - 357.4 (53.2)"
[1] "hr=" "1.1"
D56V3, continuous
                 vv
clus              DISTANT METASTASIS PRIMARY TUMOR
  XIRP2 MUTATED                   18             2
  XIRP2 WILD-TYPE                 17             2
                 vv
clus              REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  XIRP2 MUTATED                                          19                  50
  XIRP2 WILD-TYPE                                        39                 120
D56V4, multiclass
                                           clus
vv                                          XIRP2 MUTATED XIRP2 WILD-TYPE
  DISTANT METASTASIS                                   18              17
  PRIMARY TUMOR                                         2               2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE            19              39
  REGIONAL LYMPH NODE                                  50             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              I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  XIRP2 MUTATED             3       1       6        5        8        9
  XIRP2 WILD-TYPE           7       5      16        5       16        8
                 vv
clus              STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  XIRP2 MUTATED           6         6         2        10          2          6
  XIRP2 WILD-TYPE         4         8         7        21         11         16
                 vv
clus              STAGE IIIC STAGE IV
  XIRP2 MUTATED           15        4
  XIRP2 WILD-TYPE         29        8
D56V5, multiclass
             clus
vv            XIRP2 MUTATED XIRP2 WILD-TYPE
  I OR II NOS             3               7
  STAGE 0                 1               5
  STAGE I                 6              16
  STAGE IA                5               5
  STAGE IB                8              16
  STAGE II                9               8
  STAGE IIA               6               4
  STAGE IIB               6               8
  STAGE IIC               2               7
  STAGE III              10              21
  STAGE IIIA              2              11
  STAGE IIIB              6              16
  STAGE IIIC             15              29
  STAGE IV                4               8
[1] 14  2
[1] 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
  XIRP2 MUTATED      17 20 21 19
  XIRP2 WILD-TYPE    34 38 32 36
D56V6, multiclass
       clus
vv      XIRP2 MUTATED XIRP2 WILD-TYPE
  T0+T1            17              34
  T2               20              38
  T3               21              32
  T4               19              36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  XIRP2 MUTATED   49 16 11  9
  XIRP2 WILD-TYPE 89 32 21 24
D56V7, multiclass
    clus
vv   XIRP2 MUTATED XIRP2 WILD-TYPE
  N0            49              89
  N1            16              32
  N2            11              21
  N3             9              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               M0  M1 M1A M1B M1C
  XIRP2 MUTATED    83   1   1   0   2
  XIRP2 WILD-TYPE 157   3   1   2   3
D56V8, multiclass
     clus
vv    XIRP2 MUTATED XIRP2 WILD-TYPE
  M0             83             157
  M1              1               3
  M1A             1               1
  M1B             0               2
  M1C             2               3
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V9, binary
                 cls
clus               0  1
  XIRP2 MUTATED   39 24
  XIRP2 WILD-TYPE 63 43
[1] "tbl2"
                 cls
clus              [,1] [,2]
  XIRP2 MUTATED     39   24
  XIRP2 WILD-TYPE   63   43
     clus
vv    XIRP2 MUTATED XIRP2 WILD-TYPE
  NO             39              63
  YES            24              43
[1] 2 2
[1] FALSE
D56V10, binary
                 cls
clus                0   1
  XIRP2 MUTATED     9  80
  XIRP2 WILD-TYPE  24 155
[1] "tbl2"
                 cls
clus              [,1] [,2]
  XIRP2 MUTATED      9   80
  XIRP2 WILD-TYPE   24  155
     clus
vv    XIRP2 MUTATED XIRP2 WILD-TYPE
  NO              9              24
  YES            80             155
[1] 2 2
[1] FALSE
D56V11, continuous
D56V12, binary
                 cls
clus                0   1
  XIRP2 MUTATED    37  52
  XIRP2 WILD-TYPE  66 113
[1] "tbl2"
                 cls
clus              [,1] [,2]
  XIRP2 MUTATED     37   52
  XIRP2 WILD-TYPE   66  113
        clus
vv       XIRP2 MUTATED XIRP2 WILD-TYPE
  FEMALE            37              66
  MALE              52             113
[1] 2 2
[1] FALSE
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  XIRP2 MUTATED       0                         0    89
  XIRP2 WILD-TYPE     3                         1   175
D56V13, multiclass
                           clus
vv                          XIRP2 MUTATED XIRP2 WILD-TYPE
  ASIAN                                 0               3
  BLACK OR AFRICAN AMERICAN             0               1
  WHITE                                89             175
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V14, binary
                 cls
clus                0   1
  XIRP2 MUTATED     1  87
  XIRP2 WILD-TYPE   2 174
[1] "tbl2"
                 cls
clus              [,1] [,2]
  XIRP2 MUTATED      1   87
  XIRP2 WILD-TYPE    2  174
                        clus
vv                       XIRP2 MUTATED XIRP2 WILD-TYPE
  HISPANIC OR LATINO                 1               2
  NOT HISPANIC OR LATINO            87             174
[1] 2 2
[1] FALSE

Clustering(57) Variable = USH2A MUTATION ANALYSIS
D57V1, survival
                 sevent
clus2              0  1
  USH2A MUTATED   43 42
  USH2A WILD-TYPE 85 88
  USH2A MUTATED USH2A WILD-TYPE 
             85             173 
  USH2A MUTATED USH2A WILD-TYPE 
             42              88 
$`USH2A MUTATED`
TCGA-D3-A2JD TCGA-D3-A2JH TCGA-D3-A2JP TCGA-D3-A3C7 TCGA-D3-A3MR TCGA-D3-A3MV 
       11.41        36.16        45.11        46.98       103.59         5.39 
TCGA-D3-A51J TCGA-D3-A51T TCGA-D3-A5GO TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1HV 
       41.10        13.94        47.87        11.31        13.22        48.79 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F3 TCGA-DA-A3F8 
       51.12        10.03        22.36         6.64         7.00        14.83 
TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A185 TCGA-EE-A20C TCGA-EE-A29C TCGA-EE-A29D 
        1.12         1.35         4.31         4.34        37.97        11.15 
TCGA-EE-A29E TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29S 
       38.63         1.08        27.12         9.50        12.03         9.99 
TCGA-EE-A29V TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A6 TCGA-EE-A2GJ TCGA-EE-A2GM 
        2.43        11.31        49.22         8.94        19.43        28.31 
TCGA-EE-A2GO TCGA-EE-A2GR TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M8 TCGA-EE-A2MC 
       30.84         1.15        36.33         8.84         6.18        47.51 
TCGA-EE-A2MD TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MQ 
        9.53        14.56        63.42       111.91        56.02        21.60 
TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD 
       29.65        27.16       124.31       122.73        25.84         3.68 
TCGA-EE-A3AF TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J8 TCGA-EE-A3JD TCGA-EE-A3JE 
       13.81        22.92        21.60        16.14        27.35         0.46 
TCGA-ER-A193 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19C TCGA-ER-A19E TCGA-ER-A19F 
       31.40        38.40         5.72         3.78        11.90        11.11 
TCGA-ER-A19S TCGA-ER-A2NC TCGA-ER-A3PL TCGA-FR-A44A TCGA-FS-A1Z3 TCGA-FS-A1ZA 
       36.07        11.80         1.71        85.74        14.24         7.30 
TCGA-FS-A1ZC TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZR TCGA-FS-A1ZW TCGA-FS-A1ZZ 
       20.38        12.89        47.38         8.81        27.39         5.23 
TCGA-FS-A4F0 TCGA-FS-A4FD TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-GF-A3OT TCGA-GN-A266 
       53.85         2.27         0.99         0.13         9.90        10.13 
TCGA-QB-A6FS 
        5.79 

$`USH2A WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.47         8.52       111.09        32.42        70.16       110.79 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       28.08        22.55        45.83        81.24        10.29        85.32 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JF 
        8.38        21.14        88.50        68.22        69.90        30.87 
TCGA-D3-A2JG TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A3BZ 
        7.50         6.31        92.42        56.19        64.44       114.67 
TCGA-D3-A3C6 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF 
       15.25        46.32        82.29        61.38        13.32        24.00 
TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H 
        6.31         9.34        26.37        80.22        42.71        15.09 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS 
       17.72         8.84        20.48        52.01         1.55         6.97 
TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-DA-A1HW TCGA-DA-A1I1 
       23.11         4.01         2.89         9.90        35.80        39.19 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA 
       13.68         9.99        44.52        36.69        25.15         4.93 
TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH 
       19.36        17.56        13.15         0.20         0.00         0.00 
TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A183 
       13.22        11.57        10.55         6.31         8.12        12.20 
TCGA-EE-A184 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A 
        5.13        36.07         5.13         9.21         1.18         7.99 
TCGA-EE-A29B TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29W 
        9.90         8.55         4.41         8.09         8.84         8.68 
TCGA-EE-A29X TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD 
        8.09        23.90         9.67        39.39        34.29        17.98 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GN 
       34.92        47.21        30.08        16.01        35.54        33.83 
TCGA-EE-A2GP TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2ME 
        5.42        13.02        34.98        98.27         2.70        29.46 
TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MK TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MT 
       44.25         7.96       111.78        25.08        26.99        23.05 
TCGA-EE-A2MU TCGA-EE-A3AE TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J7 
        5.56        30.15        15.95        12.72         3.22        21.60 
TCGA-EE-A3JA TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A19A 
       22.22        13.94        33.60        18.61        12.95        76.41 
TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L 
       25.18         3.52       114.15        34.88         4.21        13.45 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19W TCGA-ER-A1A1 
       28.60        42.84        34.68         9.57        17.72        78.44 
TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES 
        1.87         1.51        13.08        12.62        11.74         9.04 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-FR-A3YN TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX 
        6.58        22.49        18.41         4.90        64.47         3.45 
TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZB TCGA-FS-A1ZD 
       11.01        23.80        15.52         7.33         3.39         8.22 
TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZP 
       19.53        11.08         7.17        30.87        12.92        52.08 
TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZY TCGA-FS-A4F4 
        8.65        49.15        40.64         8.68         0.82         7.36 
TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FW-A3I3 
       28.73        14.20        10.78         5.98         6.41         0.20 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 
        0.16         0.43         7.23        12.85        24.85        31.33 
TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D 
       84.72        16.24        15.42        12.16        14.70 

  USH2A MUTATED USH2A WILD-TYPE 
           0.13            0.00 
  USH2A MUTATED USH2A WILD-TYPE 
         124.31          114.67 
  USH2A MUTATED USH2A WILD-TYPE 
          13.94           15.42 
[1] "0.1 - 124.3 (13.9)" "0.0 - 114.7 (15.4)"
[1] "hr=" "1"  
D57V2, survival
                 sevent
clus2              0  1
  USH2A MUTATED   44 42
  USH2A WILD-TYPE 88 89
  USH2A MUTATED USH2A WILD-TYPE 
             86             177 
  USH2A MUTATED USH2A WILD-TYPE 
             42              89 
$`USH2A MUTATED`
TCGA-D3-A2JD TCGA-D3-A2JH TCGA-D3-A2JP TCGA-D3-A3C7 TCGA-D3-A3MR TCGA-D3-A3MV 
       11.87        42.08        45.11        46.98       103.59        21.47 
TCGA-D3-A51J TCGA-D3-A51T TCGA-D3-A5GO TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1HV 
      131.90        15.06       137.92        25.18        66.25        48.89 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F3 TCGA-DA-A3F8 
      117.21        20.38        23.44        68.09        10.49        15.68 
TCGA-EB-A5UL TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A185 TCGA-EE-A20C TCGA-EE-A29C 
        3.55        33.73        14.70         4.96       151.27        47.84 
TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P 
       13.97        39.62         2.60        44.35        18.61        56.42 
TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A6 TCGA-EE-A2GJ 
       55.92        25.87        46.82       102.90        58.75        89.33 
TCGA-EE-A2GM TCGA-EE-A2GO TCGA-EE-A2GR TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M8 
       75.48       101.95        14.30        94.82        21.67        19.76 
TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MM 
       61.51        47.28       204.66        96.23       203.05       167.90 
TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC 
       43.23       103.56       136.47       124.31       122.73        25.84 
TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J8 TCGA-EE-A3JD 
        3.68        13.81       127.20        36.95        34.32        27.35 
TCGA-EE-A3JE TCGA-ER-A193 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19C TCGA-ER-A19E 
       33.40        31.40        50.76         9.17        48.89        13.02 
TCGA-ER-A19F TCGA-ER-A19S TCGA-ER-A2NC TCGA-ER-A3PL TCGA-FR-A44A TCGA-FS-A1Z3 
       26.37        37.25        43.82        33.21       174.21        20.91 
TCGA-FS-A1ZA TCGA-FS-A1ZC TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZR TCGA-FS-A1ZW 
       27.72       357.37        23.93       101.26        11.41        49.48 
TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4FD TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-GF-A3OT 
       27.02        77.82        77.88        22.92        47.54         9.90 
TCGA-GN-A266 TCGA-QB-A6FS 
       10.13         6.67 

$`USH2A WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.57        16.67       112.04       112.57        71.80       133.25 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       28.08        31.59        90.90        95.74        43.43       103.10 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JF 
       65.49        23.77       115.53       168.00        69.90        48.76 
TCGA-D3-A2JG TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A3BZ 
      113.52        12.10       171.58        56.19        66.08       130.72 
TCGA-D3-A3C6 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF 
       58.06        46.32       166.52        86.93        60.23        24.53 
TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H 
       13.87         9.34        39.75       161.85        43.69        40.14 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS 
       18.38        10.03        51.68       135.75       166.19         7.43 
TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 
      125.19       151.53        54.67         3.65         6.41        11.34 
TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-DA-A1HW TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 
        3.25         9.90        36.03       194.83       176.55        35.93 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A3F2 TCGA-DA-A3F5 
      107.34        61.18        53.92        65.92        28.60       215.44 
TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EE-A17X 
       13.87        10.16        45.11        35.01        52.01        29.82 
TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A20B 
       27.22         8.65        94.98        26.89        68.15       109.64 
TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29G 
       78.87       168.26        13.55        63.35        80.61        72.07 
TCGA-EE-A29H TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A2 
       32.19        37.35        14.47       171.55        17.92        24.43 
TCGA-EE-A2A5 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH 
       39.29        47.54        67.43       314.56       135.95       208.04 
TCGA-EE-A2GI TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GS 
       48.72        54.74        79.66        90.97        13.91        55.59 
TCGA-EE-A2GT TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH 
       44.88       129.27        28.83       103.27       103.20        16.96 
TCGA-EE-A2MK TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AE 
      144.76        47.54       248.65        41.59        53.26        54.51 
TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J7 TCGA-EE-A3JA TCGA-EE-A3JH 
       23.47       138.81       172.18        64.08        53.19       101.79 
TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19D 
      148.08        35.44        13.94        77.75        98.40        12.59 
TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N 
      268.93       152.35         6.44       131.51        61.05        44.05 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2ND TCGA-ER-A2NE 
      162.08        50.89       148.18        79.99        23.34        20.15 
TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV 
       16.37        31.27        32.05       247.04        80.32        46.98 
TCGA-FR-A3YN TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 
       92.98         4.90       216.92        48.59       228.59       202.65 
TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZB TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF 
       28.08         7.79        48.85        53.52        40.27        15.45 
TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZS 
        9.70        32.75        47.38        74.73       133.55       148.80 
TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZY TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 
       53.16        26.56        27.09        66.67        28.73       174.84 
TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FW-A3I3 TCGA-FW-A3TV TCGA-FW-A5DY 
       12.43        26.73        49.45         0.20         0.16         2.40 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 
        7.23        14.04       120.46       117.93        84.72        64.44 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D 
       62.79        32.48        39.58 

  USH2A MUTATED USH2A WILD-TYPE 
           2.60            0.16 
  USH2A MUTATED USH2A WILD-TYPE 
         357.37          314.56 
  USH2A MUTATED USH2A WILD-TYPE 
         42.655          53.190 
[1] "2.6 - 357.4 (42.7)" "0.2 - 314.6 (53.2)"
[1] "hr=" "1.2"
D57V3, continuous
                 vv
clus              DISTANT METASTASIS PRIMARY TUMOR
  USH2A MUTATED                   12             2
  USH2A WILD-TYPE                 23             2
                 vv
clus              REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  USH2A MUTATED                                          20                  55
  USH2A WILD-TYPE                                        38                 115
D57V4, multiclass
                                           clus
vv                                          USH2A MUTATED USH2A WILD-TYPE
  DISTANT METASTASIS                                   12              23
  PRIMARY TUMOR                                         2               2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE            20              38
  REGIONAL LYMPH NODE                                  55             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              I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  USH2A MUTATED             4       2       5        3        6       11
  USH2A WILD-TYPE           6       4      17        7       18        6
                 vv
clus              STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  USH2A MUTATED           2         4         2        14          3          9
  USH2A WILD-TYPE         8        10         7        17         10         13
                 vv
clus              STAGE IIIC STAGE IV
  USH2A MUTATED           16        3
  USH2A WILD-TYPE         28        9
D57V5, multiclass
             clus
vv            USH2A MUTATED USH2A WILD-TYPE
  I OR II NOS             4               6
  STAGE 0                 2               4
  STAGE I                 5              17
  STAGE IA                3               7
  STAGE IB                6              18
  STAGE II               11               6
  STAGE IIA               2               8
  STAGE IIB               4              10
  STAGE IIC               2               7
  STAGE III              14              17
  STAGE IIIA              3              10
  STAGE IIIB              9              13
  STAGE IIIC             16              28
  STAGE IV                3               9
[1] 14  2
[1] 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
  USH2A MUTATED      16 19 21 19
  USH2A WILD-TYPE    35 39 32 36
D57V6, multiclass
       clus
vv      USH2A MUTATED USH2A WILD-TYPE
  T0+T1            16              35
  T2               19              39
  T3               21              32
  T4               19              36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  USH2A MUTATED   42 18 13 11
  USH2A WILD-TYPE 96 30 19 22
D57V7, multiclass
    clus
vv   USH2A MUTATED USH2A WILD-TYPE
  N0            42              96
  N1            18              30
  N2            13              19
  N3            11              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               M0  M1 M1A M1B M1C
  USH2A MUTATED    83   1   2   0   0
  USH2A WILD-TYPE 157   3   0   2   5
D57V8, multiclass
     clus
vv    USH2A MUTATED USH2A WILD-TYPE
  M0             83             157
  M1              1               3
  M1A             2               0
  M1B             0               2
  M1C             0               5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V9, binary
                 cls
clus               0  1
  USH2A MUTATED   31 22
  USH2A WILD-TYPE 71 45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USH2A MUTATED     31   22
  USH2A WILD-TYPE   71   45
     clus
vv    USH2A MUTATED USH2A WILD-TYPE
  NO             31              71
  YES            22              45
[1] 2 2
[1] FALSE
D57V10, binary
                 cls
clus                0   1
  USH2A MUTATED    16  73
  USH2A WILD-TYPE  17 162
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USH2A MUTATED     16   73
  USH2A WILD-TYPE   17  162
     clus
vv    USH2A MUTATED USH2A WILD-TYPE
  NO             16              17
  YES            73             162
[1] 2 2
[1] FALSE
D57V11, continuous
D57V12, binary
                 cls
clus                0   1
  USH2A MUTATED    30  59
  USH2A WILD-TYPE  73 106
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USH2A MUTATED     30   59
  USH2A WILD-TYPE   73  106
        clus
vv       USH2A MUTATED USH2A WILD-TYPE
  FEMALE            30              73
  MALE              59             106
[1] 2 2
[1] FALSE
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  USH2A MUTATED       0                         0    89
  USH2A WILD-TYPE     3                         1   175
D57V13, multiclass
                           clus
vv                          USH2A MUTATED USH2A WILD-TYPE
  ASIAN                                 0               3
  BLACK OR AFRICAN AMERICAN             0               1
  WHITE                                89             175
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V14, binary
                 cls
clus                0   1
  USH2A MUTATED     1  88
  USH2A WILD-TYPE   2 173
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USH2A MUTATED      1   88
  USH2A WILD-TYPE    2  173
                        clus
vv                       USH2A MUTATED USH2A WILD-TYPE
  HISPANIC OR LATINO                 1               2
  NOT HISPANIC OR LATINO            88             173
[1] 2 2
[1] FALSE

Clustering(58) Variable = DDX3X MUTATION ANALYSIS
D58V1, survival
                 sevent
clus2               0   1
  DDX3X MUTATED    10   8
  DDX3X WILD-TYPE 118 122
  DDX3X MUTATED DDX3X WILD-TYPE 
             18             240 
  DDX3X MUTATED DDX3X WILD-TYPE 
              8             122 
$`DDX3X MUTATED`
TCGA-D3-A2J8 TCGA-D9-A6EA TCGA-DA-A1I0 TCGA-DA-A3F8 TCGA-EE-A20B TCGA-EE-A29E 
        8.38        11.31        10.03        14.83        36.07        38.63 
TCGA-EE-A2A1 TCGA-EE-A2GC TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2ML TCGA-EE-A2MU 
       49.22        34.29        33.83         5.42       111.91         5.56 
TCGA-EE-A3AA TCGA-EE-A3AF TCGA-EE-A3J7 TCGA-ER-A193 TCGA-FS-A1Z3 TCGA-FS-A1ZK 
      124.31        13.81        21.60        31.40        14.24        12.89 

$`DDX3X WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.47         8.52       111.09        32.42        70.16       110.79 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       28.08        22.55        45.83        81.24        10.29        85.32 
TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF 
       21.14        88.50        68.22        69.90        11.41        30.87 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO 
        7.50        36.16         6.31        92.42        56.19        64.44 
TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB 
       45.11       114.67        15.25        46.98        46.32        82.29 
TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR 
       61.38        13.32        24.00         6.31         9.34       103.59 
TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J 
       26.37         5.39        80.22        42.71        15.09        41.10 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO 
       17.72         8.84        20.48        13.94        52.01        47.87 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 
        1.55         6.97        23.11         4.01         2.89         9.90 
TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 
       13.22        48.79        35.80        51.12        39.19        13.68 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB 
        9.99        44.52        36.69        25.15         4.93        22.36 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-EB-A44Q TCGA-EB-A44R 
        6.64        19.36         7.00        17.56        13.15         0.20 
TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z 
        0.00         0.00        13.22        11.57        10.55         6.31 
TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 
        8.12         1.12         1.35        12.20         5.13         4.31 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B 
        4.34         5.13         9.21         1.18         7.99         9.90 
TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M 
       37.97        11.15         8.55         4.41         1.08        27.12 
TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V 
        9.50        12.03         8.09         8.84         9.99         2.43 
TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 
        8.68         8.09        11.31        23.90         9.67         8.94 
TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ 
       39.39        17.98        34.92        47.21        30.08        19.43 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GO TCGA-EE-A2GR TCGA-EE-A2GS 
       16.01        35.54        28.31        30.84         1.15        13.02 
TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 
       34.98        36.33         8.84        98.27         2.70         6.18 
TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI 
       47.51         9.53        29.46        44.25         7.96        14.56 
TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ 
       63.42       111.78        56.02        25.08        26.99        21.60 
TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD 
       29.65        27.16        23.05       122.73        25.84         3.68 
TCGA-EE-A3AE TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 
       30.15        15.95        12.72         3.22        22.92        21.60 
TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI 
       16.14        22.22        27.35         0.46        13.94        33.60 
TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B 
       18.61        12.95        38.40         5.72        76.41        25.18 
TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H 
        3.78         3.52        11.90        11.11       114.15        34.88 
TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q 
        4.21        13.45        28.60        42.84        34.68         9.57 
TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE 
       36.07        17.72        78.44        11.80         1.87         1.51 
TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV 
       13.08        12.62        11.74         9.04         6.58        22.49 
TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX 
        1.71        18.41        85.74         4.90        64.47         3.45 
TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB 
       11.01        23.80        15.52         7.33         7.30         3.39 
TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH 
       20.38         8.22        19.53        11.08         7.17        30.87 
TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS 
       12.92        47.38        52.08         8.65         8.81        49.15 
TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 
       40.64         8.68        27.39         0.82         5.23        53.85 
TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC 
        7.36        28.73        14.20        10.78         5.98         6.41 
TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY 
        2.27         0.20         0.99         0.13         0.16         0.43 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        9.90         7.23        12.85        24.85        31.33        84.72 
TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS 
       10.13        16.24        15.42        12.16        14.70         5.79 

  DDX3X MUTATED DDX3X WILD-TYPE 
           5.42            0.00 
  DDX3X MUTATED DDX3X WILD-TYPE 
         124.31          122.73 
  DDX3X MUTATED DDX3X WILD-TYPE 
         18.215          14.630 
[1] "5.4 - 124.3 (18.2)" "0.0 - 122.7 (14.6)"
[1] "hr=" "1.4"
D58V2, survival
                 sevent
clus2               0   1
  DDX3X MUTATED    11   8
  DDX3X WILD-TYPE 121 123
  DDX3X MUTATED DDX3X WILD-TYPE 
             19             244 
  DDX3X MUTATED DDX3X WILD-TYPE 
              8             123 
$`DDX3X MUTATED`
TCGA-D3-A2J8 TCGA-D9-A148 TCGA-D9-A6EA TCGA-DA-A1I0 TCGA-DA-A3F8 TCGA-EE-A20B 
       65.49       151.53        25.18        20.38        15.68       109.64 
TCGA-EE-A29E TCGA-EE-A2A1 TCGA-EE-A2GC TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2ML 
       39.62       102.90        67.43        90.97        13.91       203.05 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AF TCGA-EE-A3J7 TCGA-ER-A193 TCGA-FS-A1Z3 
       53.26       124.31        13.81        64.08        31.40        20.91 
TCGA-FS-A1ZK 
       23.93 

$`DDX3X WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.57        16.67       112.04       112.57        71.80       133.25 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       28.08        31.59        90.90        95.74        43.43       103.10 
TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF 
       23.77       115.53       168.00        69.90        11.87        48.76 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO 
      113.52        42.08        12.10       171.58        56.19        66.08 
TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB 
       45.11       130.72        58.06        46.98        46.32       166.52 
TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR 
       86.93        60.23        24.53        13.87         9.34       103.59 
TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J 
       39.75        21.47       161.85        43.69        40.14       131.90 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO 
       18.38        10.03        51.68        15.06       135.75       137.92 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX 
      166.19         7.43       125.19        54.67         3.65         6.41 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1HW 
       11.34         3.25         9.90        66.25        48.89        36.03 
TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 
      117.21       194.83       176.55        35.93       107.34        61.18 
TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 
       53.92        65.92        23.44        68.09        28.60        10.49 
TCGA-DA-A3F5 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL 
      215.44        13.87        10.16        45.11        35.01         3.55 
TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 
       52.01        29.82        27.22         8.65        94.98        33.73 
TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20C TCGA-EE-A20F 
       14.70        26.89        68.15         4.96       151.27        78.87 
TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D 
      168.26        13.55        63.35        80.61        47.84        13.97 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P 
       72.07        32.19         2.60        44.35        18.61        56.42 
TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X 
       37.35        14.47        55.92        25.87       171.55        17.92 
TCGA-EE-A2A0 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD 
       46.82        24.43        39.29        58.75        47.54       314.56 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
      135.95       208.04        48.72        89.33        54.74        79.66 
TCGA-EE-A2GM TCGA-EE-A2GO TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU 
       75.48       101.95        14.30        55.59        44.88        94.82 
TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD 
       21.67       129.27        28.83        19.76        61.51        47.28 
TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK 
      103.27       103.20        16.96       204.66        96.23       144.76 
TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS 
      167.90        47.54       248.65        43.23       103.56       136.47 
TCGA-EE-A2MT TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AG 
       41.59       122.73        25.84         3.68        54.51        23.47 
TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J8 TCGA-EE-A3JA 
      138.81       172.18       127.20        36.95        34.32        53.19 
TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 
       27.35        33.40       101.79       148.08        35.44        13.94 
TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D 
       50.76         9.17        77.75        98.40        48.89        12.59 
TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L 
       13.02        26.37       268.93       152.35         6.44       131.51 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W 
       61.05        44.05       162.08        50.89        37.25       148.18 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG 
       79.99        43.82        23.34        20.15        16.37        31.27 
TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN 
       32.05       247.04        80.32        46.98        33.21        92.98 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 
      174.21         4.90       216.92        48.59       228.59       202.65 
TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD 
       28.08         7.79        27.72        48.85       357.37        53.52 
TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZM 
       40.27        15.45         9.70        32.75        47.38       101.26 
TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU 
       74.73       133.55        11.41       148.80        53.16        26.56 
TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 
       49.48        27.09        27.02        77.82        66.67        28.73 
TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 
      174.84        12.43        26.73        49.45        77.88         0.20 
TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
       22.92        47.54         0.16         2.40         9.90         7.23 
TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 
       14.04       120.46       117.93        84.72        10.13        64.44 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS 
       62.79        32.48        39.58         6.67 

  DDX3X MUTATED DDX3X WILD-TYPE 
          13.81            0.16 
  DDX3X MUTATED DDX3X WILD-TYPE 
         203.05          357.37 
  DDX3X MUTATED DDX3X WILD-TYPE 
         53.260          48.215 
[1] "13.8 - 203.1 (53.3)" "0.2 - 357.4 (48.2)" 
[1] "hr=" "1.1"
D58V3, continuous
                 vv
clus              DISTANT METASTASIS PRIMARY TUMOR
  DDX3X MUTATED                    2             1
  DDX3X WILD-TYPE                 33             3
                 vv
clus              REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  DDX3X MUTATED                                           6                  10
  DDX3X WILD-TYPE                                        52                 160
D58V4, multiclass
                                           clus
vv                                          DDX3X MUTATED DDX3X WILD-TYPE
  DISTANT METASTASIS                                    2              33
  PRIMARY TUMOR                                         1               3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE             6              52
  REGIONAL LYMPH NODE                                  10             160
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  DDX3X MUTATED             0       0       1        1        2        3
  DDX3X WILD-TYPE          10       6      21        9       22       14
                 vv
clus              STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DDX3X MUTATED           1         2         0         1          0          3
  DDX3X WILD-TYPE         9        12         9        30         13         19
                 vv
clus              STAGE IIIC STAGE IV
  DDX3X MUTATED            2        2
  DDX3X WILD-TYPE         42       10
D58V5, multiclass
             clus
vv            DDX3X MUTATED DDX3X WILD-TYPE
  I OR II NOS             0              10
  STAGE 0                 0               6
  STAGE I                 1              21
  STAGE IA                1               9
  STAGE IB                2              22
  STAGE II                3              14
  STAGE IIA               1               9
  STAGE IIB               2              12
  STAGE IIC               0               9
  STAGE III               1              30
  STAGE IIIA              0              13
  STAGE IIIB              3              19
  STAGE IIIC              2              42
  STAGE IV                2              10
[1] 14  2
[1] 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       3  5  5  4
  DDX3X WILD-TYPE    48 53 48 51
D58V6, multiclass
       clus
vv      DDX3X MUTATED DDX3X WILD-TYPE
  T0+T1             3              48
  T2                5              53
  T3                5              48
  T4                4              51
[1] 4 2
[1] TRUE
[1] "dimension 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    11   3   1   4
  DDX3X WILD-TYPE 127  45  31  29
D58V7, multiclass
    clus
vv   DDX3X MUTATED DDX3X WILD-TYPE
  N0            11             127
  N1             3              45
  N2             1              31
  N3             4              29
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               M0  M1 M1A M1B M1C
  DDX3X MUTATED    16   1   1   1   0
  DDX3X WILD-TYPE 224   3   1   1   5
D58V8, multiclass
     clus
vv    DDX3X MUTATED DDX3X WILD-TYPE
  M0             16             224
  M1              1               3
  M1A             1               1
  M1B             1               1
  M1C             0               5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V9, binary
                 cls
clus               0  1
  DDX3X MUTATED    9  5
  DDX3X WILD-TYPE 93 62
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX3X MUTATED      9    5
  DDX3X WILD-TYPE   93   62
     clus
vv    DDX3X MUTATED DDX3X WILD-TYPE
  NO              9              93
  YES             5              62
[1] 2 2
[1] FALSE
D58V10, binary
                 cls
clus                0   1
  DDX3X MUTATED     3  16
  DDX3X WILD-TYPE  30 219
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX3X MUTATED      3   16
  DDX3X WILD-TYPE   30  219
     clus
vv    DDX3X MUTATED DDX3X WILD-TYPE
  NO              3              30
  YES            16             219
[1] 2 2
[1] FALSE
D58V11, continuous
D58V12, binary
                 cls
clus                0   1
  DDX3X MUTATED     3  16
  DDX3X WILD-TYPE 100 149
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX3X MUTATED      3   16
  DDX3X WILD-TYPE  100  149
        clus
vv       DDX3X MUTATED DDX3X WILD-TYPE
  FEMALE             3             100
  MALE              16             149
[1] 2 2
[1] FALSE
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DDX3X MUTATED       0                         0    19
  DDX3X WILD-TYPE     3                         1   245
D58V13, multiclass
                           clus
vv                          DDX3X MUTATED DDX3X WILD-TYPE
  ASIAN                                 0               3
  BLACK OR AFRICAN AMERICAN             0               1
  WHITE                                19             245
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V14, binary
                 cls
clus                0   1
  DDX3X MUTATED     0  19
  DDX3X WILD-TYPE   3 242
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX3X MUTATED      0   19
  DDX3X WILD-TYPE    3  242
                        clus
vv                       DDX3X MUTATED DDX3X WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO            19             242
[1] 2 2
[1] FALSE

Clustering(59) Variable = PTPN22 MUTATION ANALYSIS
D59V1, survival
                  sevent
clus2                0   1
  PTPN22 MUTATED    14   7
  PTPN22 WILD-TYPE 114 123
  PTPN22 MUTATED PTPN22 WILD-TYPE 
              21              237 
  PTPN22 MUTATED PTPN22 WILD-TYPE 
               7              123 
$`PTPN22 MUTATED`
TCGA-D3-A1Q9 TCGA-D3-A2JC TCGA-D3-A2JH TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A5GO 
       22.55        69.90        36.16       103.59        26.37        47.87 
TCGA-D9-A6EC TCGA-EB-A5SH TCGA-EE-A183 TCGA-EE-A29E TCGA-EE-A2MM TCGA-EE-A2MR 
       13.22         0.00        12.20        38.63        56.02        29.65 
TCGA-EE-A3AA TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3JA TCGA-ER-A19N TCGA-FS-A1ZW 
      124.31        13.81        15.95        22.22        42.84        27.39 
TCGA-FS-A4FC TCGA-FW-A3R5 TCGA-GN-A266 
        6.41         0.99        10.13 

$`PTPN22 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.47         8.52       111.09        32.42        70.16       110.79 
TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 
       28.08        45.83        81.24        10.29        85.32         8.38 
TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JG 
       21.14        88.50        68.22        11.41        30.87         7.50 
TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ 
        6.31        92.42        56.19        64.44        45.11       114.67 
TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE 
       15.25        46.98        46.32        82.29        61.38        13.32 
TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F 
       24.00         6.31         9.34         5.39        80.22        42.71 
TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T 
       15.09        41.10        17.72         8.84        20.48        13.94 
TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 
       52.01         1.55         6.97        23.11         4.01         2.89 
TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 
        9.90        11.31        48.79        35.80        51.12        10.03 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 
       39.19        13.68         9.99        44.52        36.69        25.15 
TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 
        4.93        22.36         6.64        19.36         7.00        17.56 
TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5UN TCGA-EE-A17X 
       14.83        13.15         0.20         0.00        13.22        11.57 
TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A184 
       10.55         6.31         8.12         1.12         1.35         5.13 
TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I 
        4.31        36.07         4.34         5.13         9.21         1.18 
TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29H 
        7.99         9.90        37.97        11.15         8.55         4.41 
TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R 
        1.08        27.12         9.50        12.03         8.09         8.84 
TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 
        9.99         2.43         8.68         8.09        11.31        49.22 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD 
       23.90         9.67         8.94        39.39        34.29        17.98 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
       34.92        47.21        30.08        19.43        16.01        35.54 
TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS 
       28.31        33.83        30.84         5.42         1.15        13.02 
TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 
       34.98        36.33         8.84        98.27         2.70         6.18 
TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI 
       47.51         9.53        29.46        44.25         7.96        14.56 
TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ 
       63.42       111.78       111.91        25.08        26.99        21.60 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD 
       27.16        23.05         5.56       122.73        25.84         3.68 
TCGA-EE-A3AE TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 
       30.15        12.72         3.22        22.92        21.60        21.60 
TCGA-EE-A3J8 TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 
       16.14        27.35         0.46        13.94        33.60        31.40 
TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B 
       18.61        12.95        38.40         5.72        76.41        25.18 
TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H 
        3.78         3.52        11.90        11.11       114.15        34.88 
TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S 
        4.21        13.45        28.60        34.68         9.57        36.07 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF 
       17.72        78.44        11.80         1.87         1.51        13.08 
TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL 
       12.62        11.74         9.04         6.58        22.49         1.71 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY 
       18.41        85.74         4.90        64.47         3.45        11.01 
TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB 
       23.80        14.24        15.52         7.33         7.30         3.39 
TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH 
       20.38         8.22        19.53        11.08         7.17        30.87 
TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR 
       12.92        12.89        47.38        52.08         8.65         8.81 
TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 
       49.15        40.64         8.68         0.82         5.23        53.85 
TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FD 
        7.36        28.73        14.20        10.78         5.98         2.27 
TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
        0.20         0.13         0.16         0.43         9.90         7.23 
TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 
       12.85        24.85        31.33        84.72        16.24        15.42 
TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS 
       12.16        14.70         5.79 

  PTPN22 MUTATED PTPN22 WILD-TYPE 
               0                0 
  PTPN22 MUTATED PTPN22 WILD-TYPE 
          124.31           122.73 
  PTPN22 MUTATED PTPN22 WILD-TYPE 
           26.37            14.20 
[1] "0.0 - 124.3 (26.4)" "0.0 - 122.7 (14.2)"
[1] "hr=" "2"  
D59V2, survival
                  sevent
clus2                0   1
  PTPN22 MUTATED    14   7
  PTPN22 WILD-TYPE 118 124
  PTPN22 MUTATED PTPN22 WILD-TYPE 
              21              242 
  PTPN22 MUTATED PTPN22 WILD-TYPE 
               7              124 
$`PTPN22 MUTATED`
TCGA-D3-A1Q9 TCGA-D3-A2JC TCGA-D3-A2JH TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A5GO 
       31.59        69.90        42.08       103.59        39.75       137.92 
TCGA-D9-A6EC TCGA-EB-A5SH TCGA-EE-A183 TCGA-EE-A29E TCGA-EE-A2MM TCGA-EE-A2MR 
       66.25        35.01        26.89        39.62       167.90       103.56 
TCGA-EE-A3AA TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3JA TCGA-ER-A19N TCGA-FS-A1ZW 
      124.31        13.81        23.47        53.19        44.05        49.48 
TCGA-FS-A4FC TCGA-FW-A3R5 TCGA-GN-A266 
       49.45        22.92        10.13 

$`PTPN22 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.57        16.67       112.04       112.57        71.80       133.25 
TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 
       28.08        90.90        95.74        43.43       103.10        65.49 
TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JG 
       23.77       115.53       168.00        11.87        48.76       113.52 
TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ 
       12.10       171.58        56.19        66.08        45.11       130.72 
TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE 
       58.06        46.98        46.32       166.52        86.93        60.23 
TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F 
       24.53        13.87         9.34        21.47       161.85        43.69 
TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T 
       40.14       131.90        18.38        10.03        51.68        15.06 
TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 
      135.75       166.19         7.43       125.19       151.53        54.67 
TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA 
        3.65         6.41        11.34         3.25         9.90        25.18 
TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 
       48.89        36.03       117.21        20.38       194.83       176.55 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB 
       35.93       107.34        61.18        53.92        65.92        23.44 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q 
       68.09        28.60        10.49       215.44        15.68        13.87 
TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y 
       10.16        45.11         3.55        52.01        29.82        27.22 
TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A184 TCGA-EE-A185 
        8.65        94.98        33.73        14.70        68.15         4.96 
TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A 
      109.64       151.27        78.87       168.26        13.55        63.35 
TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L 
       80.61        47.84        13.97        72.07        32.19         2.60 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S 
       44.35        18.61        56.42        37.35        14.47        55.92 
TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 
       25.87       171.55        17.92        46.82       102.90        24.43 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE 
       39.29        58.75        47.54        67.43       314.56       135.95 
TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM 
      208.04        48.72        89.33        54.74        79.66        75.48 
TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT 
       90.97       101.95        13.91        14.30        55.59        44.88 
TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC 
       94.82        21.67       129.27        28.83        19.76        61.51 
TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ 
       47.28       103.27       103.20        16.96       204.66        96.23 
TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MS 
      144.76       203.05        47.54       248.65        43.23       136.47 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE 
       41.59        53.26       122.73        25.84         3.68        54.51 
TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 
      138.81       172.18       127.20        36.95        64.08        34.32 
TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 
       27.35        33.40       101.79       148.08        31.40        35.44 
TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C 
       13.94        50.76         9.17        77.75        98.40        48.89 
TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J 
       12.59        13.02        26.37       268.93       152.35         6.44 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W 
      131.51        61.05       162.08        50.89        37.25       148.18 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG 
       79.99        43.82        23.34        20.15        16.37        31.27 
TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN 
       32.05       247.04        80.32        46.98        33.21        92.98 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 
      174.21         4.90       216.92        48.59       228.59       202.65 
TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC 
       20.91        28.08         7.79        27.72        48.85       357.37 
TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ 
       53.52        40.27        15.45         9.70        32.75        47.38 
TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS 
       23.93       101.26        74.73       133.55        11.41       148.80 
TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 
       53.16        26.56        27.09        27.02        77.82        66.67 
TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FD TCGA-FW-A3I3 
       28.73       174.84        12.43        26.73        77.88         0.20 
TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 
       47.54         0.16         2.40         9.90         7.23        14.04 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
      120.46       117.93        84.72        64.44        62.79        32.48 
TCGA-GN-A26D TCGA-QB-A6FS 
       39.58         6.67 

  PTPN22 MUTATED PTPN22 WILD-TYPE 
           10.13             0.16 
  PTPN22 MUTATED PTPN22 WILD-TYPE 
          167.90           357.37 
  PTPN22 MUTATED PTPN22 WILD-TYPE 
          44.050           48.655 
[1] "10.1 - 167.9 (44.0)" "0.2 - 357.4 (48.7)" 
[1] "hr=" "1.3"
D59V3, continuous
                  vv
clus               DISTANT METASTASIS PRIMARY TUMOR
  PTPN22 MUTATED                    1             1
  PTPN22 WILD-TYPE                 34             3
                  vv
clus               REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  PTPN22 MUTATED                                           5
  PTPN22 WILD-TYPE                                        53
                  vv
clus               REGIONAL LYMPH NODE
  PTPN22 MUTATED                    14
  PTPN22 WILD-TYPE                 156
D59V4, multiclass
                                           clus
vv                                          PTPN22 MUTATED PTPN22 WILD-TYPE
  DISTANT METASTASIS                                     1               34
  PRIMARY TUMOR                                          1                3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE              5               53
  REGIONAL LYMPH NODE                                   14              156
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  PTPN22 MUTATED             0       1       2        0        2        1
  PTPN22 WILD-TYPE          10       5      20       10       22       16
                  vv
clus               STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  PTPN22 MUTATED           1         0         0         6          2
  PTPN22 WILD-TYPE         9        14         9        25         11
                  vv
clus               STAGE IIIB STAGE IIIC STAGE IV
  PTPN22 MUTATED            3          1        0
  PTPN22 WILD-TYPE         19         43       12
D59V5, multiclass
             clus
vv            PTPN22 MUTATED PTPN22 WILD-TYPE
  I OR II NOS              0               10
  STAGE 0                  1                5
  STAGE I                  2               20
  STAGE IA                 0               10
  STAGE IB                 2               22
  STAGE II                 1               16
  STAGE IIA                1                9
  STAGE IIB                0               14
  STAGE IIC                0                9
  STAGE III                6               25
  STAGE IIIA               2               11
  STAGE IIIB               3               19
  STAGE IIIC               1               43
  STAGE IV                 0               12
[1] 14  2
[1] 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
  PTPN22 MUTATED       6  4  4  3
  PTPN22 WILD-TYPE    45 54 49 52
D59V6, multiclass
       clus
vv      PTPN22 MUTATED PTPN22 WILD-TYPE
  T0+T1              6               45
  T2                 4               54
  T3                 4               49
  T4                 3               52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  PTPN22 MUTATED     8   5   5   1
  PTPN22 WILD-TYPE 130  43  27  32
D59V7, multiclass
    clus
vv   PTPN22 MUTATED PTPN22 WILD-TYPE
  N0              8              130
  N1              5               43
  N2              5               27
  N3              1               32
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                M0  M1 M1A M1B M1C
  PTPN22 MUTATED    19   0   0   0   0
  PTPN22 WILD-TYPE 221   4   2   2   5
D59V8, multiclass
     clus
vv    PTPN22 MUTATED PTPN22 WILD-TYPE
  M0              19              221
  M1               0                4
  M1A              0                2
  M1B              0                2
  M1C              0                5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V9, binary
                  cls
clus                0  1
  PTPN22 MUTATED    7  3
  PTPN22 WILD-TYPE 95 64
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PTPN22 MUTATED      7    3
  PTPN22 WILD-TYPE   95   64
     clus
vv    PTPN22 MUTATED PTPN22 WILD-TYPE
  NO               7               95
  YES              3               64
[1] 2 2
[1] FALSE
D59V10, binary
                  cls
clus                 0   1
  PTPN22 MUTATED     7  14
  PTPN22 WILD-TYPE  26 221
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PTPN22 MUTATED      7   14
  PTPN22 WILD-TYPE   26  221
     clus
vv    PTPN22 MUTATED PTPN22 WILD-TYPE
  NO               7               26
  YES             14              221
[1] 2 2
[1] FALSE
D59V11, continuous
D59V12, binary
                  cls
clus                 0   1
  PTPN22 MUTATED     6  15
  PTPN22 WILD-TYPE  97 150
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PTPN22 MUTATED      6   15
  PTPN22 WILD-TYPE   97  150
        clus
vv       PTPN22 MUTATED PTPN22 WILD-TYPE
  FEMALE              6               97
  MALE               15              150
[1] 2 2
[1] FALSE
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PTPN22 MUTATED       0                         0    21
  PTPN22 WILD-TYPE     3                         1   243
D59V13, multiclass
                           clus
vv                          PTPN22 MUTATED PTPN22 WILD-TYPE
  ASIAN                                  0                3
  BLACK OR AFRICAN AMERICAN              0                1
  WHITE                                 21              243
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V14, binary
                  cls
clus                 0   1
  PTPN22 MUTATED     0  21
  PTPN22 WILD-TYPE   3 240
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PTPN22 MUTATED      0   21
  PTPN22 WILD-TYPE    3  240
                        clus
vv                       PTPN22 MUTATED PTPN22 WILD-TYPE
  HISPANIC OR LATINO                  0                3
  NOT HISPANIC OR LATINO             21              240
[1] 2 2
[1] FALSE

Clustering(60) Variable = C3ORF71 MUTATION ANALYSIS
D60V1, survival
                   sevent
clus2                 0   1
  C3ORF71 MUTATED     1   3
  C3ORF71 WILD-TYPE 127 127
  C3ORF71 MUTATED C3ORF71 WILD-TYPE 
                4               254 
  C3ORF71 MUTATED C3ORF71 WILD-TYPE 
                3               127 
$`C3ORF71 MUTATED`
TCGA-D3-A1Q5 TCGA-EE-A2GL TCGA-EE-A2MC TCGA-ER-A2NC 
       32.42        35.54        47.51        11.80 

$`C3ORF71 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       16.47         8.52       111.09        70.16       110.79        28.08 
TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 
       22.55        45.83        81.24        10.29        85.32         8.38 
TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF 
       21.14        88.50        68.22        69.90        11.41        30.87 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO 
        7.50        36.16         6.31        92.42        56.19        64.44 
TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB 
       45.11       114.67        15.25        46.98        46.32        82.29 
TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR 
       61.38        13.32        24.00         6.31         9.34       103.59 
TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J 
       26.37         5.39        80.22        42.71        15.09        41.10 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO 
       17.72         8.84        20.48        13.94        52.01        47.87 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 
        1.55         6.97        23.11         4.01         2.89         9.90 
TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 
       11.31        13.22        48.79        35.80        51.12        10.03 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 
       39.19        13.68         9.99        44.52        36.69        25.15 
TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 
        4.93        22.36         6.64        19.36         7.00        17.56 
TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN 
       14.83        13.15         0.20         0.00         0.00        13.22 
TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 
       11.57        10.55         6.31         8.12         1.12         1.35 
TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F 
       12.20         5.13         4.31        36.07         4.34         5.13 
TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D 
        9.21         1.18         7.99         9.90        37.97        11.15 
TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N 
       38.63         8.55         4.41         1.08        27.12         9.50 
TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W 
       12.03         8.09         8.84         9.99         2.43         8.68 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 
        8.09        11.31        49.22        23.90         9.67         8.94 
TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI 
       39.39        34.29        17.98        34.92        47.21        30.08 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP 
       19.43        16.01        28.31        33.83        30.84         5.42 
TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 
        1.15        13.02        34.98        36.33         8.84        98.27 
TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH 
        2.70         6.18         9.53        29.46        44.25         7.96 
TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN 
       14.56        63.42       111.78       111.91        56.02        25.08 
TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU 
       26.99        21.60        29.65        27.16        23.05         5.56 
TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF 
      124.31       122.73        25.84         3.68        30.15        13.81 
TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 
       15.95        12.72         3.22        22.92        21.60        21.60 
TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI 
       16.14        22.22        27.35         0.46        13.94        33.60 
TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A 
       31.40        18.61        12.95        38.40         5.72        76.41 
TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G 
       25.18         3.78         3.52        11.90        11.11       114.15 
TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P 
       34.88         4.21        13.45        28.60        42.84        34.68 
TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2ND TCGA-ER-A2NE 
        9.57        36.07        17.72        78.44         1.87         1.51 
TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV 
       13.08        12.62        11.74         9.04         6.58        22.49 
TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX 
        1.71        18.41        85.74         4.90        64.47         3.45 
TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA 
       11.01        23.80        14.24        15.52         7.33         7.30 
TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG 
        3.39        20.38         8.22        19.53        11.08         7.17 
TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ 
       30.87        12.92        12.89        47.38        52.08         8.65 
TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY 
        8.81        49.15        40.64         8.68        27.39         0.82 
TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 
        5.23        53.85         7.36        28.73        14.20        10.78 
TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU 
        5.98         6.41         2.27         0.20         0.99         0.13 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 
        0.16         0.43         9.90         7.23        12.85        24.85 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
       31.33        84.72        10.13        16.24        15.42        12.16 
TCGA-GN-A26D TCGA-QB-A6FS 
       14.70         5.79 

  C3ORF71 MUTATED C3ORF71 WILD-TYPE 
             11.8               0.0 
  C3ORF71 MUTATED C3ORF71 WILD-TYPE 
            47.51            124.31 
  C3ORF71 MUTATED C3ORF71 WILD-TYPE 
            33.98             14.63 
[1] "11.8 - 47.5 (34.0)" "0.0 - 124.3 (14.6)"
[1] "hr=" "1.1"
D60V2, survival
                   sevent
clus2                 0   1
  C3ORF71 MUTATED     1   3
  C3ORF71 WILD-TYPE 131 128
  C3ORF71 MUTATED C3ORF71 WILD-TYPE 
                4               259 
  C3ORF71 MUTATED C3ORF71 WILD-TYPE 
                3               128 
$`C3ORF71 MUTATED`
TCGA-D3-A1Q5 TCGA-EE-A2GL TCGA-EE-A2MC TCGA-ER-A2NC 
      112.57        79.66        61.51        43.82 

$`C3ORF71 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       16.57        16.67       112.04        71.80       133.25        28.08 
TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 
       31.59        90.90        95.74        43.43       103.10        65.49 
TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF 
       23.77       115.53       168.00        69.90        11.87        48.76 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO 
      113.52        42.08        12.10       171.58        56.19        66.08 
TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB 
       45.11       130.72        58.06        46.98        46.32       166.52 
TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR 
       86.93        60.23        24.53        13.87         9.34       103.59 
TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J 
       39.75        21.47       161.85        43.69        40.14       131.90 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO 
       18.38        10.03        51.68        15.06       135.75       137.92 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW 
      166.19         7.43       125.19       151.53        54.67         3.65 
TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC 
        6.41        11.34         3.25         9.90        25.18        66.25 
TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 
       48.89        36.03       117.21        20.38       194.83       176.55 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB 
       35.93       107.34        61.18        53.92        65.92        23.44 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q 
       68.09        28.60        10.49       215.44        15.68        13.87 
TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X 
       10.16        45.11        35.01         3.55        52.01        29.82 
TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 
       27.22         8.65        94.98        33.73        14.70        26.89 
TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H 
       68.15         4.96       109.64       151.27        78.87       168.26 
TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E 
       13.55        63.35        80.61        47.84        13.97        39.62 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P 
       72.07        32.19         2.60        44.35        18.61        56.42 
TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X 
       37.35        14.47        55.92        25.87       171.55        17.92 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB 
       46.82       102.90        24.43        39.29        58.75        47.54 
TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ 
       67.43       314.56       135.95       208.04        48.72        89.33 
TCGA-EE-A2GK TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR 
       54.74        75.48        90.97       101.95        13.91        14.30 
TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 
       55.59        44.88        94.82        21.67       129.27        28.83 
TCGA-EE-A2M8 TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI 
       19.76        47.28       103.27       103.20        16.96       204.66 
TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP 
       96.23       144.76       203.05       167.90        47.54       248.65 
TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA 
       43.23       103.56       136.47        41.59        53.26       124.31 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG 
      122.73        25.84         3.68        54.51        13.81        23.47 
TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 
      138.81       172.18       127.20        36.95        64.08        34.32 
TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 
       53.19        27.35        33.40       101.79       148.08        31.40 
TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B 
       35.44        13.94        50.76         9.17        77.75        98.40 
TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H 
       48.89        12.59        13.02        26.37       268.93       152.35 
TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q 
        6.44       131.51        61.05        44.05       162.08        50.89 
TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF 
       37.25       148.18        79.99        23.34        20.15        16.37 
TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL 
       31.27        32.05       247.04        80.32        46.98        33.21 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY 
       92.98       174.21         4.90       216.92        48.59       228.59 
TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB 
      202.65        20.91        28.08         7.79        27.72        48.85 
TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH 
      357.37        53.52        40.27        15.45         9.70        32.75 
TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR 
       47.38        23.93       101.26        74.73       133.55        11.41 
TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ 
      148.80        53.16        26.56        49.48        27.09        27.02 
TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB 
       77.82        66.67        28.73       174.84        12.43        26.73 
TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV 
       49.45        77.88         0.20        22.92        47.54         0.16 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 
        2.40         9.90         7.23        14.04       120.46       117.93 
TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D 
       84.72        10.13        64.44        62.79        32.48        39.58 
TCGA-QB-A6FS 
        6.67 

  C3ORF71 MUTATED C3ORF71 WILD-TYPE 
            43.82              0.16 
  C3ORF71 MUTATED C3ORF71 WILD-TYPE 
           112.57            357.37 
  C3ORF71 MUTATED C3ORF71 WILD-TYPE 
           70.585            47.840 
[1] "43.8 - 112.6 (70.6)" "0.2 - 357.4 (47.8)" 
[1] "hr=" "1.4"
D60V3, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  C3ORF71 MUTATED                    1             0
  C3ORF71 WILD-TYPE                 34             4
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  C3ORF71 MUTATED                                           0
  C3ORF71 WILD-TYPE                                        58
                   vv
clus                REGIONAL LYMPH NODE
  C3ORF71 MUTATED                     3
  C3ORF71 WILD-TYPE                 167
D60V4, multiclass
                                           clus
vv                                          C3ORF71 MUTATED C3ORF71 WILD-TYPE
  DISTANT METASTASIS                                      1                34
  PRIMARY TUMOR                                           0                 4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE               0                58
  REGIONAL LYMPH NODE                                     3               167
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  C3ORF71 MUTATED             1       0       1        0        1        0
  C3ORF71 WILD-TYPE           9       6      21       10       23       17
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  C3ORF71 MUTATED           1         0         0         0          0
  C3ORF71 WILD-TYPE         9        14         9        31         13
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  C3ORF71 MUTATED            0          0        0
  C3ORF71 WILD-TYPE         22         44       12
D60V5, multiclass
             clus
vv            C3ORF71 MUTATED C3ORF71 WILD-TYPE
  I OR II NOS               1                 9
  STAGE 0                   0                 6
  STAGE I                   1                21
  STAGE IA                  0                10
  STAGE IB                  1                23
  STAGE II                  0                17
  STAGE IIA                 1                 9
  STAGE IIB                 0                14
  STAGE IIC                 0                 9
  STAGE III                 0                31
  STAGE IIIA                0                13
  STAGE IIIB                0                22
  STAGE IIIC                0                44
  STAGE IV                  0                12
[1] 14  2
[1] 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
  C3ORF71 MUTATED       0  2  1  0
  C3ORF71 WILD-TYPE    51 56 52 55
D60V6, multiclass
       clus
vv      C3ORF71 MUTATED C3ORF71 WILD-TYPE
  T0+T1               0                51
  T2                  2                56
  T3                  1                52
  T4                  0                55
[1] 4 2
[1] TRUE
[1] "dimension 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
  C3ORF71 MUTATED     4   0   0   0
  C3ORF71 WILD-TYPE 134  48  32  33
D60V7, multiclass
    clus
vv   C3ORF71 MUTATED C3ORF71 WILD-TYPE
  N0               4               134
  N1               0                48
  N2               0                32
  N3               0                33
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1 M1A M1B M1C
  C3ORF71 MUTATED     4   0   0   0   0
  C3ORF71 WILD-TYPE 236   4   2   2   5
D60V8, multiclass
     clus
vv    C3ORF71 MUTATED C3ORF71 WILD-TYPE
  M0                4               236
  M1                0                 4
  M1A               0                 2
  M1B               0                 2
  M1C               0                 5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V9, binary
                   cls
clus                 0  1
  C3ORF71 MUTATED    3  0
  C3ORF71 WILD-TYPE 99 67
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C3ORF71 MUTATED      3    0
  C3ORF71 WILD-TYPE   99   67
     clus
vv    C3ORF71 MUTATED C3ORF71 WILD-TYPE
  NO                3                99
  YES               0                67
[1] 2 2
[1] FALSE
D60V10, binary
                   cls
clus                  0   1
  C3ORF71 MUTATED     0   4
  C3ORF71 WILD-TYPE  33 231
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C3ORF71 MUTATED      0    4
  C3ORF71 WILD-TYPE   33  231
     clus
vv    C3ORF71 MUTATED C3ORF71 WILD-TYPE
  NO                0                33
  YES               4               231
[1] 2 2
[1] FALSE
D60V11, continuous
D60V12, binary
                   cls
clus                  0   1
  C3ORF71 MUTATED     1   3
  C3ORF71 WILD-TYPE 102 162
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C3ORF71 MUTATED      1    3
  C3ORF71 WILD-TYPE  102  162
        clus
vv       C3ORF71 MUTATED C3ORF71 WILD-TYPE
  FEMALE               1               102
  MALE                 3               162
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  C3ORF71 MUTATED       0                         0     4
  C3ORF71 WILD-TYPE     3                         1   260
D60V13, multiclass
                           clus
vv                          C3ORF71 MUTATED C3ORF71 WILD-TYPE
  ASIAN                                   0                 3
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                   4               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"
D60V14, binary
                   cls
clus                  0   1
  C3ORF71 MUTATED     0   4
  C3ORF71 WILD-TYPE   3 257
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C3ORF71 MUTATED      0    4
  C3ORF71 WILD-TYPE    3  257
                        clus
vv                       C3ORF71 MUTATED C3ORF71 WILD-TYPE
  HISPANIC OR LATINO                   0                 3
  NOT HISPANIC OR LATINO               4               257
[1] 2 2
[1] FALSE

Clustering(61) Variable = CEACAM6 MUTATION ANALYSIS
D61V1, survival
                   sevent
clus2                 0   1
  CEACAM6 MUTATED     5  10
  CEACAM6 WILD-TYPE 123 120
  CEACAM6 MUTATED CEACAM6 WILD-TYPE 
               15               243 
  CEACAM6 MUTATED CEACAM6 WILD-TYPE 
               10               120 
$`CEACAM6 MUTATED`
TCGA-D9-A3Z1 TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A29L TCGA-EE-A2GC TCGA-EE-A2GJ 
        4.01         8.12         1.12         1.08        34.29        19.43 
TCGA-EE-A2MJ TCGA-EE-A2MS TCGA-EE-A3AH TCGA-EE-A3J8 TCGA-ER-A19A TCGA-ER-A19E 
       63.42        27.16        12.72        16.14        76.41        11.90 
TCGA-ER-A2NC TCGA-FS-A4F0 TCGA-GN-A266 
       11.80        53.85        10.13 

$`CEACAM6 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.47         8.52       111.09        32.42        70.16       110.79 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       28.08        22.55        45.83        81.24        10.29        85.32 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
        8.38        21.14        88.50        68.22        69.90        11.41 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       30.87         7.50        36.16         6.31        92.42        56.19 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 
       64.44        45.11       114.67        15.25        46.98        46.32 
TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO 
       82.29        61.38        13.32        24.00         6.31         9.34 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H 
      103.59        26.37         5.39        80.22        42.71        15.09 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN 
       41.10        17.72         8.84        20.48        13.94        52.01 
TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z3 TCGA-D9-A6E9 
       47.87         1.55         6.97        23.11         2.89         9.90 
TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 
       11.31        13.22        48.79        35.80        51.12        10.03 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 
       39.19        13.68         9.99        44.52        36.69        25.15 
TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 
        4.93        22.36         6.64        19.36         7.00        17.56 
TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN 
       14.83        13.15         0.20         0.00         0.00        13.22 
TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 
       11.57        10.55         6.31         1.35        12.20         5.13 
TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I 
        4.31        36.07         4.34         5.13         9.21         1.18 
TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G 
        7.99         9.90        37.97        11.15        38.63         8.55 
TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R 
        4.41        27.12         9.50        12.03         8.09         8.84 
TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 
        9.99         2.43         8.68         8.09        11.31        49.22 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE 
       23.90         9.67         8.94        39.39        17.98        34.92 
TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN 
       47.21        30.08        16.01        35.54        28.31        33.83 
TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU 
       30.84         5.42         1.15        13.02        34.98        36.33 
TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD 
        8.84        98.27         2.70         6.18        47.51         9.53 
TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2ML 
       29.46        44.25         7.96        14.56       111.78       111.91 
TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MT 
       56.02        25.08        26.99        21.60        29.65        23.05 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE 
        5.56       124.31       122.73        25.84         3.68        30.15 
TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 
       13.81        15.95         3.22        22.92        21.60        21.60 
TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 
       22.22        27.35         0.46        13.94        33.60        31.40 
TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19B TCGA-ER-A19C 
       18.61        12.95        38.40         5.72        25.18         3.78 
TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L 
        3.52        11.11       114.15        34.88         4.21        13.45 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W 
       28.60        42.84        34.68         9.57        36.07        17.72 
TCGA-ER-A1A1 TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH 
       78.44         1.87         1.51        13.08        12.62        11.74 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A 
        9.04         6.58        22.49         1.71        18.41        85.74 
TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
        4.90        64.47         3.45        11.01        23.80        14.24 
TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD 
       15.52         7.33         7.30         3.39        20.38         8.22 
TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK 
       19.53        11.08         7.17        30.87        12.92        12.89 
TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT 
       47.38        52.08         8.65         8.81        49.15        40.64 
TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F4 TCGA-FS-A4F5 
        8.68        27.39         0.82         5.23         7.36        28.73 
TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 
       14.20        10.78         5.98         6.41         2.27         0.20 
TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
        0.99         0.13         0.16         0.43         9.90         7.23 
TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 
       12.85        24.85        31.33        84.72        16.24        15.42 
TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS 
       12.16        14.70         5.79 

  CEACAM6 MUTATED CEACAM6 WILD-TYPE 
             1.08              0.00 
  CEACAM6 MUTATED CEACAM6 WILD-TYPE 
            76.41            124.31 
  CEACAM6 MUTATED CEACAM6 WILD-TYPE 
            12.72             14.83 
[1] "1.1 - 76.4 (12.7)"  "0.0 - 124.3 (14.8)"
[1] "hr=" "1.4"
D61V2, survival
                   sevent
clus2                 0   1
  CEACAM6 MUTATED     5  10
  CEACAM6 WILD-TYPE 127 121
  CEACAM6 MUTATED CEACAM6 WILD-TYPE 
               15               248 
  CEACAM6 MUTATED CEACAM6 WILD-TYPE 
               10               121 
$`CEACAM6 MUTATED`
TCGA-D9-A3Z1 TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A29L TCGA-EE-A2GC TCGA-EE-A2GJ 
       11.34        94.98        33.73         2.60        67.43        89.33 
TCGA-EE-A2MJ TCGA-EE-A2MS TCGA-EE-A3AH TCGA-EE-A3J8 TCGA-ER-A19A TCGA-ER-A19E 
       96.23       136.47       138.81        34.32        77.75        13.02 
TCGA-ER-A2NC TCGA-FS-A4F0 TCGA-GN-A266 
       43.82        77.82        10.13 

$`CEACAM6 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.57        16.67       112.04       112.57        71.80       133.25 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       28.08        31.59        90.90        95.74        43.43       103.10 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
       65.49        23.77       115.53       168.00        69.90        11.87 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       48.76       113.52        42.08        12.10       171.58        56.19 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 
       66.08        45.11       130.72        58.06        46.98        46.32 
TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO 
      166.52        86.93        60.23        24.53        13.87         9.34 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H 
      103.59        39.75        21.47       161.85        43.69        40.14 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN 
      131.90        18.38        10.03        51.68        15.06       135.75 
TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 
      137.92       166.19         7.43       125.19       151.53        54.67 
TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC 
        3.65         6.41         3.25         9.90        25.18        66.25 
TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 
       48.89        36.03       117.21        20.38       194.83       176.55 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB 
       35.93       107.34        61.18        53.92        65.92        23.44 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q 
       68.09        28.60        10.49       215.44        15.68        13.87 
TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X 
       10.16        45.11        35.01         3.55        52.01        29.82 
TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 
       27.22         8.65        14.70        26.89        68.15         4.96 
TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A 
      109.64       151.27        78.87       168.26        13.55        63.35 
TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H 
       80.61        47.84        13.97        39.62        72.07        32.19 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S 
       44.35        18.61        56.42        37.35        14.47        55.92 
TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 
       25.87       171.55        17.92        46.82       102.90        24.43 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH 
       39.29        58.75        47.54       314.56       135.95       208.04 
TCGA-EE-A2GI TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO 
       48.72        54.74        79.66        75.48        90.97       101.95 
TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 
       13.91        14.30        55.59        44.88        94.82        21.67 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME 
      129.27        28.83        19.76        61.51        47.28       103.27 
TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM 
      103.20        16.96       204.66       144.76       203.05       167.90 
TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MT TCGA-EE-A2MU 
       47.54       248.65        43.23       103.56        41.59        53.26 
TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF 
      124.31       122.73        25.84         3.68        54.51        13.81 
TCGA-EE-A3AG TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3JA 
       23.47       172.18       127.20        36.95        64.08        53.19 
TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 
       27.35        33.40       101.79       148.08        31.40        35.44 
TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D 
       13.94        50.76         9.17        98.40        48.89        12.59 
TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M 
       26.37       268.93       152.35         6.44       131.51        61.05 
TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 
       44.05       162.08        50.89        37.25       148.18        79.99 
TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES 
       23.34        20.15        16.37        31.27        32.05       247.04 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
       80.32        46.98        33.21        92.98       174.21         4.90 
TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 
      216.92        48.59       228.59       202.65        20.91        28.08 
TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE 
        7.79        27.72        48.85       357.37        53.52        40.27 
TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM 
       15.45         9.70        32.75        47.38        23.93       101.26 
TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU 
       74.73       133.55        11.41       148.80        53.16        26.56 
TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 
       49.48        27.09        27.02        66.67        28.73       174.84 
TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 
       12.43        26.73        49.45        77.88         0.20        22.92 
TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 
       47.54         0.16         2.40         9.90         7.23        14.04 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
      120.46       117.93        84.72        64.44        62.79        32.48 
TCGA-GN-A26D TCGA-QB-A6FS 
       39.58         6.67 

  CEACAM6 MUTATED CEACAM6 WILD-TYPE 
             2.60              0.16 
  CEACAM6 MUTATED CEACAM6 WILD-TYPE 
           138.81            357.37 
  CEACAM6 MUTATED CEACAM6 WILD-TYPE 
           67.430            48.215 
[1] "2.6 - 138.8 (67.4)" "0.2 - 357.4 (48.2)"
[1] "hr=" "1.6"
D61V3, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  CEACAM6 MUTATED                    2             0
  CEACAM6 WILD-TYPE                 33             4
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  CEACAM6 MUTATED                                           4
  CEACAM6 WILD-TYPE                                        54
                   vv
clus                REGIONAL LYMPH NODE
  CEACAM6 MUTATED                     9
  CEACAM6 WILD-TYPE                 161
D61V4, multiclass
                                           clus
vv                                          CEACAM6 MUTATED CEACAM6 WILD-TYPE
  DISTANT METASTASIS                                      2                33
  PRIMARY TUMOR                                           0                 4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE               4                54
  REGIONAL LYMPH NODE                                     9               161
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  CEACAM6 MUTATED             0       0       0        1        2        3
  CEACAM6 WILD-TYPE          10       6      22        9       22       14
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  CEACAM6 MUTATED           0         2         0         2          1
  CEACAM6 WILD-TYPE        10        12         9        29         12
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  CEACAM6 MUTATED            0          2        1
  CEACAM6 WILD-TYPE         22         42       11
D61V5, multiclass
             clus
vv            CEACAM6 MUTATED CEACAM6 WILD-TYPE
  I OR II NOS               0                10
  STAGE 0                   0                 6
  STAGE I                   0                22
  STAGE IA                  1                 9
  STAGE IB                  2                22
  STAGE II                  3                14
  STAGE IIA                 0                10
  STAGE IIB                 2                12
  STAGE IIC                 0                 9
  STAGE III                 2                29
  STAGE IIIA                1                12
  STAGE IIIB                0                22
  STAGE IIIC                2                42
  STAGE IV                  1                11
[1] 14  2
[1] 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
  CEACAM6 MUTATED       1  3  4  5
  CEACAM6 WILD-TYPE    50 55 49 50
D61V6, multiclass
       clus
vv      CEACAM6 MUTATED CEACAM6 WILD-TYPE
  T0+T1               1                50
  T2                  3                55
  T3                  4                49
  T4                  5                50
[1] 4 2
[1] TRUE
[1] "dimension 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
  CEACAM6 MUTATED    11   1   0   2
  CEACAM6 WILD-TYPE 127  47  32  31
D61V7, multiclass
    clus
vv   CEACAM6 MUTATED CEACAM6 WILD-TYPE
  N0              11               127
  N1               1                47
  N2               0                32
  N3               2                31
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1 M1A M1B M1C
  CEACAM6 MUTATED    13   1   0   0   0
  CEACAM6 WILD-TYPE 227   3   2   2   5
D61V8, multiclass
     clus
vv    CEACAM6 MUTATED CEACAM6 WILD-TYPE
  M0               13               227
  M1                1                 3
  M1A               0                 2
  M1B               0                 2
  M1C               0                 5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V9, binary
                   cls
clus                 0  1
  CEACAM6 MUTATED    9  2
  CEACAM6 WILD-TYPE 93 65
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CEACAM6 MUTATED      9    2
  CEACAM6 WILD-TYPE   93   65
     clus
vv    CEACAM6 MUTATED CEACAM6 WILD-TYPE
  NO                9                93
  YES               2                65
[1] 2 2
[1] FALSE
D61V10, binary
                   cls
clus                  0   1
  CEACAM6 MUTATED     2  13
  CEACAM6 WILD-TYPE  31 222
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CEACAM6 MUTATED      2   13
  CEACAM6 WILD-TYPE   31  222
     clus
vv    CEACAM6 MUTATED CEACAM6 WILD-TYPE
  NO                2                31
  YES              13               222
[1] 2 2
[1] FALSE
D61V11, continuous
D61V12, binary
                   cls
clus                  0   1
  CEACAM6 MUTATED     3  12
  CEACAM6 WILD-TYPE 100 153
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CEACAM6 MUTATED      3   12
  CEACAM6 WILD-TYPE  100  153
        clus
vv       CEACAM6 MUTATED CEACAM6 WILD-TYPE
  FEMALE               3               100
  MALE                12               153
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CEACAM6 MUTATED       0                         0    15
  CEACAM6 WILD-TYPE     3                         1   249
D61V13, multiclass
                           clus
vv                          CEACAM6 MUTATED CEACAM6 WILD-TYPE
  ASIAN                                   0                 3
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  15               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"
D61V14, binary
                   cls
clus                  0   1
  CEACAM6 MUTATED     0  15
  CEACAM6 WILD-TYPE   3 246
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CEACAM6 MUTATED      0   15
  CEACAM6 WILD-TYPE    3  246
                        clus
vv                       CEACAM6 MUTATED CEACAM6 WILD-TYPE
  HISPANIC OR LATINO                   0                 3
  NOT HISPANIC OR LATINO              15               246
[1] 2 2
[1] FALSE

Clustering(62) Variable = MUC7 MUTATION ANALYSIS
D62V1, survival
                sevent
clus2              0   1
  MUC7 MUTATED    10   6
  MUC7 WILD-TYPE 118 124
  MUC7 MUTATED MUC7 WILD-TYPE 
            16            242 
  MUC7 MUTATED MUC7 WILD-TYPE 
             6            124 
$`MUC7 MUTATED`
TCGA-D3-A5GO TCGA-D9-A6EC TCGA-DA-A1IC TCGA-EE-A181 TCGA-EE-A20C TCGA-EE-A29D 
       47.87        13.22         6.64         1.12         4.34        11.15 
TCGA-EE-A29E TCGA-EE-A2GC TCGA-EE-A2GJ TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A2MS 
       38.63        34.29        19.43        30.84        29.65        27.16 
TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-FS-A1ZK TCGA-FS-A4FC 
       21.60        21.60        12.89         6.41 

$`MUC7 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.47         8.52       111.09        32.42        70.16       110.79 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       28.08        22.55        45.83        81.24        10.29        85.32 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
        8.38        21.14        88.50        68.22        69.90        11.41 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       30.87         7.50        36.16         6.31        92.42        56.19 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 
       64.44        45.11       114.67        15.25        46.98        46.32 
TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO 
       82.29        61.38        13.32        24.00         6.31         9.34 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H 
      103.59        26.37         5.39        80.22        42.71        15.09 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN 
       41.10        17.72         8.84        20.48        13.94        52.01 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 
        1.55         6.97        23.11         4.01         2.89         9.90 
TCGA-D9-A6EA TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 
       11.31        48.79        35.80        51.12        10.03        39.19 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA 
       13.68         9.99        44.52        36.69        25.15         4.93 
TCGA-DA-A1IB TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q 
       22.36        19.36         7.00        17.56        14.83        13.15 
TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y 
        0.20         0.00         0.00        13.22        11.57        10.55 
TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 
        6.31         8.12         1.35        12.20         5.13         4.31 
TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B 
       36.07         5.13         9.21         1.18         7.99         9.90 
TCGA-EE-A29C TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N 
       37.97         8.55         4.41         1.08        27.12         9.50 
TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W 
       12.03         8.09         8.84         9.99         2.43         8.68 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 
        8.09        11.31        49.22        23.90         9.67         8.94 
TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GK 
       39.39        17.98        34.92        47.21        30.08        16.01 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS 
       35.54        28.31        33.83         5.42         1.15        13.02 
TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 
       34.98        36.33         8.84        98.27         2.70         6.18 
TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI 
       47.51         9.53        29.46        44.25         7.96        14.56 
TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP 
       63.42       111.78       111.91        56.02        25.08        26.99 
TCGA-EE-A2MQ TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC 
       21.60        23.05         5.56       124.31       122.73        25.84 
TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 
        3.68        30.15        13.81        15.95        12.72         3.22 
TCGA-EE-A3J4 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH 
       22.92        16.14        22.22        27.35         0.46        13.94 
TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 
       33.60        31.40        18.61        12.95        38.40         5.72 
TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F 
       76.41        25.18         3.78         3.52        11.90        11.11 
TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N 
      114.15        34.88         4.21        13.45        28.60        42.84 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
       34.68         9.57        36.07        17.72        78.44        11.80 
TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES 
        1.87         1.51        13.08        12.62        11.74         9.04 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
        6.58        22.49         1.71        18.41        85.74         4.90 
TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 
       64.47         3.45        11.01        23.80        14.24        15.52 
TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE 
        7.33         7.30         3.39        20.38         8.22        19.53 
TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZP 
       11.08         7.17        30.87        12.92        47.38        52.08 
TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW 
        8.65         8.81        49.15        40.64         8.68        27.39 
TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 
        0.82         5.23        53.85         7.36        28.73        14.20 
TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU 
       10.78         5.98         2.27         0.20         0.99         0.13 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 
        0.16         0.43         9.90         7.23        12.85        24.85 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
       31.33        84.72        10.13        16.24        15.42        12.16 
TCGA-GN-A26D TCGA-QB-A6FS 
       14.70         5.79 

  MUC7 MUTATED MUC7 WILD-TYPE 
          1.12           0.00 
  MUC7 MUTATED MUC7 WILD-TYPE 
         47.87         124.31 
  MUC7 MUTATED MUC7 WILD-TYPE 
        20.515         14.630 
[1] "1.1 - 47.9 (20.5)"  "0.0 - 124.3 (14.6)"
[1] "hr=" "1.3"
D62V2, survival
                sevent
clus2              0   1
  MUC7 MUTATED    10   6
  MUC7 WILD-TYPE 122 125
  MUC7 MUTATED MUC7 WILD-TYPE 
            16            247 
  MUC7 MUTATED MUC7 WILD-TYPE 
             6            125 
$`MUC7 MUTATED`
TCGA-D3-A5GO TCGA-D9-A6EC TCGA-DA-A1IC TCGA-EE-A181 TCGA-EE-A20C TCGA-EE-A29D 
      137.92        66.25        68.09        33.73       151.27        13.97 
TCGA-EE-A29E TCGA-EE-A2GC TCGA-EE-A2GJ TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A2MS 
       39.62        67.43        89.33       101.95       103.56       136.47 
TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-FS-A1ZK TCGA-FS-A4FC 
       36.95        64.08        23.93        49.45 

$`MUC7 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.57        16.67       112.04       112.57        71.80       133.25 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       28.08        31.59        90.90        95.74        43.43       103.10 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
       65.49        23.77       115.53       168.00        69.90        11.87 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       48.76       113.52        42.08        12.10       171.58        56.19 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 
       66.08        45.11       130.72        58.06        46.98        46.32 
TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO 
      166.52        86.93        60.23        24.53        13.87         9.34 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H 
      103.59        39.75        21.47       161.85        43.69        40.14 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN 
      131.90        18.38        10.03        51.68        15.06       135.75 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW 
      166.19         7.43       125.19       151.53        54.67         3.65 
TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-DA-A1HV 
        6.41        11.34         3.25         9.90        25.18        48.89 
TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 
       36.03       117.21        20.38       194.83       176.55        35.93 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A3F2 
      107.34        61.18        53.92        65.92        23.44        28.60 
TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG 
       10.49       215.44        15.68        13.87        10.16        45.11 
TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z 
       35.01         3.55        52.01        29.82        27.22         8.65 
TCGA-EE-A180 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B 
       94.98        14.70        26.89        68.15         4.96       109.64 
TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C 
       78.87       168.26        13.55        63.35        80.61        47.84 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P 
       72.07        32.19         2.60        44.35        18.61        56.42 
TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X 
       37.35        14.47        55.92        25.87       171.55        17.92 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB 
       46.82       102.90        24.43        39.29        58.75        47.54 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GK TCGA-EE-A2GL 
      314.56       135.95       208.04        48.72        54.74        79.66 
TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT 
       75.48        90.97        13.91        14.30        55.59        44.88 
TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC 
       94.82        21.67       129.27        28.83        19.76        61.51 
TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ 
       47.28       103.27       103.20        16.96       204.66        96.23 
TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ 
      144.76       203.05       167.90        47.54       248.65        43.23 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD 
       41.59        53.26       124.31       122.73        25.84         3.68 
TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 
       54.51        13.81        23.47       138.81       172.18       127.20 
TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI 
       34.32        53.19        27.35        33.40       101.79       148.08 
TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A 
       31.40        35.44        13.94        50.76         9.17        77.75 
TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G 
       98.40        48.89        12.59        13.02        26.37       268.93 
TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P 
      152.35         6.44       131.51        61.05        44.05       162.08 
TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
       50.89        37.25       148.18        79.99        43.82        23.34 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET 
       20.15        16.37        31.27        32.05       247.04        80.32 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW 
       46.98        33.21        92.98       174.21         4.90       216.92 
TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 
       48.59       228.59       202.65        20.91        28.08         7.79 
TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF 
       27.72        48.85       357.37        53.52        40.27        15.45 
TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ 
        9.70        32.75        47.38       101.26        74.73       133.55 
TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY 
       11.41       148.80        53.16        26.56        49.48        27.09 
TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 
       27.02        77.82        66.67        28.73       174.84        12.43 
TCGA-FS-A4FB TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV 
       26.73        77.88         0.20        22.92        47.54         0.16 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 
        2.40         9.90         7.23        14.04       120.46       117.93 
TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D 
       84.72        10.13        64.44        62.79        32.48        39.58 
TCGA-QB-A6FS 
        6.67 

  MUC7 MUTATED MUC7 WILD-TYPE 
         13.97           0.16 
  MUC7 MUTATED MUC7 WILD-TYPE 
        151.27         357.37 
  MUC7 MUTATED MUC7 WILD-TYPE 
         66.84          47.54 
[1] "14.0 - 151.3 (66.8)" "0.2 - 357.4 (47.5)" 
[1] "hr=" "1.5"
D62V3, continuous
                vv
clus             DISTANT METASTASIS PRIMARY TUMOR
  MUC7 MUTATED                    3             1
  MUC7 WILD-TYPE                 32             3
                vv
clus             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  MUC7 MUTATED                                           5                   7
  MUC7 WILD-TYPE                                        53                 163
D62V4, multiclass
                                           clus
vv                                          MUC7 MUTATED MUC7 WILD-TYPE
  DISTANT METASTASIS                                   3             32
  PRIMARY TUMOR                                        1              3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE            5             53
  REGIONAL LYMPH NODE                                  7            163
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  MUC7 MUTATED             0       1       2        1        0        5
  MUC7 WILD-TYPE          10       5      20        9       24       12
                vv
clus             STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  MUC7 MUTATED           1         1         0         1          1          2
  MUC7 WILD-TYPE         9        13         9        30         12         20
                vv
clus             STAGE IIIC STAGE IV
  MUC7 MUTATED            1        0
  MUC7 WILD-TYPE         43       12
D62V5, multiclass
             clus
vv            MUC7 MUTATED MUC7 WILD-TYPE
  I OR II NOS            0             10
  STAGE 0                1              5
  STAGE I                2             20
  STAGE IA               1              9
  STAGE IB               0             24
  STAGE II               5             12
  STAGE IIA              1              9
  STAGE IIB              1             13
  STAGE IIC              0              9
  STAGE III              1             30
  STAGE IIIA             1             12
  STAGE IIIB             2             20
  STAGE IIIC             1             43
  STAGE IV               0             12
[1] 14  2
[1] 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
  MUC7 MUTATED       1  2  9  3
  MUC7 WILD-TYPE    50 56 44 52
D62V6, multiclass
       clus
vv      MUC7 MUTATED MUC7 WILD-TYPE
  T0+T1            1             50
  T2               2             56
  T3               9             44
  T4               3             52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  MUC7 MUTATED    11   4   1   0
  MUC7 WILD-TYPE 127  44  31  33
D62V7, multiclass
    clus
vv   MUC7 MUTATED MUC7 WILD-TYPE
  N0           11            127
  N1            4             44
  N2            1             31
  N3            0             33
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              M0  M1 M1A M1B M1C
  MUC7 MUTATED    16   0   0   0   0
  MUC7 WILD-TYPE 224   4   2   2   5
D62V8, multiclass
     clus
vv    MUC7 MUTATED MUC7 WILD-TYPE
  M0            16            224
  M1             0              4
  M1A            0              2
  M1B            0              2
  M1C            0              5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V9, binary
                cls
clus              0  1
  MUC7 MUTATED    9  3
  MUC7 WILD-TYPE 93 64
[1] "tbl2"
                cls
clus             [,1] [,2]
  MUC7 MUTATED      9    3
  MUC7 WILD-TYPE   93   64
     clus
vv    MUC7 MUTATED MUC7 WILD-TYPE
  NO             9             93
  YES            3             64
[1] 2 2
[1] FALSE
D62V10, binary
                cls
clus               0   1
  MUC7 MUTATED     0  16
  MUC7 WILD-TYPE  33 219
[1] "tbl2"
                cls
clus             [,1] [,2]
  MUC7 MUTATED      0   16
  MUC7 WILD-TYPE   33  219
     clus
vv    MUC7 MUTATED MUC7 WILD-TYPE
  NO             0             33
  YES           16            219
[1] 2 2
[1] FALSE
D62V11, continuous
D62V12, binary
                cls
clus               0   1
  MUC7 MUTATED     4  12
  MUC7 WILD-TYPE  99 153
[1] "tbl2"
                cls
clus             [,1] [,2]
  MUC7 MUTATED      4   12
  MUC7 WILD-TYPE   99  153
        clus
vv       MUC7 MUTATED MUC7 WILD-TYPE
  FEMALE            4             99
  MALE             12            153
[1] 2 2
[1] FALSE
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MUC7 MUTATED       0                         0    16
  MUC7 WILD-TYPE     3                         1   248
D62V13, multiclass
                           clus
vv                          MUC7 MUTATED MUC7 WILD-TYPE
  ASIAN                                0              3
  BLACK OR AFRICAN AMERICAN            0              1
  WHITE                               16            248
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V14, binary
                cls
clus               0   1
  MUC7 MUTATED     0  16
  MUC7 WILD-TYPE   3 245
[1] "tbl2"
                cls
clus             [,1] [,2]
  MUC7 MUTATED      0   16
  MUC7 WILD-TYPE    3  245
                        clus
vv                       MUC7 MUTATED MUC7 WILD-TYPE
  HISPANIC OR LATINO                0              3
  NOT HISPANIC OR LATINO           16            245
[1] 2 2
[1] FALSE

Clustering(63) Variable = SELP MUTATION ANALYSIS
D63V1, survival
                sevent
clus2              0   1
  SELP MUTATED    19  13
  SELP WILD-TYPE 109 117
  SELP MUTATED SELP WILD-TYPE 
            32            226 
  SELP MUTATED SELP WILD-TYPE 
            13            117 
$`SELP MUTATED`
TCGA-D3-A1Q8 TCGA-D3-A2JF TCGA-D3-A2JO TCGA-D3-A3C7 TCGA-D3-A3MU TCGA-D3-A5GU 
       28.08        30.87        64.44        46.98        26.37        23.11 
TCGA-DA-A1HV TCGA-EE-A17Y TCGA-EE-A181 TCGA-EE-A20C TCGA-EE-A29D TCGA-EE-A29E 
       48.79        10.55         1.12         4.34        11.15        38.63 
TCGA-EE-A29M TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A2GB TCGA-EE-A2GO TCGA-EE-A2MD 
       27.12         8.84         9.99        39.39        30.84         9.53 
TCGA-EE-A3AC TCGA-EE-A3AF TCGA-ER-A193 TCGA-ER-A19E TCGA-ER-A2NG TCGA-FR-A69P 
       25.84        13.81        31.40        11.90        12.62         4.90 
TCGA-FS-A1ZA TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F5 TCGA-FS-A4FC TCGA-FW-A3R5 
        7.30         5.23        53.85        28.73         6.41         0.99 
TCGA-FW-A5DY TCGA-GN-A266 
        0.43        10.13 

$`SELP WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.47         8.52       111.09        32.42        70.16       110.79 
TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 
       22.55        45.83        81.24        10.29        85.32         8.38 
TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JG 
       21.14        88.50        68.22        69.90        11.41         7.50 
TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3BZ 
       36.16         6.31        92.42        56.19        45.11       114.67 
TCGA-D3-A3C6 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF 
       15.25        46.32        82.29        61.38        13.32        24.00 
TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F 
        6.31         9.34       103.59         5.39        80.22        42.71 
TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T 
       15.09        41.10        17.72         8.84        20.48        13.94 
TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D9-A3Z1 TCGA-D9-A3Z3 
       52.01        47.87         1.55         6.97         4.01         2.89 
TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 
        9.90        11.31        13.22        35.80        51.12        10.03 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 
       39.19        13.68         9.99        44.52        36.69        25.15 
TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 
        4.93        22.36         6.64        19.36         7.00        17.56 
TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN 
       14.83        13.15         0.20         0.00         0.00        13.22 
TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 
       11.57         6.31         8.12         1.35        12.20         5.13 
TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A 
        4.31        36.07         5.13         9.21         1.18         7.99 
TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29N 
        9.90        37.97         8.55         4.41         1.08         9.50 
TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 
       12.03         8.09         2.43         8.68         8.09        11.31 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GC TCGA-EE-A2GD 
       49.22        23.90         9.67         8.94        34.29        17.98 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
       34.92        47.21        30.08        19.43        16.01        35.54 
TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT 
       28.31        33.83         5.42         1.15        13.02        34.98 
TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC 
       36.33         8.84        98.27         2.70         6.18        47.51 
TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK 
       29.46        44.25         7.96        14.56        63.42       111.78 
TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR 
      111.91        56.02        25.08        26.99        21.60        29.65 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AD 
       27.16        23.05         5.56       124.31       122.73         3.68 
TCGA-EE-A3AE TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 
       30.15        15.95        12.72         3.22        22.92        21.60 
TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH 
       21.60        16.14        22.22        27.35         0.46        13.94 
TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A 
       33.60        18.61        12.95        38.40         5.72        76.41 
TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H 
       25.18         3.78         3.52        11.11       114.15        34.88 
TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q 
        4.21        13.45        28.60        42.84        34.68         9.57 
TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE 
       36.07        17.72        78.44        11.80         1.87         1.51 
TCGA-ER-A2NF TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL 
       13.08        11.74         9.04         6.58        22.49         1.71 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 
       18.41        85.74        64.47         3.45        11.01        23.80 
TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD 
       14.24        15.52         7.33         3.39        20.38         8.22 
TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK 
       19.53        11.08         7.17        30.87        12.92        12.89 
TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT 
       47.38        52.08         8.65         8.81        49.15        40.64 
TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 
        8.68        27.39         0.82         7.36        14.20        10.78 
TCGA-FS-A4FB TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-GF-A3OT 
        5.98         2.27         0.20         0.13         0.16         9.90 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 
        7.23        12.85        24.85        31.33        84.72        16.24 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS 
       15.42        12.16        14.70         5.79 

  SELP MUTATED SELP WILD-TYPE 
          0.43           0.00 
  SELP MUTATED SELP WILD-TYPE 
         64.44         124.31 
  SELP MUTATED SELP WILD-TYPE 
        13.215         14.960 
[1] "0.4 - 64.4 (13.2)"  "0.0 - 124.3 (15.0)"
[1] "hr=" "1.2"
D63V2, survival
                sevent
clus2              0   1
  SELP MUTATED    19  13
  SELP WILD-TYPE 113 118
  SELP MUTATED SELP WILD-TYPE 
            32            231 
  SELP MUTATED SELP WILD-TYPE 
            13            118 
$`SELP MUTATED`
TCGA-D3-A1Q8 TCGA-D3-A2JF TCGA-D3-A2JO TCGA-D3-A3C7 TCGA-D3-A3MU TCGA-D3-A5GU 
       28.08        48.76        66.08        46.98        39.75       125.19 
TCGA-DA-A1HV TCGA-EE-A17Y TCGA-EE-A181 TCGA-EE-A20C TCGA-EE-A29D TCGA-EE-A29E 
       48.89        27.22        33.73       151.27        13.97        39.62 
TCGA-EE-A29M TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A2GB TCGA-EE-A2GO TCGA-EE-A2MD 
       44.35        14.47        55.92        47.54       101.95        47.28 
TCGA-EE-A3AC TCGA-EE-A3AF TCGA-ER-A193 TCGA-ER-A19E TCGA-ER-A2NG TCGA-FR-A69P 
       25.84        13.81        31.40        13.02        31.27         4.90 
TCGA-FS-A1ZA TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F5 TCGA-FS-A4FC TCGA-FW-A3R5 
       27.72        27.02        77.82        28.73        49.45        22.92 
TCGA-FW-A5DY TCGA-GN-A266 
        2.40        10.13 

$`SELP WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.57        16.67       112.04       112.57        71.80       133.25 
TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 
       31.59        90.90        95.74        43.43       103.10        65.49 
TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JG 
       23.77       115.53       168.00        69.90        11.87       113.52 
TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3BZ 
       42.08        12.10       171.58        56.19        45.11       130.72 
TCGA-D3-A3C6 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF 
       58.06        46.32       166.52        86.93        60.23        24.53 
TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F 
       13.87         9.34       103.59        21.47       161.85        43.69 
TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T 
       40.14       131.90        18.38        10.03        51.68        15.06 
TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D9-A148 TCGA-D9-A149 
      135.75       137.92       166.19         7.43       151.53        54.67 
TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA 
        3.65         6.41        11.34         3.25         9.90        25.18 
TCGA-D9-A6EC TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 
       66.25        36.03       117.21        20.38       194.83       176.55 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB 
       35.93       107.34        61.18        53.92        65.92        23.44 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q 
       68.09        28.60        10.49       215.44        15.68        13.87 
TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X 
       10.16        45.11        35.01         3.55        52.01        29.82 
TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 
        8.65        94.98        14.70        26.89        68.15         4.96 
TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B 
      109.64        78.87       168.26        13.55        63.35        80.61 
TCGA-EE-A29C TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P 
       47.84        72.07        32.19         2.60        18.61        56.42 
TCGA-EE-A29Q TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 
       37.35        25.87       171.55        17.92        46.82       102.90 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE 
       24.43        39.29        58.75        67.43       314.56       135.95 
TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM 
      208.04        48.72        89.33        54.74        79.66        75.48 
TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU 
       90.97        13.91        14.30        55.59        44.88        94.82 
TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2ME 
       21.67       129.27        28.83        19.76        61.51       103.27 
TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML 
      103.20        16.96       204.66        96.23       144.76       203.05 
TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS 
      167.90        47.54       248.65        43.23       103.56       136.47 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AE 
       41.59        53.26       124.31       122.73         3.68        54.51 
TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 
       23.47       138.81       172.18       127.20        36.95        64.08 
TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI 
       34.32        53.19        27.35        33.40       101.79       148.08 
TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B 
       35.44        13.94        50.76         9.17        77.75        98.40 
TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J 
       48.89        12.59        26.37       268.93       152.35         6.44 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S 
      131.51        61.05        44.05       162.08        50.89        37.25 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF 
      148.18        79.99        43.82        23.34        20.15        16.37 
TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN 
       32.05       247.04        80.32        46.98        33.21        92.98 
TCGA-FR-A44A TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
      174.21       216.92        48.59       228.59       202.65        20.91 
TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE 
       28.08         7.79        48.85       357.37        53.52        40.27 
TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM 
       15.45         9.70        32.75        47.38        23.93       101.26 
TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU 
       74.73       133.55        11.41       148.80        53.16        26.56 
TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB 
       49.48        27.09        66.67       174.84        12.43        26.73 
TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-GF-A3OT TCGA-GF-A4EO 
       77.88         0.20        47.54         0.16         9.90         7.23 
TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 
       14.04       120.46       117.93        84.72        64.44        62.79 
TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS 
       32.48        39.58         6.67 

  SELP MUTATED SELP WILD-TYPE 
          2.40           0.16 
  SELP MUTATED SELP WILD-TYPE 
        151.27         357.37 
  SELP MUTATED SELP WILD-TYPE 
        32.565         51.680 
[1] "2.4 - 151.3 (32.6)" "0.2 - 357.4 (51.7)"
[1] "hr=" "1.3"
D63V3, continuous
                vv
clus             DISTANT METASTASIS PRIMARY TUMOR
  SELP MUTATED                    5             0
  SELP WILD-TYPE                 30             4
                vv
clus             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  SELP MUTATED                                           7                  21
  SELP WILD-TYPE                                        51                 149
D63V4, multiclass
                                           clus
vv                                          SELP MUTATED SELP WILD-TYPE
  DISTANT METASTASIS                                   5             30
  PRIMARY TUMOR                                        0              4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE            7             51
  REGIONAL LYMPH NODE                                 21            149
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  SELP MUTATED             1       1       0        1        4        3
  SELP WILD-TYPE           9       5      22        9       20       14
                vv
clus             STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  SELP MUTATED           2         3         0         4          1          5
  SELP WILD-TYPE         8        11         9        27         12         17
                vv
clus             STAGE IIIC STAGE IV
  SELP MUTATED            6        1
  SELP WILD-TYPE         38       11
D63V5, multiclass
             clus
vv            SELP MUTATED SELP WILD-TYPE
  I OR II NOS            1              9
  STAGE 0                1              5
  STAGE I                0             22
  STAGE IA               1              9
  STAGE IB               4             20
  STAGE II               3             14
  STAGE IIA              2              8
  STAGE IIB              3             11
  STAGE IIC              0              9
  STAGE III              4             27
  STAGE IIIA             1             12
  STAGE IIIB             5             17
  STAGE IIIC             6             38
  STAGE IV               1             11
[1] 14  2
[1] 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
  SELP MUTATED       7  5 14  2
  SELP WILD-TYPE    44 53 39 53
D63V6, multiclass
       clus
vv      SELP MUTATED SELP WILD-TYPE
  T0+T1            7             44
  T2               5             53
  T3              14             39
  T4               2             53
[1] 4 2
[1] TRUE
[1] "dimension 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
  SELP MUTATED    15   7   5   5
  SELP WILD-TYPE 123  41  27  28
D63V7, multiclass
    clus
vv   SELP MUTATED SELP WILD-TYPE
  N0           15            123
  N1            7             41
  N2            5             27
  N3            5             28
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              M0  M1 M1A M1B M1C
  SELP MUTATED    29   0   0   1   0
  SELP WILD-TYPE 211   4   2   1   5
D63V8, multiclass
     clus
vv    SELP MUTATED SELP WILD-TYPE
  M0            29            211
  M1             0              4
  M1A            0              2
  M1B            1              1
  M1C            0              5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V9, binary
                cls
clus              0  1
  SELP MUTATED   12  9
  SELP WILD-TYPE 90 58
[1] "tbl2"
                cls
clus             [,1] [,2]
  SELP MUTATED     12    9
  SELP WILD-TYPE   90   58
     clus
vv    SELP MUTATED SELP WILD-TYPE
  NO            12             90
  YES            9             58
[1] 2 2
[1] FALSE
D63V10, binary
                cls
clus               0   1
  SELP MUTATED     7  26
  SELP WILD-TYPE  26 209
[1] "tbl2"
                cls
clus             [,1] [,2]
  SELP MUTATED      7   26
  SELP WILD-TYPE   26  209
     clus
vv    SELP MUTATED SELP WILD-TYPE
  NO             7             26
  YES           26            209
[1] 2 2
[1] FALSE
D63V11, continuous
D63V12, binary
                cls
clus               0   1
  SELP MUTATED    18  15
  SELP WILD-TYPE  85 150
[1] "tbl2"
                cls
clus             [,1] [,2]
  SELP MUTATED     18   15
  SELP WILD-TYPE   85  150
        clus
vv       SELP MUTATED SELP WILD-TYPE
  FEMALE           18             85
  MALE             15            150
[1] 2 2
[1] FALSE
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SELP MUTATED       1                         0    32
  SELP WILD-TYPE     2                         1   232
D63V13, multiclass
                           clus
vv                          SELP MUTATED SELP WILD-TYPE
  ASIAN                                1              2
  BLACK OR AFRICAN AMERICAN            0              1
  WHITE                               32            232
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V14, binary
                cls
clus               0   1
  SELP MUTATED     1  31
  SELP WILD-TYPE   2 230
[1] "tbl2"
                cls
clus             [,1] [,2]
  SELP MUTATED      1   31
  SELP WILD-TYPE    2  230
                        clus
vv                       SELP MUTATED SELP WILD-TYPE
  HISPANIC OR LATINO                1              2
  NOT HISPANIC OR LATINO           31            230
[1] 2 2
[1] FALSE

Clustering(64) Variable = LIPH MUTATION ANALYSIS
D64V1, survival
                sevent
clus2              0   1
  LIPH MUTATED     8   5
  LIPH WILD-TYPE 120 125
  LIPH MUTATED LIPH WILD-TYPE 
            13            245 
  LIPH MUTATED LIPH WILD-TYPE 
             5            125 
$`LIPH MUTATED`
TCGA-D3-A2JC TCGA-D3-A2JO TCGA-D3-A3ML TCGA-D3-A5GO TCGA-D9-A6EC TCGA-EE-A181 
       69.90        64.44         6.31        47.87        13.22         1.12 
TCGA-EE-A29E TCGA-EE-A29L TCGA-EE-A29S TCGA-EE-A2GP TCGA-EE-A2MC TCGA-EE-A2MT 
       38.63         1.08         9.99         5.42        47.51        23.05 
TCGA-FW-A3R5 
        0.99 

$`LIPH WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.47         8.52       111.09        32.42        70.16       110.79 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       28.08        22.55        45.83        81.24        10.29        85.32 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JD TCGA-D3-A2JF 
        8.38        21.14        88.50        68.22        11.41        30.87 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JP 
        7.50        36.16         6.31        92.42        56.19        45.11 
TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC 
      114.67        15.25        46.98        46.32        82.29        61.38 
TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV 
       13.32        24.00         9.34       103.59        26.37         5.39 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N 
       80.22        42.71        15.09        41.10        17.72         8.84 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU 
       20.48        13.94        52.01         1.55         6.97        23.11 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-DA-A1HV TCGA-DA-A1HW 
        4.01         2.89         9.90        11.31        48.79        35.80 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 
       51.12        10.03        39.19        13.68         9.99        44.52 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
       36.69        25.15         4.93        22.36         6.64        19.36 
TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG 
        7.00        17.56        14.83        13.15         0.20         0.00 
TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 
        0.00        13.22        11.57        10.55         6.31         8.12 
TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C 
        1.35        12.20         5.13         4.31        36.07         4.34 
TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C 
        5.13         9.21         1.18         7.99         9.90        37.97 
TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P 
       11.15         8.55         4.41        27.12         9.50        12.03 
TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 
        8.09         8.84         2.43         8.68         8.09        11.31 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC 
       49.22        23.90         9.67         8.94        39.39        34.29 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK 
       17.98        34.92        47.21        30.08        19.43        16.01 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GR TCGA-EE-A2GS 
       35.54        28.31        33.83        30.84         1.15        13.02 
TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 
       34.98        36.33         8.84        98.27         2.70         6.18 
TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ 
        9.53        29.46        44.25         7.96        14.56        63.42 
TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ 
      111.78       111.91        56.02        25.08        26.99        21.60 
TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC 
       29.65        27.16         5.56       124.31       122.73        25.84 
TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 
        3.68        30.15        13.81        15.95        12.72         3.22 
TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JD 
       22.92        21.60        21.60        16.14        22.22        27.35 
TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 
        0.46        13.94        33.60        31.40        18.61        12.95 
TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D 
       38.40         5.72        76.41        25.18         3.78         3.52 
TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L 
       11.90        11.11       114.15        34.88         4.21        13.45 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W 
       28.60        42.84        34.68         9.57        36.07        17.72 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG 
       78.44        11.80         1.87         1.51        13.08        12.62 
TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN 
       11.74         9.04         6.58        22.49         1.71        18.41 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 
       85.74         4.90        64.47         3.45        11.01        23.80 
TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC 
       14.24        15.52         7.33         7.30         3.39        20.38 
TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ 
        8.22        19.53        11.08         7.17        30.87        12.92 
TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS 
       12.89        47.38        52.08         8.65         8.81        49.15 
TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 
       40.64         8.68        27.39         0.82         5.23        53.85 
TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC 
        7.36        28.73        14.20        10.78         5.98         6.41 
TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
        2.27         0.20         0.13         0.16         0.43         9.90 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 
        7.23        12.85        24.85        31.33        84.72        10.13 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS 
       16.24        15.42        12.16        14.70         5.79 

  LIPH MUTATED LIPH WILD-TYPE 
          0.99           0.00 
  LIPH MUTATED LIPH WILD-TYPE 
         69.90         124.31 
  LIPH MUTATED LIPH WILD-TYPE 
         13.22          14.83 
[1] "1.0 - 69.9 (13.2)"  "0.0 - 124.3 (14.8)"
[1] "hr=" "1.3"
D64V2, survival
                sevent
clus2              0   1
  LIPH MUTATED     8   5
  LIPH WILD-TYPE 124 126
  LIPH MUTATED LIPH WILD-TYPE 
            13            250 
  LIPH MUTATED LIPH WILD-TYPE 
             5            126 
$`LIPH MUTATED`
TCGA-D3-A2JC TCGA-D3-A2JO TCGA-D3-A3ML TCGA-D3-A5GO TCGA-D9-A6EC TCGA-EE-A181 
       69.90        66.08        13.87       137.92        66.25        33.73 
TCGA-EE-A29E TCGA-EE-A29L TCGA-EE-A29S TCGA-EE-A2GP TCGA-EE-A2MC TCGA-EE-A2MT 
       39.62         2.60        55.92        13.91        61.51        41.59 
TCGA-FW-A3R5 
       22.92 

$`LIPH WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.57        16.67       112.04       112.57        71.80       133.25 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       28.08        31.59        90.90        95.74        43.43       103.10 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JD TCGA-D3-A2JF 
       65.49        23.77       115.53       168.00        11.87        48.76 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JP 
      113.52        42.08        12.10       171.58        56.19        45.11 
TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC 
      130.72        58.06        46.98        46.32       166.52        86.93 
TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV 
       60.23        24.53         9.34       103.59        39.75        21.47 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N 
      161.85        43.69        40.14       131.90        18.38        10.03 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU 
       51.68        15.06       135.75       166.19         7.43       125.19 
TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 
      151.53        54.67         3.65         6.41        11.34         3.25 
TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 
        9.90        25.18        48.89        36.03       117.21        20.38 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 
      194.83       176.55        35.93       107.34        61.18        53.92 
TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 
       65.92        23.44        68.09        28.60        10.49       215.44 
TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL 
       15.68        13.87        10.16        45.11        35.01         3.55 
TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A182 
       52.01        29.82        27.22         8.65        94.98        14.70 
TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F 
       26.89        68.15         4.96       109.64       151.27        78.87 
TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D 
      168.26        13.55        63.35        80.61        47.84        13.97 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
       72.07        32.19        44.35        18.61        56.42        37.35 
TCGA-EE-A29R TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 
       14.47        25.87       171.55        17.92        46.82       102.90 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD 
       24.43        39.29        58.75        47.54        67.43       314.56 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
      135.95       208.04        48.72        89.33        54.74        79.66 
TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT 
       75.48        90.97       101.95        14.30        55.59        44.88 
TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MD 
       94.82        21.67       129.27        28.83        19.76        47.28 
TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK 
      103.27       103.20        16.96       204.66        96.23       144.76 
TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR 
      203.05       167.90        47.54       248.65        43.23       103.56 
TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD 
      136.47        53.26       124.31       122.73        25.84         3.68 
TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 
       54.51        13.81        23.47       138.81       172.18       127.20 
TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE 
       36.95        64.08        34.32        53.19        27.35        33.40 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 
      101.79       148.08        31.40        35.44        13.94        50.76 
TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E 
        9.17        77.75        98.40        48.89        12.59        13.02 
TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M 
       26.37       268.93       152.35         6.44       131.51        61.05 
TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 
       44.05       162.08        50.89        37.25       148.18        79.99 
TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH 
       43.82        23.34        20.15        16.37        31.27        32.05 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A 
      247.04        80.32        46.98        33.21        92.98       174.21 
TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
        4.90       216.92        48.59       228.59       202.65        20.91 
TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD 
       28.08         7.79        27.72        48.85       357.37        53.52 
TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK 
       40.27        15.45         9.70        32.75        47.38        23.93 
TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT 
      101.26        74.73       133.55        11.41       148.80        53.16 
TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 
       26.56        49.48        27.09        27.02        77.82        66.67 
TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD 
       28.73       174.84        12.43        26.73        49.45        77.88 
TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
        0.20        47.54         0.16         2.40         9.90         7.23 
TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 
       14.04       120.46       117.93        84.72        10.13        64.44 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS 
       62.79        32.48        39.58         6.67 

  LIPH MUTATED LIPH WILD-TYPE 
          2.60           0.16 
  LIPH MUTATED LIPH WILD-TYPE 
        137.92         357.37 
  LIPH MUTATED LIPH WILD-TYPE 
        41.590         48.655 
[1] "2.6 - 137.9 (41.6)" "0.2 - 357.4 (48.7)"
[1] "hr=" "1"  
D64V3, continuous
                vv
clus             DISTANT METASTASIS PRIMARY TUMOR
  LIPH MUTATED                    1             1
  LIPH WILD-TYPE                 34             3
                vv
clus             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  LIPH MUTATED                                           2                   9
  LIPH WILD-TYPE                                        56                 161
D64V4, multiclass
                                           clus
vv                                          LIPH MUTATED LIPH WILD-TYPE
  DISTANT METASTASIS                                   1             34
  PRIMARY TUMOR                                        1              3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE            2             56
  REGIONAL LYMPH NODE                                  9            161
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  LIPH MUTATED             0       0       1        0        1        2
  LIPH WILD-TYPE          10       6      21       10       23       15
                vv
clus             STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  LIPH MUTATED           1         0         0         2          2          2
  LIPH WILD-TYPE         9        14         9        29         11         20
                vv
clus             STAGE IIIC STAGE IV
  LIPH MUTATED            2        0
  LIPH WILD-TYPE         42       12
D64V5, multiclass
             clus
vv            LIPH MUTATED LIPH WILD-TYPE
  I OR II NOS            0             10
  STAGE 0                0              6
  STAGE I                1             21
  STAGE IA               0             10
  STAGE IB               1             23
  STAGE II               2             15
  STAGE IIA              1              9
  STAGE IIB              0             14
  STAGE IIC              0              9
  STAGE III              2             29
  STAGE IIIA             2             11
  STAGE IIIB             2             20
  STAGE IIIC             2             42
  STAGE IV               0             12
[1] 14  2
[1] 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
  LIPH MUTATED       1  2  5  3
  LIPH WILD-TYPE    50 56 48 52
D64V6, multiclass
       clus
vv      LIPH MUTATED LIPH WILD-TYPE
  T0+T1            1             50
  T2               2             56
  T3               5             48
  T4               3             52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  LIPH MUTATED     5   3   3   2
  LIPH WILD-TYPE 133  45  29  31
D64V7, multiclass
    clus
vv   LIPH MUTATED LIPH WILD-TYPE
  N0            5            133
  N1            3             45
  N2            3             29
  N3            2             31
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              M0  M1 M1A M1B M1C
  LIPH MUTATED    13   0   0   0   0
  LIPH WILD-TYPE 227   4   2   2   5
D64V8, multiclass
     clus
vv    LIPH MUTATED LIPH WILD-TYPE
  M0            13            227
  M1             0              4
  M1A            0              2
  M1B            0              2
  M1C            0              5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V9, binary
                cls
clus              0  1
  LIPH MUTATED    6  3
  LIPH WILD-TYPE 96 64
[1] "tbl2"
                cls
clus             [,1] [,2]
  LIPH MUTATED      6    3
  LIPH WILD-TYPE   96   64
     clus
vv    LIPH MUTATED LIPH WILD-TYPE
  NO             6             96
  YES            3             64
[1] 2 2
[1] FALSE
D64V10, binary
                cls
clus               0   1
  LIPH MUTATED     1  12
  LIPH WILD-TYPE  32 223
[1] "tbl2"
                cls
clus             [,1] [,2]
  LIPH MUTATED      1   12
  LIPH WILD-TYPE   32  223
     clus
vv    LIPH MUTATED LIPH WILD-TYPE
  NO             1             32
  YES           12            223
[1] 2 2
[1] FALSE
D64V11, continuous
D64V12, binary
                cls
clus               0   1
  LIPH MUTATED     4   9
  LIPH WILD-TYPE  99 156
[1] "tbl2"
                cls
clus             [,1] [,2]
  LIPH MUTATED      4    9
  LIPH WILD-TYPE   99  156
        clus
vv       LIPH MUTATED LIPH WILD-TYPE
  FEMALE            4             99
  MALE              9            156
[1] 2 2
[1] FALSE
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  LIPH MUTATED       0                         0    13
  LIPH WILD-TYPE     3                         1   251
D64V13, multiclass
                           clus
vv                          LIPH MUTATED LIPH WILD-TYPE
  ASIAN                                0              3
  BLACK OR AFRICAN AMERICAN            0              1
  WHITE                               13            251
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V14, binary
                cls
clus               0   1
  LIPH MUTATED     0  13
  LIPH WILD-TYPE   3 248
[1] "tbl2"
                cls
clus             [,1] [,2]
  LIPH MUTATED      0   13
  LIPH WILD-TYPE    3  248
                        clus
vv                       LIPH MUTATED LIPH WILD-TYPE
  HISPANIC OR LATINO                0              3
  NOT HISPANIC OR LATINO           13            248
[1] 2 2
[1] FALSE

Clustering(65) Variable = MMP1 MUTATION ANALYSIS
D65V1, survival
                sevent
clus2              0   1
  MMP1 MUTATED     7   7
  MMP1 WILD-TYPE 121 123
  MMP1 MUTATED MMP1 WILD-TYPE 
            14            244 
  MMP1 MUTATED MMP1 WILD-TYPE 
             7            123 
$`MMP1 MUTATED`
TCGA-D3-A51F TCGA-D9-A6EC TCGA-EE-A17X TCGA-EE-A183 TCGA-EE-A20C TCGA-EE-A20H 
       42.71        13.22        11.57        12.20         4.34         9.21 
TCGA-EE-A2GO TCGA-EE-A2MU TCGA-EE-A3AH TCGA-EE-A3JI TCGA-ER-A193 TCGA-FS-A1Z3 
       30.84         5.56        12.72        33.60        31.40        14.24 
TCGA-FS-A4F0 TCGA-FW-A3R5 
       53.85         0.99 

$`MMP1 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.47         8.52       111.09        32.42        70.16       110.79 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       28.08        22.55        45.83        81.24        10.29        85.32 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
        8.38        21.14        88.50        68.22        69.90        11.41 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       30.87         7.50        36.16         6.31        92.42        56.19 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 
       64.44        45.11       114.67        15.25        46.98        46.32 
TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO 
       82.29        61.38        13.32        24.00         6.31         9.34 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51H TCGA-D3-A51J 
      103.59        26.37         5.39        80.22        15.09        41.10 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO 
       17.72         8.84        20.48        13.94        52.01        47.87 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 
        1.55         6.97        23.11         4.01         2.89         9.90 
TCGA-D9-A6EA TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 
       11.31        48.79        35.80        51.12        10.03        39.19 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA 
       13.68         9.99        44.52        36.69        25.15         4.93 
TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 
       22.36         6.64        19.36         7.00        17.56        14.83 
TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EE-A17Y 
       13.15         0.20         0.00         0.00        13.22        10.55 
TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A184 TCGA-EE-A185 
        6.31         8.12         1.12         1.35         5.13         4.31 
TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C 
       36.07         5.13         1.18         7.99         9.90        37.97 
TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M 
       11.15        38.63         8.55         4.41         1.08        27.12 
TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V 
        9.50        12.03         8.09         8.84         9.99         2.43 
TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 
        8.68         8.09        11.31        49.22        23.90         9.67 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH 
        8.94        39.39        34.29        17.98        34.92        47.21 
TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN 
       30.08        19.43        16.01        35.54        28.31        33.83 
TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 
        5.42         1.15        13.02        34.98        36.33         8.84 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME 
       98.27         2.70         6.18        47.51         9.53        29.46 
TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML 
       44.25         7.96        14.56        63.42       111.78       111.91 
TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS 
       56.02        25.08        26.99        21.60        29.65        27.16 
TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE 
       23.05       124.31       122.73        25.84         3.68        30.15 
TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 
       13.81        15.95         3.22        22.92        21.60        21.60 
TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A195 
       16.14        22.22        27.35         0.46        13.94        18.61 
TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C 
       12.95        38.40         5.72        76.41        25.18         3.78 
TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J 
        3.52        11.90        11.11       114.15        34.88         4.21 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S 
       13.45        28.60        42.84        34.68         9.57        36.07 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF 
       17.72        78.44        11.80         1.87         1.51        13.08 
TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL 
       12.62        11.74         9.04         6.58        22.49         1.71 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY 
       18.41        85.74         4.90        64.47         3.45        11.01 
TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC 
       23.80        15.52         7.33         7.30         3.39        20.38 
TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ 
        8.22        19.53        11.08         7.17        30.87        12.92 
TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS 
       12.89        47.38        52.08         8.65         8.81        49.15 
TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F4 
       40.64         8.68        27.39         0.82         5.23         7.36 
TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD 
       28.73        14.20        10.78         5.98         6.41         2.27 
TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
        0.20         0.13         0.16         0.43         9.90         7.23 
TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 
       12.85        24.85        31.33        84.72        10.13        16.24 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS 
       15.42        12.16        14.70         5.79 

  MMP1 MUTATED MMP1 WILD-TYPE 
          0.99           0.00 
  MMP1 MUTATED MMP1 WILD-TYPE 
         53.85         124.31 
  MMP1 MUTATED MMP1 WILD-TYPE 
         12.97          15.17 
[1] "1.0 - 53.9 (13.0)"  "0.0 - 124.3 (15.2)"
[1] "hr=" "1.1"
D65V2, survival
                sevent
clus2              0   1
  MMP1 MUTATED     7   7
  MMP1 WILD-TYPE 125 124
  MMP1 MUTATED MMP1 WILD-TYPE 
            14            249 
  MMP1 MUTATED MMP1 WILD-TYPE 
             7            124 
$`MMP1 MUTATED`
TCGA-D3-A51F TCGA-D9-A6EC TCGA-EE-A17X TCGA-EE-A183 TCGA-EE-A20C TCGA-EE-A20H 
       43.69        66.25        29.82        26.89       151.27       168.26 
TCGA-EE-A2GO TCGA-EE-A2MU TCGA-EE-A3AH TCGA-EE-A3JI TCGA-ER-A193 TCGA-FS-A1Z3 
      101.95        53.26       138.81       148.08        31.40        20.91 
TCGA-FS-A4F0 TCGA-FW-A3R5 
       77.82        22.92 

$`MMP1 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.57        16.67       112.04       112.57        71.80       133.25 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       28.08        31.59        90.90        95.74        43.43       103.10 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
       65.49        23.77       115.53       168.00        69.90        11.87 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       48.76       113.52        42.08        12.10       171.58        56.19 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 
       66.08        45.11       130.72        58.06        46.98        46.32 
TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO 
      166.52        86.93        60.23        24.53        13.87         9.34 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51H TCGA-D3-A51J 
      103.59        39.75        21.47       161.85        40.14       131.90 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO 
       18.38        10.03        51.68        15.06       135.75       137.92 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW 
      166.19         7.43       125.19       151.53        54.67         3.65 
TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-DA-A1HV 
        6.41        11.34         3.25         9.90        25.18        48.89 
TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 
       36.03       117.21        20.38       194.83       176.55        35.93 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC 
      107.34        61.18        53.92        65.92        23.44        68.09 
TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R 
       28.60        10.49       215.44        15.68        13.87        10.16 
TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17Y TCGA-EE-A17Z 
       45.11        35.01         3.55        52.01        27.22         8.65 
TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B 
       94.98        33.73        14.70        68.15         4.96       109.64 
TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D 
       78.87        13.55        63.35        80.61        47.84        13.97 
TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N 
       39.62        72.07        32.19         2.60        44.35        18.61 
TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W 
       56.42        37.35        14.47        55.92        25.87       171.55 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 
       17.92        46.82       102.90        24.43        39.29        58.75 
TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI 
       47.54        67.43       314.56       135.95       208.04        48.72 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP 
       89.33        54.74        79.66        75.48        90.97        13.91 
TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 
       14.30        55.59        44.88        94.82        21.67       129.27 
TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG 
       28.83        19.76        61.51        47.28       103.27       103.20 
TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM 
       16.96       204.66        96.23       144.76       203.05       167.90 
TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT 
       47.54       248.65        43.23       103.56       136.47        41.59 
TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF 
      124.31       122.73        25.84         3.68        54.51        13.81 
TCGA-EE-A3AG TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 
       23.47       172.18       127.20        36.95        64.08        34.32 
TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A195 TCGA-ER-A197 
       53.19        27.35        33.40       101.79        35.44        13.94 
TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D 
       50.76         9.17        77.75        98.40        48.89        12.59 
TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L 
       13.02        26.37       268.93       152.35         6.44       131.51 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W 
       61.05        44.05       162.08        50.89        37.25       148.18 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG 
       79.99        43.82        23.34        20.15        16.37        31.27 
TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN 
       32.05       247.04        80.32        46.98        33.21        92.98 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 
      174.21         4.90       216.92        48.59       228.59       202.65 
TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD 
       28.08         7.79        27.72        48.85       357.37        53.52 
TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK 
       40.27        15.45         9.70        32.75        47.38        23.93 
TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT 
      101.26        74.73       133.55        11.41       148.80        53.16 
TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F4 TCGA-FS-A4F5 
       26.56        49.48        27.09        27.02        66.67        28.73 
TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 
      174.84        12.43        26.73        49.45        77.88         0.20 
TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 
       47.54         0.16         2.40         9.90         7.23        14.04 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 
      120.46       117.93        84.72        10.13        64.44        62.79 
TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS 
       32.48        39.58         6.67 

  MMP1 MUTATED MMP1 WILD-TYPE 
         20.91           0.16 
  MMP1 MUTATED MMP1 WILD-TYPE 
        168.26         357.37 
  MMP1 MUTATED MMP1 WILD-TYPE 
        59.755         47.840 
[1] "20.9 - 168.3 (59.8)" "0.2 - 357.4 (47.8)" 
[1] "hr=" "1.1"
D65V3, continuous
                vv
clus             DISTANT METASTASIS PRIMARY TUMOR
  MMP1 MUTATED                    3             1
  MMP1 WILD-TYPE                 32             3
                vv
clus             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  MMP1 MUTATED                                           3                   7
  MMP1 WILD-TYPE                                        55                 163
D65V4, multiclass
                                           clus
vv                                          MMP1 MUTATED MMP1 WILD-TYPE
  DISTANT METASTASIS                                   3             32
  PRIMARY TUMOR                                        1              3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE            3             55
  REGIONAL LYMPH NODE                                  7            163
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  MMP1 MUTATED             0       2       2        2        0        2
  MMP1 WILD-TYPE          10       4      20        8       24       15
                vv
clus             STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  MMP1 MUTATED           0         2         0         1          1          0
  MMP1 WILD-TYPE        10        12         9        30         12         22
                vv
clus             STAGE IIIC STAGE IV
  MMP1 MUTATED            1        1
  MMP1 WILD-TYPE         43       11
D65V5, multiclass
             clus
vv            MMP1 MUTATED MMP1 WILD-TYPE
  I OR II NOS            0             10
  STAGE 0                2              4
  STAGE I                2             20
  STAGE IA               2              8
  STAGE IB               0             24
  STAGE II               2             15
  STAGE IIA              0             10
  STAGE IIB              2             12
  STAGE IIC              0              9
  STAGE III              1             30
  STAGE IIIA             1             12
  STAGE IIIB             0             22
  STAGE IIIC             1             43
  STAGE IV               1             11
[1] 14  2
[1] 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
  MMP1 MUTATED       2  2  4  2
  MMP1 WILD-TYPE    49 56 49 53
D65V6, multiclass
       clus
vv      MMP1 MUTATED MMP1 WILD-TYPE
  T0+T1            2             49
  T2               2             56
  T3               4             49
  T4               2             53
[1] 4 2
[1] TRUE
[1] "dimension 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
  MMP1 MUTATED    11   2   1   0
  MMP1 WILD-TYPE 127  46  31  33
D65V7, multiclass
    clus
vv   MMP1 MUTATED MMP1 WILD-TYPE
  N0           11            127
  N1            2             46
  N2            1             31
  N3            0             33
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              M0  M1 M1A M1B M1C
  MMP1 MUTATED    13   1   0   0   0
  MMP1 WILD-TYPE 227   3   2   2   5
D65V8, multiclass
     clus
vv    MMP1 MUTATED MMP1 WILD-TYPE
  M0            13            227
  M1             1              3
  M1A            0              2
  M1B            0              2
  M1C            0              5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V9, binary
                cls
clus              0  1
  MMP1 MUTATED    8  1
  MMP1 WILD-TYPE 94 66
[1] "tbl2"
                cls
clus             [,1] [,2]
  MMP1 MUTATED      8    1
  MMP1 WILD-TYPE   94   66
     clus
vv    MMP1 MUTATED MMP1 WILD-TYPE
  NO             8             94
  YES            1             66
[1] 2 2
[1] FALSE
D65V10, binary
                cls
clus               0   1
  MMP1 MUTATED     1  13
  MMP1 WILD-TYPE  32 222
[1] "tbl2"
                cls
clus             [,1] [,2]
  MMP1 MUTATED      1   13
  MMP1 WILD-TYPE   32  222
     clus
vv    MMP1 MUTATED MMP1 WILD-TYPE
  NO             1             32
  YES           13            222
[1] 2 2
[1] FALSE
D65V11, continuous
D65V12, binary
                cls
clus               0   1
  MMP1 MUTATED     4  10
  MMP1 WILD-TYPE  99 155
[1] "tbl2"
                cls
clus             [,1] [,2]
  MMP1 MUTATED      4   10
  MMP1 WILD-TYPE   99  155
        clus
vv       MMP1 MUTATED MMP1 WILD-TYPE
  FEMALE            4             99
  MALE             10            155
[1] 2 2
[1] FALSE
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MMP1 MUTATED       0                         0    14
  MMP1 WILD-TYPE     3                         1   250
D65V13, multiclass
                           clus
vv                          MMP1 MUTATED MMP1 WILD-TYPE
  ASIAN                                0              3
  BLACK OR AFRICAN AMERICAN            0              1
  WHITE                               14            250
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V14, binary
                cls
clus               0   1
  MMP1 MUTATED     0  13
  MMP1 WILD-TYPE   3 248
[1] "tbl2"
                cls
clus             [,1] [,2]
  MMP1 MUTATED      0   13
  MMP1 WILD-TYPE    3  248
                        clus
vv                       MMP1 MUTATED MMP1 WILD-TYPE
  HISPANIC OR LATINO                0              3
  NOT HISPANIC OR LATINO           13            248
[1] 2 2
[1] FALSE

Clustering(66) Variable = KLF11 MUTATION ANALYSIS
D66V1, survival
                 sevent
clus2               0   1
  KLF11 MUTATED     5   4
  KLF11 WILD-TYPE 123 126
  KLF11 MUTATED KLF11 WILD-TYPE 
              9             249 
  KLF11 MUTATED KLF11 WILD-TYPE 
              4             126 
$`KLF11 MUTATED`
TCGA-D3-A1Q6 TCGA-D3-A1QA TCGA-D3-A2JF TCGA-EE-A180 TCGA-EE-A183 TCGA-EE-A29L 
       70.16        45.83        30.87         8.12        12.20         1.08 
TCGA-FW-A3R5 TCGA-GN-A262 TCGA-GN-A265 
        0.99        24.85        84.72 

$`KLF11 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       16.47         8.52       111.09        32.42       110.79        28.08 
TCGA-D3-A1Q9 TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 
       22.55        81.24        10.29        85.32         8.38        21.14 
TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JH 
       88.50        68.22        69.90        11.41         7.50        36.16 
TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ 
        6.31        92.42        56.19        64.44        45.11       114.67 
TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE 
       15.25        46.98        46.32        82.29        61.38        13.32 
TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV 
       24.00         6.31         9.34       103.59        26.37         5.39 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N 
       80.22        42.71        15.09        41.10        17.72         8.84 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS 
       20.48        13.94        52.01        47.87         1.55         6.97 
TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC 
       23.11         4.01         2.89         9.90        11.31        13.22 
TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 
       48.79        35.80        51.12        10.03        39.19        13.68 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB 
        9.99        44.52        36.69        25.15         4.93        22.36 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q 
        6.64        19.36         7.00        17.56        14.83        13.15 
TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y 
        0.20         0.00         0.00        13.22        11.57        10.55 
TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B 
        6.31         1.12         1.35         5.13         4.31        36.07 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B 
        4.34         5.13         9.21         1.18         7.99         9.90 
TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M 
       37.97        11.15        38.63         8.55         4.41        27.12 
TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V 
        9.50        12.03         8.09         8.84         9.99         2.43 
TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 
        8.68         8.09        11.31        49.22        23.90         9.67 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH 
        8.94        39.39        34.29        17.98        34.92        47.21 
TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN 
       30.08        19.43        16.01        35.54        28.31        33.83 
TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU 
       30.84         5.42         1.15        13.02        34.98        36.33 
TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD 
        8.84        98.27         2.70         6.18        47.51         9.53 
TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK 
       29.46        44.25         7.96        14.56        63.42       111.78 
TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR 
      111.91        56.02        25.08        26.99        21.60        29.65 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC 
       27.16        23.05         5.56       124.31       122.73        25.84 
TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 
        3.68        30.15        13.81        15.95        12.72         3.22 
TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JD 
       22.92        21.60        21.60        16.14        22.22        27.35 
TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 
        0.46        13.94        33.60        31.40        18.61        12.95 
TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D 
       38.40         5.72        76.41        25.18         3.78         3.52 
TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L 
       11.90        11.11       114.15        34.88         4.21        13.45 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W 
       28.60        42.84        34.68         9.57        36.07        17.72 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG 
       78.44        11.80         1.87         1.51        13.08        12.62 
TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN 
       11.74         9.04         6.58        22.49         1.71        18.41 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 
       85.74         4.90        64.47         3.45        11.01        23.80 
TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC 
       14.24        15.52         7.33         7.30         3.39        20.38 
TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ 
        8.22        19.53        11.08         7.17        30.87        12.92 
TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS 
       12.89        47.38        52.08         8.65         8.81        49.15 
TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 
       40.64         8.68        27.39         0.82         5.23        53.85 
TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC 
        7.36        28.73        14.20        10.78         5.98         6.41 
TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
        2.27         0.20         0.13         0.16         0.43         9.90 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A264 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 
        7.23        12.85        31.33        10.13        16.24        15.42 
TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS 
       12.16        14.70         5.79 

  KLF11 MUTATED KLF11 WILD-TYPE 
           0.99            0.00 
  KLF11 MUTATED KLF11 WILD-TYPE 
          84.72          124.31 
  KLF11 MUTATED KLF11 WILD-TYPE 
          24.85           14.70 
[1] "1.0 - 84.7 (24.9)"  "0.0 - 124.3 (14.7)"
[1] "hr=" "1.3"
D66V2, survival
                 sevent
clus2               0   1
  KLF11 MUTATED     5   4
  KLF11 WILD-TYPE 127 127
  KLF11 MUTATED KLF11 WILD-TYPE 
              9             254 
  KLF11 MUTATED KLF11 WILD-TYPE 
              4             127 
$`KLF11 MUTATED`
TCGA-D3-A1Q6 TCGA-D3-A1QA TCGA-D3-A2JF TCGA-EE-A180 TCGA-EE-A183 TCGA-EE-A29L 
       71.80        90.90        48.76        94.98        26.89         2.60 
TCGA-FW-A3R5 TCGA-GN-A262 TCGA-GN-A265 
       22.92       120.46        84.72 

$`KLF11 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       16.57        16.67       112.04       112.57       133.25        28.08 
TCGA-D3-A1Q9 TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 
       31.59        95.74        43.43       103.10        65.49        23.77 
TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JH 
      115.53       168.00        69.90        11.87       113.52        42.08 
TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ 
       12.10       171.58        56.19        66.08        45.11       130.72 
TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE 
       58.06        46.98        46.32       166.52        86.93        60.23 
TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV 
       24.53        13.87         9.34       103.59        39.75        21.47 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N 
      161.85        43.69        40.14       131.90        18.38        10.03 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS 
       51.68        15.06       135.75       137.92       166.19         7.43 
TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 
      125.19       151.53        54.67         3.65         6.41        11.34 
TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1HW 
        3.25         9.90        25.18        66.25        48.89        36.03 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 
      117.21        20.38       194.83       176.55        35.93       107.34 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
       61.18        53.92        65.92        23.44        68.09        28.60 
TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG 
       10.49       215.44        15.68        13.87        10.16        45.11 
TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z 
       35.01         3.55        52.01        29.82        27.22         8.65 
TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C 
       33.73        14.70        68.15         4.96       109.64       151.27 
TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C 
       78.87       168.26        13.55        63.35        80.61        47.84 
TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29N 
       13.97        39.62        72.07        32.19        44.35        18.61 
TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W 
       56.42        37.35        14.47        55.92        25.87       171.55 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 
       17.92        46.82       102.90        24.43        39.29        58.75 
TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI 
       47.54        67.43       314.56       135.95       208.04        48.72 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO 
       89.33        54.74        79.66        75.48        90.97       101.95 
TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 
       13.91        14.30        55.59        44.88        94.82        21.67 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME 
      129.27        28.83        19.76        61.51        47.28       103.27 
TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML 
      103.20        16.96       204.66        96.23       144.76       203.05 
TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS 
      167.90        47.54       248.65        43.23       103.56       136.47 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD 
       41.59        53.26       124.31       122.73        25.84         3.68 
TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 
       54.51        13.81        23.47       138.81       172.18       127.20 
TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE 
       36.95        64.08        34.32        53.19        27.35        33.40 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 
      101.79       148.08        31.40        35.44        13.94        50.76 
TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E 
        9.17        77.75        98.40        48.89        12.59        13.02 
TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M 
       26.37       268.93       152.35         6.44       131.51        61.05 
TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 
       44.05       162.08        50.89        37.25       148.18        79.99 
TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH 
       43.82        23.34        20.15        16.37        31.27        32.05 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A 
      247.04        80.32        46.98        33.21        92.98       174.21 
TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
        4.90       216.92        48.59       228.59       202.65        20.91 
TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD 
       28.08         7.79        27.72        48.85       357.37        53.52 
TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK 
       40.27        15.45         9.70        32.75        47.38        23.93 
TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT 
      101.26        74.73       133.55        11.41       148.80        53.16 
TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 
       26.56        49.48        27.09        27.02        77.82        66.67 
TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD 
       28.73       174.84        12.43        26.73        49.45        77.88 
TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
        0.20        47.54         0.16         2.40         9.90         7.23 
TCGA-GF-A6C8 TCGA-GN-A264 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
       14.04       117.93        10.13        64.44        62.79        32.48 
TCGA-GN-A26D TCGA-QB-A6FS 
       39.58         6.67 

  KLF11 MUTATED KLF11 WILD-TYPE 
           2.60            0.16 
  KLF11 MUTATED KLF11 WILD-TYPE 
         120.46          357.37 
  KLF11 MUTATED KLF11 WILD-TYPE 
          71.80           47.69 
[1] "2.6 - 120.5 (71.8)" "0.2 - 357.4 (47.7)"
[1] "hr=" "1"  
D66V3, continuous
                 vv
clus              DISTANT METASTASIS PRIMARY TUMOR
  KLF11 MUTATED                    2             0
  KLF11 WILD-TYPE                 33             4
                 vv
clus              REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  KLF11 MUTATED                                           2                   5
  KLF11 WILD-TYPE                                        56                 165
D66V4, multiclass
                                           clus
vv                                          KLF11 MUTATED KLF11 WILD-TYPE
  DISTANT METASTASIS                                    2              33
  PRIMARY TUMOR                                         0               4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE             2              56
  REGIONAL LYMPH NODE                                   5             165
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  KLF11 MUTATED             0       1       0        1        1        0
  KLF11 WILD-TYPE          10       5      22        9       23       17
                 vv
clus              STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  KLF11 MUTATED           0         0         0         3          0          0
  KLF11 WILD-TYPE        10        14         9        28         13         22
                 vv
clus              STAGE IIIC STAGE IV
  KLF11 MUTATED            1        0
  KLF11 WILD-TYPE         43       12
D66V5, multiclass
             clus
vv            KLF11 MUTATED KLF11 WILD-TYPE
  I OR II NOS             0              10
  STAGE 0                 1               5
  STAGE I                 0              22
  STAGE IA                1               9
  STAGE IB                1              23
  STAGE II                0              17
  STAGE IIA               0              10
  STAGE IIB               0              14
  STAGE IIC               0               9
  STAGE III               3              28
  STAGE IIIA              0              13
  STAGE IIIB              0              22
  STAGE IIIC              1              43
  STAGE IV                0              12
[1] 14  2
[1] 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
  KLF11 MUTATED       1  1  0  3
  KLF11 WILD-TYPE    50 57 53 52
D66V6, multiclass
       clus
vv      KLF11 MUTATED KLF11 WILD-TYPE
  T0+T1             1              50
  T2                1              57
  T3                0              53
  T4                3              52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  KLF11 MUTATED     4   1   1   1
  KLF11 WILD-TYPE 134  47  31  32
D66V7, multiclass
    clus
vv   KLF11 MUTATED KLF11 WILD-TYPE
  N0             4             134
  N1             1              47
  N2             1              31
  N3             1              32
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               M0  M1 M1A M1B M1C
  KLF11 MUTATED     7   0   0   0   0
  KLF11 WILD-TYPE 233   4   2   2   5
D66V8, multiclass
     clus
vv    KLF11 MUTATED KLF11 WILD-TYPE
  M0              7             233
  M1              0               4
  M1A             0               2
  M1B             0               2
  M1C             0               5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V9, binary
                 cls
clus               0  1
  KLF11 MUTATED    3  1
  KLF11 WILD-TYPE 99 66
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KLF11 MUTATED      3    1
  KLF11 WILD-TYPE   99   66
     clus
vv    KLF11 MUTATED KLF11 WILD-TYPE
  NO              3              99
  YES             1              66
[1] 2 2
[1] FALSE
D66V10, binary
                 cls
clus                0   1
  KLF11 MUTATED     1   8
  KLF11 WILD-TYPE  32 227
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KLF11 MUTATED      1    8
  KLF11 WILD-TYPE   32  227
     clus
vv    KLF11 MUTATED KLF11 WILD-TYPE
  NO              1              32
  YES             8             227
[1] 2 2
[1] FALSE
D66V11, continuous
D66V12, binary
                 cls
clus                0   1
  KLF11 MUTATED     1   8
  KLF11 WILD-TYPE 102 157
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KLF11 MUTATED      1    8
  KLF11 WILD-TYPE  102  157
        clus
vv       KLF11 MUTATED KLF11 WILD-TYPE
  FEMALE             1             102
  MALE               8             157
[1] 2 2
[1] FALSE
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  KLF11 MUTATED       0                         0     9
  KLF11 WILD-TYPE     3                         1   255
D66V13, multiclass
                           clus
vv                          KLF11 MUTATED KLF11 WILD-TYPE
  ASIAN                                 0               3
  BLACK OR AFRICAN AMERICAN             0               1
  WHITE                                 9             255
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V14, binary
                 cls
clus                0   1
  KLF11 MUTATED     0   9
  KLF11 WILD-TYPE   3 252
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KLF11 MUTATED      0    9
  KLF11 WILD-TYPE    3  252
                        clus
vv                       KLF11 MUTATED KLF11 WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO             9             252
[1] 2 2
[1] FALSE

Clustering(67) Variable = USP9X MUTATION ANALYSIS
D67V1, survival
                 sevent
clus2               0   1
  USP9X MUTATED     7   5
  USP9X WILD-TYPE 121 125
  USP9X MUTATED USP9X WILD-TYPE 
             12             246 
  USP9X MUTATED USP9X WILD-TYPE 
              5             125 
$`USP9X MUTATED`
TCGA-D3-A3C7 TCGA-D9-A6EC TCGA-DA-A1HV TCGA-EE-A2MR TCGA-EE-A3AF TCGA-EE-A3J7 
       46.98        13.22        48.79        29.65        13.81        21.60 
TCGA-ER-A198 TCGA-ER-A2NH TCGA-FS-A1Z0 TCGA-FS-A1ZK TCGA-FS-A4F5 TCGA-FW-A3R5 
       38.40        11.74        23.80        12.89        28.73         0.99 

$`USP9X WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.47         8.52       111.09        32.42        70.16       110.79 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       28.08        22.55        45.83        81.24        10.29        85.32 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
        8.38        21.14        88.50        68.22        69.90        11.41 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       30.87         7.50        36.16         6.31        92.42        56.19 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C8 TCGA-D3-A3CB 
       64.44        45.11       114.67        15.25        46.32        82.29 
TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR 
       61.38        13.32        24.00         6.31         9.34       103.59 
TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J 
       26.37         5.39        80.22        42.71        15.09        41.10 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO 
       17.72         8.84        20.48        13.94        52.01        47.87 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 
        1.55         6.97        23.11         4.01         2.89         9.90 
TCGA-D9-A6EA TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 
       11.31        35.80        51.12        10.03        39.19        13.68 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB 
        9.99        44.52        36.69        25.15         4.93        22.36 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q 
        6.64        19.36         7.00        17.56        14.83        13.15 
TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y 
        0.20         0.00         0.00        13.22        11.57        10.55 
TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 
        6.31         8.12         1.12         1.35        12.20         5.13 
TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I 
        4.31        36.07         4.34         5.13         9.21         1.18 
TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G 
        7.99         9.90        37.97        11.15        38.63         8.55 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
        4.41         1.08        27.12         9.50        12.03         8.09 
TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 
        8.84         9.99         2.43         8.68         8.09        11.31 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC 
       49.22        23.90         9.67         8.94        39.39        34.29 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK 
       17.98        34.92        47.21        30.08        19.43        16.01 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR 
       35.54        28.31        33.83        30.84         5.42         1.15 
TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 
       13.02        34.98        36.33         8.84        98.27         2.70 
TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH 
        6.18        47.51         9.53        29.46        44.25         7.96 
TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN 
       14.56        63.42       111.78       111.91        56.02        25.08 
TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA 
       26.99        21.60        27.16        23.05         5.56       124.31 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AG TCGA-EE-A3AH 
      122.73        25.84         3.68        30.15        15.95        12.72 
TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JD 
        3.22        22.92        21.60        16.14        22.22        27.35 
TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 
        0.46        13.94        33.60        31.40        18.61        12.95 
TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E 
        5.72        76.41        25.18         3.78         3.52        11.90 
TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M 
       11.11       114.15        34.88         4.21        13.45        28.60 
TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 
       42.84        34.68         9.57        36.07        17.72        78.44 
TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES 
       11.80         1.87         1.51        13.08        12.62         9.04 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
        6.58        22.49         1.71        18.41        85.74         4.90 
TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 
       64.47         3.45        11.01        14.24        15.52         7.33 
TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF 
        7.30         3.39        20.38         8.22        19.53        11.08 
TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ 
        7.17        30.87        12.92        47.38        52.08         8.65 
TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY 
        8.81        49.15        40.64         8.68        27.39         0.82 
TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB 
        5.23        53.85         7.36        14.20        10.78         5.98 
TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY 
        6.41         2.27         0.20         0.13         0.16         0.43 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        9.90         7.23        12.85        24.85        31.33        84.72 
TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS 
       10.13        16.24        15.42        12.16        14.70         5.79 

  USP9X MUTATED USP9X WILD-TYPE 
           0.99            0.00 
  USP9X MUTATED USP9X WILD-TYPE 
          48.79          124.31 
  USP9X MUTATED USP9X WILD-TYPE 
          22.70           14.63 
[1] "1.0 - 48.8 (22.7)"  "0.0 - 124.3 (14.6)"
[1] "hr=" "1.4"
D67V2, survival
                 sevent
clus2               0   1
  USP9X MUTATED     8   5
  USP9X WILD-TYPE 124 126
  USP9X MUTATED USP9X WILD-TYPE 
             13             250 
  USP9X MUTATED USP9X WILD-TYPE 
              5             126 
$`USP9X MUTATED`
TCGA-D3-A3C7 TCGA-D9-A148 TCGA-D9-A6EC TCGA-DA-A1HV TCGA-EE-A2MR TCGA-EE-A3AF 
       46.98       151.53        66.25        48.89       103.56        13.81 
TCGA-EE-A3J7 TCGA-ER-A198 TCGA-ER-A2NH TCGA-FS-A1Z0 TCGA-FS-A1ZK TCGA-FS-A4F5 
       64.08        50.76        32.05       202.65        23.93        28.73 
TCGA-FW-A3R5 
       22.92 

$`USP9X WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.57        16.67       112.04       112.57        71.80       133.25 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       28.08        31.59        90.90        95.74        43.43       103.10 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
       65.49        23.77       115.53       168.00        69.90        11.87 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       48.76       113.52        42.08        12.10       171.58        56.19 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C8 TCGA-D3-A3CB 
       66.08        45.11       130.72        58.06        46.32       166.52 
TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR 
       86.93        60.23        24.53        13.87         9.34       103.59 
TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J 
       39.75        21.47       161.85        43.69        40.14       131.90 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO 
       18.38        10.03        51.68        15.06       135.75       137.92 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX 
      166.19         7.43       125.19        54.67         3.65         6.41 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-DA-A1HW TCGA-DA-A1HY 
       11.34         3.25         9.90        25.18        36.03       117.21 
TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 
       20.38       194.83       176.55        35.93       107.34        61.18 
TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 
       53.92        65.92        23.44        68.09        28.60        10.49 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH 
      215.44        15.68        13.87        10.16        45.11        35.01 
TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 
        3.55        52.01        29.82        27.22         8.65        94.98 
TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B 
       33.73        14.70        26.89        68.15         4.96       109.64 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B 
      151.27        78.87       168.26        13.55        63.35        80.61 
TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L 
       47.84        13.97        39.62        72.07        32.19         2.60 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S 
       44.35        18.61        56.42        37.35        14.47        55.92 
TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 
       25.87       171.55        17.92        46.82       102.90        24.43 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE 
       39.29        58.75        47.54        67.43       314.56       135.95 
TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM 
      208.04        48.72        89.33        54.74        79.66        75.48 
TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT 
       90.97       101.95        13.91        14.30        55.59        44.88 
TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC 
       94.82        21.67       129.27        28.83        19.76        61.51 
TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ 
       47.28       103.27       103.20        16.96       204.66        96.23 
TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ 
      144.76       203.05       167.90        47.54       248.65        43.23 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC 
      136.47        41.59        53.26       124.31       122.73        25.84 
TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 
        3.68        54.51        23.47       138.81       172.18       127.20 
TCGA-EE-A3J5 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH 
       36.95        34.32        53.19        27.35        33.40       101.79 
TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A 
      148.08        31.40        35.44        13.94         9.17        77.75 
TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G 
       98.40        48.89        12.59        13.02        26.37       268.93 
TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P 
      152.35         6.44       131.51        61.05        44.05       162.08 
TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
       50.89        37.25       148.18        79.99        43.82        23.34 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV 
       20.15        16.37        31.27       247.04        80.32        46.98 
TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX 
       33.21        92.98       174.21         4.90       216.92        48.59 
TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB 
      228.59        20.91        28.08         7.79        27.72        48.85 
TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH 
      357.37        53.52        40.27        15.45         9.70        32.75 
TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS 
       47.38       101.26        74.73       133.55        11.41       148.80 
TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 
       53.16        26.56        49.48        27.09        27.02        77.82 
TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD 
       66.67       174.84        12.43        26.73        49.45        77.88 
TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
        0.20        47.54         0.16         2.40         9.90         7.23 
TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 
       14.04       120.46       117.93        84.72        10.13        64.44 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS 
       62.79        32.48        39.58         6.67 

  USP9X MUTATED USP9X WILD-TYPE 
          13.81            0.16 
  USP9X MUTATED USP9X WILD-TYPE 
         202.65          357.37 
  USP9X MUTATED USP9X WILD-TYPE 
         48.890          48.215 
[1] "13.8 - 202.7 (48.9)" "0.2 - 357.4 (48.2)" 
[1] "hr=" "1.3"
D67V3, continuous
                 vv
clus              DISTANT METASTASIS PRIMARY TUMOR
  USP9X MUTATED                    2             1
  USP9X WILD-TYPE                 33             3
                 vv
clus              REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  USP9X MUTATED                                           4                   7
  USP9X WILD-TYPE                                        54                 163
D67V4, multiclass
                                           clus
vv                                          USP9X MUTATED USP9X WILD-TYPE
  DISTANT METASTASIS                                    2              33
  PRIMARY TUMOR                                         1               3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE             4              54
  REGIONAL LYMPH NODE                                   7             163
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  USP9X MUTATED             0       1       2        1        1        1
  USP9X WILD-TYPE          10       5      20        9       23       16
                 vv
clus              STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  USP9X MUTATED           0         0         0         2          1          1
  USP9X WILD-TYPE        10        14         9        29         12         21
                 vv
clus              STAGE IIIC STAGE IV
  USP9X MUTATED            2        0
  USP9X WILD-TYPE         42       12
D67V5, multiclass
             clus
vv            USP9X MUTATED USP9X WILD-TYPE
  I OR II NOS             0              10
  STAGE 0                 1               5
  STAGE I                 2              20
  STAGE IA                1               9
  STAGE IB                1              23
  STAGE II                1              16
  STAGE IIA               0              10
  STAGE IIB               0              14
  STAGE IIC               0               9
  STAGE III               2              29
  STAGE IIIA              1              12
  STAGE IIIB              1              21
  STAGE IIIC              2              42
  STAGE IV                0              12
[1] 14  2
[1] 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
  USP9X MUTATED       4  3  1  2
  USP9X WILD-TYPE    47 55 52 53
D67V6, multiclass
       clus
vv      USP9X MUTATED USP9X WILD-TYPE
  T0+T1             4              47
  T2                3              55
  T3                1              52
  T4                2              53
[1] 4 2
[1] TRUE
[1] "dimension 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
  USP9X MUTATED     6   2   2   3
  USP9X WILD-TYPE 132  46  30  30
D67V7, multiclass
    clus
vv   USP9X MUTATED USP9X WILD-TYPE
  N0             6             132
  N1             2              46
  N2             2              30
  N3             3              30
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               M0  M1 M1A M1B M1C
  USP9X MUTATED    13   0   0   1   0
  USP9X WILD-TYPE 227   4   2   1   5
D67V8, multiclass
     clus
vv    USP9X MUTATED USP9X WILD-TYPE
  M0             13             227
  M1              0               4
  M1A             0               2
  M1B             1               1
  M1C             0               5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V9, binary
                 cls
clus               0  1
  USP9X MUTATED    6  2
  USP9X WILD-TYPE 96 65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP9X MUTATED      6    2
  USP9X WILD-TYPE   96   65
     clus
vv    USP9X MUTATED USP9X WILD-TYPE
  NO              6              96
  YES             2              65
[1] 2 2
[1] FALSE
D67V10, binary
                 cls
clus                0   1
  USP9X MUTATED     3  11
  USP9X WILD-TYPE  30 224
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP9X MUTATED      3   11
  USP9X WILD-TYPE   30  224
     clus
vv    USP9X MUTATED USP9X WILD-TYPE
  NO              3              30
  YES            11             224
[1] 2 2
[1] FALSE
D67V11, continuous
D67V12, binary
                 cls
clus                0   1
  USP9X MUTATED     6   8
  USP9X WILD-TYPE  97 157
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP9X MUTATED      6    8
  USP9X WILD-TYPE   97  157
        clus
vv       USP9X MUTATED USP9X WILD-TYPE
  FEMALE             6              97
  MALE               8             157
[1] 2 2
[1] FALSE
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  USP9X MUTATED       0                         0    14
  USP9X WILD-TYPE     3                         1   250
D67V13, multiclass
                           clus
vv                          USP9X MUTATED USP9X WILD-TYPE
  ASIAN                                 0               3
  BLACK OR AFRICAN AMERICAN             0               1
  WHITE                                14             250
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V14, binary
                 cls
clus                0   1
  USP9X MUTATED     0  14
  USP9X WILD-TYPE   3 247
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP9X MUTATED      0   14
  USP9X WILD-TYPE    3  247
                        clus
vv                       USP9X MUTATED USP9X WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO            14             247
[1] 2 2
[1] FALSE

Clustering(68) Variable = PTK7 MUTATION ANALYSIS
D68V1, survival
                sevent
clus2              0   1
  PTK7 MUTATED     8   7
  PTK7 WILD-TYPE 120 123
  PTK7 MUTATED PTK7 WILD-TYPE 
            15            243 
  PTK7 MUTATED PTK7 WILD-TYPE 
             7            123 
$`PTK7 MUTATED`
TCGA-D3-A2J8 TCGA-D9-A6EC TCGA-DA-A1I8 TCGA-EE-A181 TCGA-EE-A20I TCGA-EE-A29E 
        8.38        13.22        25.15         1.12         1.18        38.63 
TCGA-EE-A3AA TCGA-EE-A3AD TCGA-EE-A3JI TCGA-ER-A19M TCGA-ER-A3PL TCGA-FR-A3YN 
      124.31         3.68        33.60        28.60         1.71        18.41 
TCGA-FS-A1ZZ TCGA-FS-A4FD TCGA-FW-A3R5 
        5.23         2.27         0.99 

$`PTK7 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.47         8.52       111.09        32.42        70.16       110.79 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       28.08        22.55        45.83        81.24        10.29        85.32 
TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF 
       21.14        88.50        68.22        69.90        11.41        30.87 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO 
        7.50        36.16         6.31        92.42        56.19        64.44 
TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB 
       45.11       114.67        15.25        46.98        46.32        82.29 
TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR 
       61.38        13.32        24.00         6.31         9.34       103.59 
TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J 
       26.37         5.39        80.22        42.71        15.09        41.10 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO 
       17.72         8.84        20.48        13.94        52.01        47.87 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 
        1.55         6.97        23.11         4.01         2.89         9.90 
TCGA-D9-A6EA TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 
       11.31        48.79        35.80        51.12        10.03        39.19 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IB 
       13.68         9.99        44.52        36.69         4.93        22.36 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q 
        6.64        19.36         7.00        17.56        14.83        13.15 
TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y 
        0.20         0.00         0.00        13.22        11.57        10.55 
TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 
        6.31         8.12         1.35        12.20         5.13         4.31 
TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29B 
       36.07         4.34         5.13         9.21         7.99         9.90 
TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M 
       37.97        11.15         8.55         4.41         1.08        27.12 
TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V 
        9.50        12.03         8.09         8.84         9.99         2.43 
TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 
        8.68         8.09        11.31        49.22        23.90         9.67 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH 
        8.94        39.39        34.29        17.98        34.92        47.21 
TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN 
       30.08        19.43        16.01        35.54        28.31        33.83 
TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU 
       30.84         5.42         1.15        13.02        34.98        36.33 
TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD 
        8.84        98.27         2.70         6.18        47.51         9.53 
TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK 
       29.46        44.25         7.96        14.56        63.42       111.78 
TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR 
      111.91        56.02        25.08        26.99        21.60        29.65 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AE 
       27.16        23.05         5.56       122.73        25.84        30.15 
TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 
       13.81        15.95        12.72         3.22        22.92        21.60 
TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH 
       21.60        16.14        22.22        27.35         0.46        13.94 
TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A 
       31.40        18.61        12.95        38.40         5.72        76.41 
TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G 
       25.18         3.78         3.52        11.90        11.11       114.15 
TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q 
       34.88         4.21        13.45        42.84        34.68         9.57 
TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE 
       36.07        17.72        78.44        11.80         1.87         1.51 
TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV 
       13.08        12.62        11.74         9.04         6.58        22.49 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 
       85.74         4.90        64.47         3.45        11.01        23.80 
TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC 
       14.24        15.52         7.33         7.30         3.39        20.38 
TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ 
        8.22        19.53        11.08         7.17        30.87        12.92 
TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS 
       12.89        47.38        52.08         8.65         8.81        49.15 
TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A4F0 TCGA-FS-A4F4 
       40.64         8.68        27.39         0.82        53.85         7.36 
TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FW-A3I3 
       28.73        14.20        10.78         5.98         6.41         0.20 
TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 
        0.13         0.16         0.43         9.90         7.23        12.85 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 
       24.85        31.33        84.72        10.13        16.24        15.42 
TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS 
       12.16        14.70         5.79 

  PTK7 MUTATED PTK7 WILD-TYPE 
          0.99           0.00 
  PTK7 MUTATED PTK7 WILD-TYPE 
        124.31         122.73 
  PTK7 MUTATED PTK7 WILD-TYPE 
          8.38          15.09 
[1] "1.0 - 124.3 (8.4)"  "0.0 - 122.7 (15.1)"
[1] "hr=" "1.2"
D68V2, survival
                sevent
clus2              0   1
  PTK7 MUTATED     8   7
  PTK7 WILD-TYPE 124 124
  PTK7 MUTATED PTK7 WILD-TYPE 
            15            248 
  PTK7 MUTATED PTK7 WILD-TYPE 
             7            124 
$`PTK7 MUTATED`
TCGA-D3-A2J8 TCGA-D9-A6EC TCGA-DA-A1I8 TCGA-EE-A181 TCGA-EE-A20I TCGA-EE-A29E 
       65.49        66.25        53.92        33.73        13.55        39.62 
TCGA-EE-A3AA TCGA-EE-A3AD TCGA-EE-A3JI TCGA-ER-A19M TCGA-ER-A3PL TCGA-FR-A3YN 
      124.31         3.68       148.08        61.05        33.21        92.98 
TCGA-FS-A1ZZ TCGA-FS-A4FD TCGA-FW-A3R5 
       27.02        77.88        22.92 

$`PTK7 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.57        16.67       112.04       112.57        71.80       133.25 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       28.08        31.59        90.90        95.74        43.43       103.10 
TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF 
       23.77       115.53       168.00        69.90        11.87        48.76 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO 
      113.52        42.08        12.10       171.58        56.19        66.08 
TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB 
       45.11       130.72        58.06        46.98        46.32       166.52 
TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR 
       86.93        60.23        24.53        13.87         9.34       103.59 
TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J 
       39.75        21.47       161.85        43.69        40.14       131.90 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO 
       18.38        10.03        51.68        15.06       135.75       137.92 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW 
      166.19         7.43       125.19       151.53        54.67         3.65 
TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-DA-A1HV 
        6.41        11.34         3.25         9.90        25.18        48.89 
TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 
       36.03       117.21        20.38       194.83       176.55        35.93 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
      107.34        61.18        65.92        23.44        68.09        28.60 
TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG 
       10.49       215.44        15.68        13.87        10.16        45.11 
TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z 
       35.01         3.55        52.01        29.82        27.22         8.65 
TCGA-EE-A180 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B 
       94.98        14.70        26.89        68.15         4.96       109.64 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C 
      151.27        78.87       168.26        63.35        80.61        47.84 
TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N 
       13.97        72.07        32.19         2.60        44.35        18.61 
TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W 
       56.42        37.35        14.47        55.92        25.87       171.55 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 
       17.92        46.82       102.90        24.43        39.29        58.75 
TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI 
       47.54        67.43       314.56       135.95       208.04        48.72 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO 
       89.33        54.74        79.66        75.48        90.97       101.95 
TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 
       13.91        14.30        55.59        44.88        94.82        21.67 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME 
      129.27        28.83        19.76        61.51        47.28       103.27 
TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML 
      103.20        16.96       204.66        96.23       144.76       203.05 
TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS 
      167.90        47.54       248.65        43.23       103.56       136.47 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AE TCGA-EE-A3AF 
       41.59        53.26       122.73        25.84        54.51        13.81 
TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 
       23.47       138.81       172.18       127.20        36.95        64.08 
TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A193 
       34.32        53.19        27.35        33.40       101.79        31.40 
TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B 
       35.44        13.94        50.76         9.17        77.75        98.40 
TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H 
       48.89        12.59        13.02        26.37       268.93       152.35 
TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S 
        6.44       131.51        44.05       162.08        50.89        37.25 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF 
      148.18        79.99        43.82        23.34        20.15        16.37 
TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-FR-A44A 
       31.27        32.05       247.04        80.32        46.98       174.21 
TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
        4.90       216.92        48.59       228.59       202.65        20.91 
TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD 
       28.08         7.79        27.72        48.85       357.37        53.52 
TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK 
       40.27        15.45         9.70        32.75        47.38        23.93 
TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT 
      101.26        74.73       133.55        11.41       148.80        53.16 
TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 
       26.56        49.48        27.09        77.82        66.67        28.73 
TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FW-A3I3 TCGA-FW-A3TU 
      174.84        12.43        26.73        49.45         0.20        47.54 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 
        0.16         2.40         9.90         7.23        14.04       120.46 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
      117.93        84.72        10.13        64.44        62.79        32.48 
TCGA-GN-A26D TCGA-QB-A6FS 
       39.58         6.67 

  PTK7 MUTATED PTK7 WILD-TYPE 
          3.68           0.16 
  PTK7 MUTATED PTK7 WILD-TYPE 
        148.08         357.37 
  PTK7 MUTATED PTK7 WILD-TYPE 
        53.920         48.215 
[1] "3.7 - 148.1 (53.9)" "0.2 - 357.4 (48.2)"
[1] "hr=" "1.1"
D68V3, continuous
                vv
clus             DISTANT METASTASIS PRIMARY TUMOR
  PTK7 MUTATED                    1             1
  PTK7 WILD-TYPE                 34             3
                vv
clus             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  PTK7 MUTATED                                           4                  10
  PTK7 WILD-TYPE                                        54                 160
D68V4, multiclass
                                           clus
vv                                          PTK7 MUTATED PTK7 WILD-TYPE
  DISTANT METASTASIS                                   1             34
  PRIMARY TUMOR                                        1              3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE            4             54
  REGIONAL LYMPH NODE                                 10            160
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  PTK7 MUTATED             0       1       1        0        3        1
  PTK7 WILD-TYPE          10       5      21       10       21       16
                vv
clus             STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  PTK7 MUTATED           0         1         0         3          1          1
  PTK7 WILD-TYPE        10        13         9        28         12         21
                vv
clus             STAGE IIIC STAGE IV
  PTK7 MUTATED            2        2
  PTK7 WILD-TYPE         42       10
D68V5, multiclass
             clus
vv            PTK7 MUTATED PTK7 WILD-TYPE
  I OR II NOS            0             10
  STAGE 0                1              5
  STAGE I                1             21
  STAGE IA               0             10
  STAGE IB               3             21
  STAGE II               1             16
  STAGE IIA              0             10
  STAGE IIB              1             13
  STAGE IIC              0              9
  STAGE III              3             28
  STAGE IIIA             1             12
  STAGE IIIB             1             21
  STAGE IIIC             2             42
  STAGE IV               2             10
[1] 14  2
[1] 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
  PTK7 MUTATED       2  5  5  1
  PTK7 WILD-TYPE    49 53 48 54
D68V6, multiclass
       clus
vv      PTK7 MUTATED PTK7 WILD-TYPE
  T0+T1            2             49
  T2               5             53
  T3               5             48
  T4               1             54
[1] 4 2
[1] TRUE
[1] "dimension 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
  PTK7 MUTATED     9   4   1   2
  PTK7 WILD-TYPE 129  44  31  31
D68V7, multiclass
    clus
vv   PTK7 MUTATED PTK7 WILD-TYPE
  N0            9            129
  N1            4             44
  N2            1             31
  N3            2             31
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              M0  M1 M1A M1B M1C
  PTK7 MUTATED    14   0   1   0   1
  PTK7 WILD-TYPE 226   4   1   2   4
D68V8, multiclass
     clus
vv    PTK7 MUTATED PTK7 WILD-TYPE
  M0            14            226
  M1             0              4
  M1A            1              1
  M1B            0              2
  M1C            1              4
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V9, binary
                cls
clus              0  1
  PTK7 MUTATED    6  4
  PTK7 WILD-TYPE 96 63
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTK7 MUTATED      6    4
  PTK7 WILD-TYPE   96   63
     clus
vv    PTK7 MUTATED PTK7 WILD-TYPE
  NO             6             96
  YES            4             63
[1] 2 2
[1] FALSE
D68V10, binary
                cls
clus               0   1
  PTK7 MUTATED     2  14
  PTK7 WILD-TYPE  31 221
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTK7 MUTATED      2   14
  PTK7 WILD-TYPE   31  221
     clus
vv    PTK7 MUTATED PTK7 WILD-TYPE
  NO             2             31
  YES           14            221
[1] 2 2
[1] FALSE
D68V11, continuous
D68V12, binary
                cls
clus               0   1
  PTK7 MUTATED     4  12
  PTK7 WILD-TYPE  99 153
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTK7 MUTATED      4   12
  PTK7 WILD-TYPE   99  153
        clus
vv       PTK7 MUTATED PTK7 WILD-TYPE
  FEMALE            4             99
  MALE             12            153
[1] 2 2
[1] FALSE
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PTK7 MUTATED       0                         0    16
  PTK7 WILD-TYPE     3                         1   248
D68V13, multiclass
                           clus
vv                          PTK7 MUTATED PTK7 WILD-TYPE
  ASIAN                                0              3
  BLACK OR AFRICAN AMERICAN            0              1
  WHITE                               16            248
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V14, binary
                cls
clus               0   1
  PTK7 MUTATED     1  15
  PTK7 WILD-TYPE   2 246
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTK7 MUTATED      1   15
  PTK7 WILD-TYPE    2  246
                        clus
vv                       PTK7 MUTATED PTK7 WILD-TYPE
  HISPANIC OR LATINO                1              2
  NOT HISPANIC OR LATINO           15            246
[1] 2 2
[1] FALSE

Clustering(69) Variable = SLC14A1 MUTATION ANALYSIS
D69V1, survival
                   sevent
clus2                 0   1
  SLC14A1 MUTATED     8   9
  SLC14A1 WILD-TYPE 120 121
  SLC14A1 MUTATED SLC14A1 WILD-TYPE 
               17               241 
  SLC14A1 MUTATED SLC14A1 WILD-TYPE 
                9               121 
$`SLC14A1 MUTATED`
TCGA-D3-A1Q6 TCGA-D3-A51T TCGA-D3-A5GO TCGA-DA-A3F5 TCGA-EE-A17X TCGA-EE-A20C 
       70.16        13.94        47.87        17.56        11.57         4.34 
TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29L TCGA-EE-A2A2 
        9.21         7.99        11.15        38.63         1.08        23.90 
TCGA-EE-A2GR TCGA-EE-A2M5 TCGA-EE-A3AC TCGA-ER-A19P TCGA-FW-A3R5 
        1.15         8.84        25.84        34.68         0.99 

$`SLC14A1 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       16.47         8.52       111.09        32.42       110.79        28.08 
TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 
       22.55        45.83        81.24        10.29        85.32         8.38 
TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF 
       21.14        88.50        68.22        69.90        11.41        30.87 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO 
        7.50        36.16         6.31        92.42        56.19        64.44 
TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB 
       45.11       114.67        15.25        46.98        46.32        82.29 
TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR 
       61.38        13.32        24.00         6.31         9.34       103.59 
TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J 
       26.37         5.39        80.22        42.71        15.09        41.10 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS 
       17.72         8.84        20.48        52.01         1.55         6.97 
TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC 
       23.11         4.01         2.89         9.90        11.31        13.22 
TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 
       48.79        35.80        51.12        10.03        39.19        13.68 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB 
        9.99        44.52        36.69        25.15         4.93        22.36 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R 
        6.64        19.36         7.00        14.83        13.15         0.20 
TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 
        0.00         0.00        13.22        10.55         6.31         8.12 
TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B 
        1.12         1.35        12.20         5.13         4.31        36.07 
TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29G TCGA-EE-A29H 
        5.13         1.18         9.90        37.97         8.55         4.41 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S 
       27.12         9.50        12.03         8.09         8.84         9.99 
TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A5 
        2.43         8.68         8.09        11.31        49.22         9.67 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH 
        8.94        39.39        34.29        17.98        34.92        47.21 
TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN 
       30.08        19.43        16.01        35.54        28.31        33.83 
TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M6 
       30.84         5.42        13.02        34.98        36.33        98.27 
TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG 
        2.70         6.18        47.51         9.53        29.46        44.25 
TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM 
        7.96        14.56        63.42       111.78       111.91        56.02 
TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT 
       25.08        26.99        21.60        29.65        27.16        23.05 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF 
        5.56       124.31       122.73         3.68        30.15        13.81 
TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 
       15.95        12.72         3.22        22.92        21.60        21.60 
TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI 
       16.14        22.22        27.35         0.46        13.94        33.60 
TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A 
       31.40        18.61        12.95        38.40         5.72        76.41 
TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G 
       25.18         3.78         3.52        11.90        11.11       114.15 
TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19Q 
       34.88         4.21        13.45        28.60        42.84         9.57 
TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE 
       36.07        17.72        78.44        11.80         1.87         1.51 
TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV 
       13.08        12.62        11.74         9.04         6.58        22.49 
TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX 
        1.71        18.41        85.74         4.90        64.47         3.45 
TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA 
       11.01        23.80        14.24        15.52         7.33         7.30 
TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG 
        3.39        20.38         8.22        19.53        11.08         7.17 
TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ 
       30.87        12.92        12.89        47.38        52.08         8.65 
TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY 
        8.81        49.15        40.64         8.68        27.39         0.82 
TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 
        5.23        53.85         7.36        28.73        14.20        10.78 
TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV 
        5.98         6.41         2.27         0.20         0.13         0.16 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 
        0.43         9.90         7.23        12.85        24.85        31.33 
TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D 
       84.72        10.13        16.24        15.42        12.16        14.70 
TCGA-QB-A6FS 
        5.79 

  SLC14A1 MUTATED SLC14A1 WILD-TYPE 
             0.99              0.00 
  SLC14A1 MUTATED SLC14A1 WILD-TYPE 
            70.16            124.31 
  SLC14A1 MUTATED SLC14A1 WILD-TYPE 
            11.57             15.09 
[1] "1.0 - 70.2 (11.6)"  "0.0 - 124.3 (15.1)"
[1] "hr=" "1.2"
D69V2, survival
                   sevent
clus2                 0   1
  SLC14A1 MUTATED     8   9
  SLC14A1 WILD-TYPE 124 122
  SLC14A1 MUTATED SLC14A1 WILD-TYPE 
               17               246 
  SLC14A1 MUTATED SLC14A1 WILD-TYPE 
                9               122 
$`SLC14A1 MUTATED`
TCGA-D3-A1Q6 TCGA-D3-A51T TCGA-D3-A5GO TCGA-DA-A3F5 TCGA-EE-A17X TCGA-EE-A20C 
       71.80        15.06       137.92       215.44        29.82       151.27 
TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29L TCGA-EE-A2A2 
      168.26        63.35        13.97        39.62         2.60        24.43 
TCGA-EE-A2GR TCGA-EE-A2M5 TCGA-EE-A3AC TCGA-ER-A19P TCGA-FW-A3R5 
       14.30        21.67        25.84       162.08        22.92 

$`SLC14A1 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       16.57        16.67       112.04       112.57       133.25        28.08 
TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 
       31.59        90.90        95.74        43.43       103.10        65.49 
TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF 
       23.77       115.53       168.00        69.90        11.87        48.76 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO 
      113.52        42.08        12.10       171.58        56.19        66.08 
TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB 
       45.11       130.72        58.06        46.98        46.32       166.52 
TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR 
       86.93        60.23        24.53        13.87         9.34       103.59 
TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J 
       39.75        21.47       161.85        43.69        40.14       131.90 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS 
       18.38        10.03        51.68       135.75       166.19         7.43 
TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 
      125.19       151.53        54.67         3.65         6.41        11.34 
TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1HW 
        3.25         9.90        25.18        66.25        48.89        36.03 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 
      117.21        20.38       194.83       176.55        35.93       107.34 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
       61.18        53.92        65.92        23.44        68.09        28.60 
TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH 
       10.49        15.68        13.87        10.16        45.11        35.01 
TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 
        3.55        52.01        27.22         8.65        94.98        33.73 
TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20F 
       14.70        26.89        68.15         4.96       109.64        78.87 
TCGA-EE-A20I TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M 
       13.55        80.61        47.84        72.07        32.19        44.35 
TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V 
       18.61        56.42        37.35        14.47        55.92        25.87 
TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A5 TCGA-EE-A2A6 
      171.55        17.92        46.82       102.90        39.29        58.75 
TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI 
       47.54        67.43       314.56       135.95       208.04        48.72 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO 
       89.33        54.74        79.66        75.48        90.97       101.95 
TCGA-EE-A2GP TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 
       13.91        55.59        44.88        94.82       129.27        28.83 
TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH 
       19.76        61.51        47.28       103.27       103.20        16.96 
TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN 
      204.66        96.23       144.76       203.05       167.90        47.54 
TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU 
      248.65        43.23       103.56       136.47        41.59        53.26 
TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG 
      124.31       122.73         3.68        54.51        13.81        23.47 
TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 
      138.81       172.18       127.20        36.95        64.08        34.32 
TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 
       53.19        27.35        33.40       101.79       148.08        31.40 
TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B 
       35.44        13.94        50.76         9.17        77.75        98.40 
TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H 
       48.89        12.59        13.02        26.37       268.93       152.35 
TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19Q TCGA-ER-A19S 
        6.44       131.51        61.05        44.05        50.89        37.25 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF 
      148.18        79.99        43.82        23.34        20.15        16.37 
TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL 
       31.27        32.05       247.04        80.32        46.98        33.21 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY 
       92.98       174.21         4.90       216.92        48.59       228.59 
TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB 
      202.65        20.91        28.08         7.79        27.72        48.85 
TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH 
      357.37        53.52        40.27        15.45         9.70        32.75 
TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR 
       47.38        23.93       101.26        74.73       133.55        11.41 
TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ 
      148.80        53.16        26.56        49.48        27.09        27.02 
TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB 
       77.82        66.67        28.73       174.84        12.43        26.73 
TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY 
       49.45        77.88         0.20        47.54         0.16         2.40 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        9.90         7.23        14.04       120.46       117.93        84.72 
TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS 
       10.13        64.44        62.79        32.48        39.58         6.67 

  SLC14A1 MUTATED SLC14A1 WILD-TYPE 
             2.60              0.16 
  SLC14A1 MUTATED SLC14A1 WILD-TYPE 
           215.44            357.37 
  SLC14A1 MUTATED SLC14A1 WILD-TYPE 
            29.82             48.74 
[1] "2.6 - 215.4 (29.8)" "0.2 - 357.4 (48.7)"
[1] "hr=" "1.1"
D69V3, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  SLC14A1 MUTATED                    4             0
  SLC14A1 WILD-TYPE                 31             4
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  SLC14A1 MUTATED                                           2
  SLC14A1 WILD-TYPE                                        56
                   vv
clus                REGIONAL LYMPH NODE
  SLC14A1 MUTATED                    11
  SLC14A1 WILD-TYPE                 159
D69V4, multiclass
                                           clus
vv                                          SLC14A1 MUTATED SLC14A1 WILD-TYPE
  DISTANT METASTASIS                                      4                31
  PRIMARY TUMOR                                           0                 4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE               2                56
  REGIONAL LYMPH NODE                                    11               159
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  SLC14A1 MUTATED             0       1       2        1        0        2
  SLC14A1 WILD-TYPE          10       5      20        9       24       15
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  SLC14A1 MUTATED           0         0         0         3          1
  SLC14A1 WILD-TYPE        10        14         9        28         12
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  SLC14A1 MUTATED            1          5        0
  SLC14A1 WILD-TYPE         21         39       12
D69V5, multiclass
             clus
vv            SLC14A1 MUTATED SLC14A1 WILD-TYPE
  I OR II NOS               0                10
  STAGE 0                   1                 5
  STAGE I                   2                20
  STAGE IA                  1                 9
  STAGE IB                  0                24
  STAGE II                  2                15
  STAGE IIA                 0                10
  STAGE IIB                 0                14
  STAGE IIC                 0                 9
  STAGE III                 3                28
  STAGE IIIA                1                12
  STAGE IIIB                1                21
  STAGE IIIC                5                39
  STAGE IV                  0                12
[1] 14  2
[1] 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
  SLC14A1 MUTATED       3  2  3  6
  SLC14A1 WILD-TYPE    48 56 50 49
D69V6, multiclass
       clus
vv      SLC14A1 MUTATED SLC14A1 WILD-TYPE
  T0+T1               3                48
  T2                  2                56
  T3                  3                50
  T4                  6                49
[1] 4 2
[1] TRUE
[1] "dimension 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
  SLC14A1 MUTATED     7   6   2   2
  SLC14A1 WILD-TYPE 131  42  30  31
D69V7, multiclass
    clus
vv   SLC14A1 MUTATED SLC14A1 WILD-TYPE
  N0               7               131
  N1               6                42
  N2               2                30
  N3               2                31
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1 M1A M1B M1C
  SLC14A1 MUTATED    17   0   0   0   0
  SLC14A1 WILD-TYPE 223   4   2   2   5
D69V8, multiclass
     clus
vv    SLC14A1 MUTATED SLC14A1 WILD-TYPE
  M0               17               223
  M1                0                 4
  M1A               0                 2
  M1B               0                 2
  M1C               0                 5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V9, binary
                   cls
clus                 0  1
  SLC14A1 MUTATED    4  4
  SLC14A1 WILD-TYPE 98 63
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC14A1 MUTATED      4    4
  SLC14A1 WILD-TYPE   98   63
     clus
vv    SLC14A1 MUTATED SLC14A1 WILD-TYPE
  NO                4                98
  YES               4                63
[1] 2 2
[1] FALSE
D69V10, binary
                   cls
clus                  0   1
  SLC14A1 MUTATED     1  16
  SLC14A1 WILD-TYPE  32 219
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC14A1 MUTATED      1   16
  SLC14A1 WILD-TYPE   32  219
     clus
vv    SLC14A1 MUTATED SLC14A1 WILD-TYPE
  NO                1                32
  YES              16               219
[1] 2 2
[1] FALSE
D69V11, continuous
D69V12, binary
                   cls
clus                  0   1
  SLC14A1 MUTATED     2  15
  SLC14A1 WILD-TYPE 101 150
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC14A1 MUTATED      2   15
  SLC14A1 WILD-TYPE  101  150
        clus
vv       SLC14A1 MUTATED SLC14A1 WILD-TYPE
  FEMALE               2               101
  MALE                15               150
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SLC14A1 MUTATED       0                         0    17
  SLC14A1 WILD-TYPE     3                         1   247
D69V13, multiclass
                           clus
vv                          SLC14A1 MUTATED SLC14A1 WILD-TYPE
  ASIAN                                   0                 3
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  17               247
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V14, binary
                   cls
clus                  0   1
  SLC14A1 MUTATED     0  15
  SLC14A1 WILD-TYPE   3 246
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC14A1 MUTATED      0   15
  SLC14A1 WILD-TYPE    3  246
                        clus
vv                       SLC14A1 MUTATED SLC14A1 WILD-TYPE
  HISPANIC OR LATINO                   0                 3
  NOT HISPANIC OR LATINO              15               246
[1] 2 2
[1] FALSE

Clustering(70) Variable = PROX2 MUTATION ANALYSIS
D70V1, survival
                 sevent
clus2               0   1
  PROX2 MUTATED     7   5
  PROX2 WILD-TYPE 121 125
  PROX2 MUTATED PROX2 WILD-TYPE 
             12             246 
  PROX2 MUTATED PROX2 WILD-TYPE 
              5             125 
$`PROX2 MUTATED`
TCGA-D3-A51R TCGA-DA-A1IC TCGA-EE-A29E TCGA-EE-A29M TCGA-EE-A2MT TCGA-EE-A3AB 
       20.48         6.64        38.63        27.12        23.05       122.73 
TCGA-EE-A3AG TCGA-EE-A3J5 TCGA-ER-A19N TCGA-FS-A1Z3 TCGA-FS-A4F5 TCGA-FW-A3R5 
       15.95        21.60        42.84        14.24        28.73         0.99 

$`PROX2 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.47         8.52       111.09        32.42        70.16       110.79 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       28.08        22.55        45.83        81.24        10.29        85.32 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
        8.38        21.14        88.50        68.22        69.90        11.41 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       30.87         7.50        36.16         6.31        92.42        56.19 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 
       64.44        45.11       114.67        15.25        46.98        46.32 
TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO 
       82.29        61.38        13.32        24.00         6.31         9.34 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H 
      103.59        26.37         5.39        80.22        42.71        15.09 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO 
       41.10        17.72         8.84        13.94        52.01        47.87 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 
        1.55         6.97        23.11         4.01         2.89         9.90 
TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 
       11.31        13.22        48.79        35.80        51.12        10.03 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 
       39.19        13.68         9.99        44.52        36.69        25.15 
TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 
        4.93        22.36        19.36         7.00        17.56        14.83 
TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EE-A17X 
       13.15         0.20         0.00         0.00        13.22        11.57 
TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 
       10.55         6.31         8.12         1.12         1.35        12.20 
TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H 
        5.13         4.31        36.07         4.34         5.13         9.21 
TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29G 
        1.18         7.99         9.90        37.97        11.15         8.55 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R 
        4.41         1.08         9.50        12.03         8.09         8.84 
TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 
        9.99         2.43         8.68         8.09        11.31        49.22 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD 
       23.90         9.67         8.94        39.39        34.29        17.98 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
       34.92        47.21        30.08        19.43        16.01        35.54 
TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS 
       28.31        33.83        30.84         5.42         1.15        13.02 
TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 
       34.98        36.33         8.84        98.27         2.70         6.18 
TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI 
       47.51         9.53        29.46        44.25         7.96        14.56 
TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP 
       63.42       111.78       111.91        56.02        25.08        26.99 
TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AC 
       21.60        29.65        27.16         5.56       124.31        25.84 
TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 
        3.68        30.15        13.81        12.72         3.22        22.92 
TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH 
       21.60        16.14        22.22        27.35         0.46        13.94 
TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 
       33.60        31.40        18.61        12.95        38.40         5.72 
TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F 
       76.41        25.18         3.78         3.52        11.90        11.11 
TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19P 
      114.15        34.88         4.21        13.45        28.60        34.68 
TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
        9.57        36.07        17.72        78.44        11.80         1.87 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET 
        1.51        13.08        12.62        11.74         9.04         6.58 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW 
       22.49         1.71        18.41        85.74         4.90        64.47 
TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA 
        3.45        11.01        23.80        15.52         7.33         7.30 
TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG 
        3.39        20.38         8.22        19.53        11.08         7.17 
TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ 
       30.87        12.92        12.89        47.38        52.08         8.65 
TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY 
        8.81        49.15        40.64         8.68        27.39         0.82 
TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB 
        5.23        53.85         7.36        14.20        10.78         5.98 
TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY 
        6.41         2.27         0.20         0.13         0.16         0.43 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        9.90         7.23        12.85        24.85        31.33        84.72 
TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS 
       10.13        16.24        15.42        12.16        14.70         5.79 

  PROX2 MUTATED PROX2 WILD-TYPE 
           0.99            0.00 
  PROX2 MUTATED PROX2 WILD-TYPE 
         122.73          124.31 
  PROX2 MUTATED PROX2 WILD-TYPE 
         22.325          14.070 
[1] "1.0 - 122.7 (22.3)" "0.0 - 124.3 (14.1)"
[1] "hr=" "1.5"
D70V2, survival
                 sevent
clus2               0   1
  PROX2 MUTATED     7   5
  PROX2 WILD-TYPE 125 126
  PROX2 MUTATED PROX2 WILD-TYPE 
             12             251 
  PROX2 MUTATED PROX2 WILD-TYPE 
              5             126 
$`PROX2 MUTATED`
TCGA-D3-A51R TCGA-DA-A1IC TCGA-EE-A29E TCGA-EE-A29M TCGA-EE-A2MT TCGA-EE-A3AB 
       51.68        68.09        39.62        44.35        41.59       122.73 
TCGA-EE-A3AG TCGA-EE-A3J5 TCGA-ER-A19N TCGA-FS-A1Z3 TCGA-FS-A4F5 TCGA-FW-A3R5 
       23.47        36.95        44.05        20.91        28.73        22.92 

$`PROX2 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.57        16.67       112.04       112.57        71.80       133.25 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       28.08        31.59        90.90        95.74        43.43       103.10 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
       65.49        23.77       115.53       168.00        69.90        11.87 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       48.76       113.52        42.08        12.10       171.58        56.19 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 
       66.08        45.11       130.72        58.06        46.98        46.32 
TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO 
      166.52        86.93        60.23        24.53        13.87         9.34 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H 
      103.59        39.75        21.47       161.85        43.69        40.14 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO 
      131.90        18.38        10.03        15.06       135.75       137.92 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW 
      166.19         7.43       125.19       151.53        54.67         3.65 
TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC 
        6.41        11.34         3.25         9.90        25.18        66.25 
TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 
       48.89        36.03       117.21        20.38       194.83       176.55 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB 
       35.93       107.34        61.18        53.92        65.92        23.44 
TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R 
       28.60        10.49       215.44        15.68        13.87        10.16 
TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y 
       45.11        35.01         3.55        52.01        29.82        27.22 
TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 
        8.65        94.98        33.73        14.70        26.89        68.15 
TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I 
        4.96       109.64       151.27        78.87       168.26        13.55 
TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29H 
       63.35        80.61        47.84        13.97        72.07        32.19 
TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S 
        2.60        18.61        56.42        37.35        14.47        55.92 
TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 
       25.87       171.55        17.92        46.82       102.90        24.43 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE 
       39.29        58.75        47.54        67.43       314.56       135.95 
TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM 
      208.04        48.72        89.33        54.74        79.66        75.48 
TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT 
       90.97       101.95        13.91        14.30        55.59        44.88 
TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC 
       94.82        21.67       129.27        28.83        19.76        61.51 
TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ 
       47.28       103.27       103.20        16.96       204.66        96.23 
TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ 
      144.76       203.05       167.90        47.54       248.65        43.23 
TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3AD 
      103.56       136.47        53.26       124.31        25.84         3.68 
TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 
       54.51        13.81       138.81       172.18       127.20        64.08 
TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI 
       34.32        53.19        27.35        33.40       101.79       148.08 
TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A 
       31.40        35.44        13.94        50.76         9.17        77.75 
TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G 
       98.40        48.89        12.59        13.02        26.37       268.93 
TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19P TCGA-ER-A19Q 
      152.35         6.44       131.51        61.05       162.08        50.89 
TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE 
       37.25       148.18        79.99        43.82        23.34        20.15 
TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV 
       16.37        31.27        32.05       247.04        80.32        46.98 
TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX 
       33.21        92.98       174.21         4.90       216.92        48.59 
TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB 
      228.59       202.65        28.08         7.79        27.72        48.85 
TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH 
      357.37        53.52        40.27        15.45         9.70        32.75 
TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR 
       47.38        23.93       101.26        74.73       133.55        11.41 
TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ 
      148.80        53.16        26.56        49.48        27.09        27.02 
TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC 
       77.82        66.67       174.84        12.43        26.73        49.45 
TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
       77.88         0.20        47.54         0.16         2.40         9.90 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 
        7.23        14.04       120.46       117.93        84.72        10.13 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS 
       64.44        62.79        32.48        39.58         6.67 

  PROX2 MUTATED PROX2 WILD-TYPE 
          20.91            0.16 
  PROX2 MUTATED PROX2 WILD-TYPE 
         122.73          357.37 
  PROX2 MUTATED PROX2 WILD-TYPE 
         40.605          48.850 
[1] "20.9 - 122.7 (40.6)" "0.2 - 357.4 (48.9)" 
[1] "hr=" "1.2"
D70V3, continuous
                 vv
clus              DISTANT METASTASIS PRIMARY TUMOR
  PROX2 MUTATED                    2             0
  PROX2 WILD-TYPE                 33             4
                 vv
clus              REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  PROX2 MUTATED                                           4                   7
  PROX2 WILD-TYPE                                        54                 163
D70V4, multiclass
                                           clus
vv                                          PROX2 MUTATED PROX2 WILD-TYPE
  DISTANT METASTASIS                                    2              33
  PRIMARY TUMOR                                         0               4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE             4              54
  REGIONAL LYMPH NODE                                   7             163
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  PROX2 MUTATED             1       0       0        0        3        0
  PROX2 WILD-TYPE           9       6      22       10       21       17
                 vv
clus              STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  PROX2 MUTATED           1         0         0         4          0          2
  PROX2 WILD-TYPE         9        14         9        27         13         20
                 vv
clus              STAGE IIIC STAGE IV
  PROX2 MUTATED            0        1
  PROX2 WILD-TYPE         44       11
D70V5, multiclass
             clus
vv            PROX2 MUTATED PROX2 WILD-TYPE
  I OR II NOS             1               9
  STAGE 0                 0               6
  STAGE I                 0              22
  STAGE IA                0              10
  STAGE IB                3              21
  STAGE II                0              17
  STAGE IIA               1               9
  STAGE IIB               0              14
  STAGE IIC               0               9
  STAGE III               4              27
  STAGE IIIA              0              13
  STAGE IIIB              2              20
  STAGE IIIC              0              44
  STAGE IV                1              11
[1] 14  2
[1] 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
  PROX2 MUTATED       2  4  3  1
  PROX2 WILD-TYPE    49 54 50 54
D70V6, multiclass
       clus
vv      PROX2 MUTATED PROX2 WILD-TYPE
  T0+T1             2              49
  T2                4              54
  T3                3              50
  T4                1              54
[1] 4 2
[1] TRUE
[1] "dimension 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
  PROX2 MUTATED     6   2   4   0
  PROX2 WILD-TYPE 132  46  28  33
D70V7, multiclass
    clus
vv   PROX2 MUTATED PROX2 WILD-TYPE
  N0             6             132
  N1             2              46
  N2             4              28
  N3             0              33
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               M0  M1 M1A M1B M1C
  PROX2 MUTATED    11   1   0   0   0
  PROX2 WILD-TYPE 229   3   2   2   5
D70V8, multiclass
     clus
vv    PROX2 MUTATED PROX2 WILD-TYPE
  M0             11             229
  M1              1               3
  M1A             0               2
  M1B             0               2
  M1C             0               5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V9, binary
                 cls
clus               0  1
  PROX2 MUTATED    7  0
  PROX2 WILD-TYPE 95 67
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PROX2 MUTATED      7    0
  PROX2 WILD-TYPE   95   67
     clus
vv    PROX2 MUTATED PROX2 WILD-TYPE
  NO              7              95
  YES             0              67
[1] 2 2
[1] FALSE
D70V10, binary
                 cls
clus                0   1
  PROX2 MUTATED     4   9
  PROX2 WILD-TYPE  29 226
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PROX2 MUTATED      4    9
  PROX2 WILD-TYPE   29  226
     clus
vv    PROX2 MUTATED PROX2 WILD-TYPE
  NO              4              29
  YES             9             226
[1] 2 2
[1] FALSE
D70V11, continuous
D70V12, binary
                 cls
clus                0   1
  PROX2 MUTATED     4   9
  PROX2 WILD-TYPE  99 156
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PROX2 MUTATED      4    9
  PROX2 WILD-TYPE   99  156
        clus
vv       PROX2 MUTATED PROX2 WILD-TYPE
  FEMALE             4              99
  MALE               9             156
[1] 2 2
[1] FALSE
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PROX2 MUTATED       0                         0    13
  PROX2 WILD-TYPE     3                         1   251
D70V13, multiclass
                           clus
vv                          PROX2 MUTATED PROX2 WILD-TYPE
  ASIAN                                 0               3
  BLACK OR AFRICAN AMERICAN             0               1
  WHITE                                13             251
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V14, binary
                 cls
clus                0   1
  PROX2 MUTATED     0  13
  PROX2 WILD-TYPE   3 248
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PROX2 MUTATED      0   13
  PROX2 WILD-TYPE    3  248
                        clus
vv                       PROX2 MUTATED PROX2 WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO            13             248
[1] 2 2
[1] FALSE

Clustering(71) Variable = DNMBP MUTATION ANALYSIS
D71V1, survival
                 sevent
clus2               0   1
  DNMBP MUTATED    10   9
  DNMBP WILD-TYPE 118 121
  DNMBP MUTATED DNMBP WILD-TYPE 
             19             239 
  DNMBP MUTATED DNMBP WILD-TYPE 
              9             121 
$`DNMBP MUTATED`
TCGA-D3-A2JD TCGA-D3-A3MR TCGA-D3-A5GN TCGA-EB-A5SG TCGA-EE-A29D TCGA-EE-A29E 
       11.41       103.59        52.01         0.00        11.15        38.63 
TCGA-EE-A29Q TCGA-EE-A2A6 TCGA-EE-A2GR TCGA-EE-A2MJ TCGA-EE-A2MR TCGA-EE-A2MS 
        8.09         8.94         1.15        63.42        29.65        27.16 
TCGA-EE-A3AC TCGA-EE-A3AG TCGA-EE-A3JA TCGA-ER-A193 TCGA-FS-A1ZP TCGA-FW-A3R5 
       25.84        15.95        22.22        31.40        52.08         0.99 
TCGA-GN-A267 
       16.24 

$`DNMBP WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.47         8.52       111.09        32.42        70.16       110.79 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       28.08        22.55        45.83        81.24        10.29        85.32 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JF 
        8.38        21.14        88.50        68.22        69.90        30.87 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO 
        7.50        36.16         6.31        92.42        56.19        64.44 
TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB 
       45.11       114.67        15.25        46.98        46.32        82.29 
TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MU 
       61.38        13.32        24.00         6.31         9.34        26.37 
TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K 
        5.39        80.22        42.71        15.09        41.10        17.72 
TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS 
        8.84        20.48        13.94        47.87         1.55         6.97 
TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC 
       23.11         4.01         2.89         9.90        11.31        13.22 
TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 
       48.79        35.80        51.12        10.03        39.19        13.68 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB 
        9.99        44.52        36.69        25.15         4.93        22.36 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q 
        6.64        19.36         7.00        17.56        14.83        13.15 
TCGA-EB-A44R TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z 
        0.20         0.00        13.22        11.57        10.55         6.31 
TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 
        8.12         1.12         1.35        12.20         5.13         4.31 
TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A 
       36.07         4.34         5.13         9.21         1.18         7.99 
TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M 
        9.90        37.97         8.55         4.41         1.08        27.12 
TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W 
        9.50        12.03         8.84         9.99         2.43         8.68 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2GB 
        8.09        11.31        49.22        23.90         9.67        39.39 
TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ 
       34.29        17.98        34.92        47.21        30.08        19.43 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP 
       16.01        35.54        28.31        33.83        30.84         5.42 
TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 
       13.02        34.98        36.33         8.84        98.27         2.70 
TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH 
        6.18        47.51         9.53        29.46        44.25         7.96 
TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP 
       14.56       111.78       111.91        56.02        25.08        26.99 
TCGA-EE-A2MQ TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AD 
       21.60        23.05         5.56       124.31       122.73         3.68 
TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 
       30.15        13.81        12.72         3.22        22.92        21.60 
TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI 
       21.60        16.14        27.35         0.46        13.94        33.60 
TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B 
       18.61        12.95        38.40         5.72        76.41        25.18 
TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H 
        3.78         3.52        11.90        11.11       114.15        34.88 
TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q 
        4.21        13.45        28.60        42.84        34.68         9.57 
TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE 
       36.07        17.72        78.44        11.80         1.87         1.51 
TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV 
       13.08        12.62        11.74         9.04         6.58        22.49 
TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX 
        1.71        18.41        85.74         4.90        64.47         3.45 
TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA 
       11.01        23.80        14.24        15.52         7.33         7.30 
TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG 
        3.39        20.38         8.22        19.53        11.08         7.17 
TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZR 
       30.87        12.92        12.89        47.38         8.65         8.81 
TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ 
       49.15        40.64         8.68        27.39         0.82         5.23 
TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB 
       53.85         7.36        28.73        14.20        10.78         5.98 
TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY 
        6.41         2.27         0.20         0.13         0.16         0.43 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        9.90         7.23        12.85        24.85        31.33        84.72 
TCGA-GN-A266 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS 
       10.13        15.42        12.16        14.70         5.79 

  DNMBP MUTATED DNMBP WILD-TYPE 
              0               0 
  DNMBP MUTATED DNMBP WILD-TYPE 
         103.59          124.31 
  DNMBP MUTATED DNMBP WILD-TYPE 
          22.22           14.24 
[1] "0.0 - 103.6 (22.2)" "0.0 - 124.3 (14.2)"
[1] "hr=" "1.2"
D71V2, survival
                 sevent
clus2               0   1
  DNMBP MUTATED    10   9
  DNMBP WILD-TYPE 122 122
  DNMBP MUTATED DNMBP WILD-TYPE 
             19             244 
  DNMBP MUTATED DNMBP WILD-TYPE 
              9             122 
$`DNMBP MUTATED`
TCGA-D3-A2JD TCGA-D3-A3MR TCGA-D3-A5GN TCGA-EB-A5SG TCGA-EE-A29D TCGA-EE-A29E 
       11.87       103.59       135.75        45.11        13.97        39.62 
TCGA-EE-A29Q TCGA-EE-A2A6 TCGA-EE-A2GR TCGA-EE-A2MJ TCGA-EE-A2MR TCGA-EE-A2MS 
       37.35        58.75        14.30        96.23       103.56       136.47 
TCGA-EE-A3AC TCGA-EE-A3AG TCGA-EE-A3JA TCGA-ER-A193 TCGA-FS-A1ZP TCGA-FW-A3R5 
       25.84        23.47        53.19        31.40        74.73        22.92 
TCGA-GN-A267 
       64.44 

$`DNMBP WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.57        16.67       112.04       112.57        71.80       133.25 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       28.08        31.59        90.90        95.74        43.43       103.10 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JF 
       65.49        23.77       115.53       168.00        69.90        48.76 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO 
      113.52        42.08        12.10       171.58        56.19        66.08 
TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB 
       45.11       130.72        58.06        46.98        46.32       166.52 
TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MU 
       86.93        60.23        24.53        13.87         9.34        39.75 
TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K 
       21.47       161.85        43.69        40.14       131.90        18.38 
TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS 
       10.03        51.68        15.06       137.92       166.19         7.43 
TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 
      125.19       151.53        54.67         3.65         6.41        11.34 
TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1HW 
        3.25         9.90        25.18        66.25        48.89        36.03 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 
      117.21        20.38       194.83       176.55        35.93       107.34 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
       61.18        53.92        65.92        23.44        68.09        28.60 
TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SH 
       10.49       215.44        15.68        13.87        10.16        35.01 
TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 
        3.55        52.01        29.82        27.22         8.65        94.98 
TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B 
       33.73        14.70        26.89        68.15         4.96       109.64 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B 
      151.27        78.87       168.26        13.55        63.35        80.61 
TCGA-EE-A29C TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N 
       47.84        72.07        32.19         2.60        44.35        18.61 
TCGA-EE-A29P TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X 
       56.42        14.47        55.92        25.87       171.55        17.92 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2GB TCGA-EE-A2GC 
       46.82       102.90        24.43        39.29        47.54        67.43 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK 
      314.56       135.95       208.04        48.72        89.33        54.74 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GS 
       79.66        75.48        90.97       101.95        13.91        55.59 
TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 
       44.88        94.82        21.67       129.27        28.83        19.76 
TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI 
       61.51        47.28       103.27       103.20        16.96       204.66 
TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ 
      144.76       203.05       167.90        47.54       248.65        43.23 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AE 
       41.59        53.26       124.31       122.73         3.68        54.51 
TCGA-EE-A3AF TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 
       13.81       138.81       172.18       127.20        36.95        64.08 
TCGA-EE-A3J8 TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 
       34.32        27.35        33.40       101.79       148.08        35.44 
TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C 
       13.94        50.76         9.17        77.75        98.40        48.89 
TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J 
       12.59        13.02        26.37       268.93       152.35         6.44 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S 
      131.51        61.05        44.05       162.08        50.89        37.25 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF 
      148.18        79.99        43.82        23.34        20.15        16.37 
TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL 
       31.27        32.05       247.04        80.32        46.98        33.21 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY 
       92.98       174.21         4.90       216.92        48.59       228.59 
TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB 
      202.65        20.91        28.08         7.79        27.72        48.85 
TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH 
      357.37        53.52        40.27        15.45         9.70        32.75 
TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS 
       47.38        23.93       101.26       133.55        11.41       148.80 
TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 
       53.16        26.56        49.48        27.09        27.02        77.82 
TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC 
       66.67        28.73       174.84        12.43        26.73        49.45 
TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
       77.88         0.20        47.54         0.16         2.40         9.90 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 
        7.23        14.04       120.46       117.93        84.72        10.13 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS 
       62.79        32.48        39.58         6.67 

  DNMBP MUTATED DNMBP WILD-TYPE 
          11.87            0.16 
  DNMBP MUTATED DNMBP WILD-TYPE 
         136.47          357.37 
  DNMBP MUTATED DNMBP WILD-TYPE 
         45.110          48.655 
[1] "11.9 - 136.5 (45.1)" "0.2 - 357.4 (48.7)" 
[1] "hr=" "1.1"
D71V3, continuous
                 vv
clus              DISTANT METASTASIS PRIMARY TUMOR
  DNMBP MUTATED                    0             0
  DNMBP WILD-TYPE                 35             4
                 vv
clus              REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  DNMBP MUTATED                                           4                  15
  DNMBP WILD-TYPE                                        54                 155
D71V4, multiclass
                                           clus
vv                                          DNMBP MUTATED DNMBP WILD-TYPE
  DISTANT METASTASIS                                    0              35
  PRIMARY TUMOR                                         0               4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE             4              54
  REGIONAL LYMPH NODE                                  15             155
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  DNMBP MUTATED             0       0       2        1        1        3
  DNMBP WILD-TYPE          10       6      20        9       23       14
                 vv
clus              STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DNMBP MUTATED           0         2         0         5          1          1
  DNMBP WILD-TYPE        10        12         9        26         12         21
                 vv
clus              STAGE IIIC STAGE IV
  DNMBP MUTATED            2        0
  DNMBP WILD-TYPE         42       12
D71V5, multiclass
             clus
vv            DNMBP MUTATED DNMBP WILD-TYPE
  I OR II NOS             0              10
  STAGE 0                 0               6
  STAGE I                 2              20
  STAGE IA                1               9
  STAGE IB                1              23
  STAGE II                3              14
  STAGE IIA               0              10
  STAGE IIB               2              12
  STAGE IIC               0               9
  STAGE III               5              26
  STAGE IIIA              1              12
  STAGE IIIB              1              21
  STAGE IIIC              2              42
  STAGE IV                0              12
[1] 14  2
[1] 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
  DNMBP MUTATED       5  2  6  4
  DNMBP WILD-TYPE    46 56 47 51
D71V6, multiclass
       clus
vv      DNMBP MUTATED DNMBP WILD-TYPE
  T0+T1             5              46
  T2                2              56
  T3                6              47
  T4                4              51
[1] 4 2
[1] TRUE
[1] "dimension 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
  DNMBP MUTATED    10   5   3   0
  DNMBP WILD-TYPE 128  43  29  33
D71V7, multiclass
    clus
vv   DNMBP MUTATED DNMBP WILD-TYPE
  N0            10             128
  N1             5              43
  N2             3              29
  N3             0              33
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               M0  M1 M1A M1B M1C
  DNMBP MUTATED    18   0   0   0   0
  DNMBP WILD-TYPE 222   4   2   2   5
D71V8, multiclass
     clus
vv    DNMBP MUTATED DNMBP WILD-TYPE
  M0             18             222
  M1              0               4
  M1A             0               2
  M1B             0               2
  M1C             0               5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V9, binary
                 cls
clus               0  1
  DNMBP MUTATED    9  3
  DNMBP WILD-TYPE 93 64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DNMBP MUTATED      9    3
  DNMBP WILD-TYPE   93   64
     clus
vv    DNMBP MUTATED DNMBP WILD-TYPE
  NO              9              93
  YES             3              64
[1] 2 2
[1] FALSE
D71V10, binary
                 cls
clus                0   1
  DNMBP MUTATED     3  16
  DNMBP WILD-TYPE  30 219
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DNMBP MUTATED      3   16
  DNMBP WILD-TYPE   30  219
     clus
vv    DNMBP MUTATED DNMBP WILD-TYPE
  NO              3              30
  YES            16             219
[1] 2 2
[1] FALSE
D71V11, continuous
D71V12, binary
                 cls
clus                0   1
  DNMBP MUTATED     3  16
  DNMBP WILD-TYPE 100 149
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DNMBP MUTATED      3   16
  DNMBP WILD-TYPE  100  149
        clus
vv       DNMBP MUTATED DNMBP WILD-TYPE
  FEMALE             3             100
  MALE              16             149
[1] 2 2
[1] FALSE
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DNMBP MUTATED       0                         0    19
  DNMBP WILD-TYPE     3                         1   245
D71V13, multiclass
                           clus
vv                          DNMBP MUTATED DNMBP WILD-TYPE
  ASIAN                                 0               3
  BLACK OR AFRICAN AMERICAN             0               1
  WHITE                                19             245
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V14, binary
                 cls
clus                0   1
  DNMBP MUTATED     0  19
  DNMBP WILD-TYPE   3 242
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DNMBP MUTATED      0   19
  DNMBP WILD-TYPE    3  242
                        clus
vv                       DNMBP MUTATED DNMBP WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO            19             242
[1] 2 2
[1] FALSE

Clustering(72) Variable = MPP7 MUTATION ANALYSIS
D72V1, survival
                sevent
clus2              0   1
  MPP7 MUTATED    15  14
  MPP7 WILD-TYPE 113 116
  MPP7 MUTATED MPP7 WILD-TYPE 
            29            229 
  MPP7 MUTATED MPP7 WILD-TYPE 
            14            116 
$`MPP7 MUTATED`
TCGA-D3-A1QA TCGA-D3-A2J8 TCGA-D3-A2JH TCGA-D3-A5GS TCGA-D9-A6EC TCGA-DA-A1I1 
       45.83         8.38        36.16         6.97        13.22        39.19 
TCGA-DA-A1IC TCGA-EE-A182 TCGA-EE-A20C TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29D 
        6.64         1.35         4.34         7.99        37.97        11.15 
TCGA-EE-A29E TCGA-EE-A2GC TCGA-EE-A2GU TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A3JD 
       38.63        34.29        36.33        29.65        27.16        27.35 
TCGA-ER-A193 TCGA-ER-A19F TCGA-ER-A19J TCGA-ER-A19N TCGA-ER-A2NC TCGA-FS-A1Z3 
       31.40        11.11         4.21        42.84        11.80        14.24 
TCGA-FS-A1ZB TCGA-FS-A4F9 TCGA-FW-A3R5 TCGA-GN-A268 TCGA-QB-A6FS 
        3.39        10.78         0.99        15.42         5.79 

$`MPP7 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.47         8.52       111.09        32.42        70.16       110.79 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J9 
       28.08        22.55        81.24        10.29        85.32        21.14 
TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JG 
       88.50        68.22        69.90        11.41        30.87         7.50 
TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ 
        6.31        92.42        56.19        64.44        45.11       114.67 
TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE 
       15.25        46.98        46.32        82.29        61.38        13.32 
TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV 
       24.00         6.31         9.34       103.59        26.37         5.39 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N 
       80.22        42.71        15.09        41.10        17.72         8.84 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GU 
       20.48        13.94        52.01        47.87         1.55        23.11 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-DA-A1HV TCGA-DA-A1HW 
        4.01         2.89         9.90        11.31        48.79        35.80 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 
       51.12        10.03        13.68         9.99        44.52        36.69 
TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 
       25.15         4.93        22.36        19.36         7.00        17.56 
TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN 
       14.83        13.15         0.20         0.00         0.00        13.22 
TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A183 
       11.57        10.55         6.31         8.12         1.12        12.20 
TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I 
        5.13         4.31        36.07         5.13         9.21         1.18 
TCGA-EE-A29B TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N 
        9.90         8.55         4.41         1.08        27.12         9.50 
TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W 
       12.03         8.09         8.84         9.99         2.43         8.68 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 
        8.09        11.31        49.22        23.90         9.67         8.94 
TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ 
       39.39        17.98        34.92        47.21        30.08        19.43 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP 
       16.01        35.54        28.31        33.83        30.84         5.42 
TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 
        1.15        13.02        34.98         8.84        98.27         2.70 
TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH 
        6.18        47.51         9.53        29.46        44.25         7.96 
TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN 
       14.56        63.42       111.78       111.91        56.02        25.08 
TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB 
       26.99        21.60        23.05         5.56       124.31       122.73 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH 
       25.84         3.68        30.15        13.81        15.95        12.72 
TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA 
        3.22        22.92        21.60        21.60        16.14        22.22 
TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 
        0.46        13.94        33.60        18.61        12.95        38.40 
TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E 
        5.72        76.41        25.18         3.78         3.52        11.90 
TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19P TCGA-ER-A19Q 
      114.15        34.88        13.45        28.60        34.68         9.57 
TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF 
       36.07        17.72        78.44         1.87         1.51        13.08 
TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL 
       12.62        11.74         9.04         6.58        22.49         1.71 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY 
       18.41        85.74         4.90        64.47         3.45        11.01 
TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZC TCGA-FS-A1ZD 
       23.80        15.52         7.33         7.30        20.38         8.22 
TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK 
       19.53        11.08         7.17        30.87        12.92        12.89 
TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT 
       47.38        52.08         8.65         8.81        49.15        40.64 
TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 
        8.68        27.39         0.82         5.23        53.85         7.36 
TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 
       28.73        14.20         5.98         6.41         2.27         0.20 
TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 
        0.13         0.16         0.43         9.90         7.23        12.85 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A26A 
       24.85        31.33        84.72        10.13        16.24        12.16 
TCGA-GN-A26D 
       14.70 

  MPP7 MUTATED MPP7 WILD-TYPE 
          0.99           0.00 
  MPP7 MUTATED MPP7 WILD-TYPE 
         45.83         124.31 
  MPP7 MUTATED MPP7 WILD-TYPE 
         13.22          15.09 
[1] "1.0 - 45.8 (13.2)"  "0.0 - 124.3 (15.1)"
[1] "hr=" "1.1"
D72V2, survival
                sevent
clus2              0   1
  MPP7 MUTATED    16  14
  MPP7 WILD-TYPE 116 117
  MPP7 MUTATED MPP7 WILD-TYPE 
            30            233 
  MPP7 MUTATED MPP7 WILD-TYPE 
            14            117 
$`MPP7 MUTATED`
TCGA-D3-A1QA TCGA-D3-A2J8 TCGA-D3-A2JH TCGA-D3-A5GS TCGA-D9-A149 TCGA-D9-A6EC 
       90.90        65.49        42.08         7.43        54.67        66.25 
TCGA-DA-A1I1 TCGA-DA-A1IC TCGA-EE-A182 TCGA-EE-A20C TCGA-EE-A29A TCGA-EE-A29C 
      194.83        68.09        14.70       151.27        63.35        47.84 
TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A2GC TCGA-EE-A2GU TCGA-EE-A2MR TCGA-EE-A2MS 
       13.97        39.62        67.43        94.82       103.56       136.47 
TCGA-EE-A3JD TCGA-ER-A193 TCGA-ER-A19F TCGA-ER-A19J TCGA-ER-A19N TCGA-ER-A2NC 
       27.35        31.40        26.37         6.44        44.05        43.82 
TCGA-FS-A1Z3 TCGA-FS-A1ZB TCGA-FS-A4F9 TCGA-FW-A3R5 TCGA-GN-A268 TCGA-QB-A6FS 
       20.91        48.85        12.43        22.92        62.79         6.67 

$`MPP7 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.57        16.67       112.04       112.57        71.80       133.25 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J9 
       28.08        31.59        95.74        43.43       103.10        23.77 
TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JG 
      115.53       168.00        69.90        11.87        48.76       113.52 
TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ 
       12.10       171.58        56.19        66.08        45.11       130.72 
TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE 
       58.06        46.98        46.32       166.52        86.93        60.23 
TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV 
       24.53        13.87         9.34       103.59        39.75        21.47 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N 
      161.85        43.69        40.14       131.90        18.38        10.03 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GU 
       51.68        15.06       135.75       137.92       166.19       125.19 
TCGA-D9-A148 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 
      151.53         3.65         6.41        11.34         3.25         9.90 
TCGA-D9-A6EA TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I2 
       25.18        48.89        36.03       117.21        20.38       176.55 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB 
       35.93       107.34        61.18        53.92        65.92        23.44 
TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R 
       28.60        10.49       215.44        15.68        13.87        10.16 
TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y 
       45.11        35.01         3.55        52.01        29.82        27.22 
TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 
        8.65        94.98        33.73        26.89        68.15         4.96 
TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29B TCGA-EE-A29G 
      109.64        78.87       168.26        13.55        80.61        72.07 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
       32.19         2.60        44.35        18.61        56.42        37.35 
TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 
       14.47        55.92        25.87       171.55        17.92        46.82 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD 
      102.90        24.43        39.29        58.75        47.54       314.56 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
      135.95       208.04        48.72        89.33        54.74        79.66 
TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS 
       75.48        90.97       101.95        13.91        14.30        55.59 
TCGA-EE-A2GT TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC 
       44.88        21.67       129.27        28.83        19.76        61.51 
TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ 
       47.28       103.27       103.20        16.96       204.66        96.23 
TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ 
      144.76       203.05       167.90        47.54       248.65        43.23 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD 
       41.59        53.26       124.31       122.73        25.84         3.68 
TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 
       54.51        13.81        23.47       138.81       172.18       127.20 
TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JE TCGA-EE-A3JH 
       36.95        64.08        34.32        53.19        33.40       101.79 
TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A 
      148.08        35.44        13.94        50.76         9.17        77.75 
TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19G TCGA-ER-A19H 
       98.40        48.89        12.59        13.02       268.93       152.35 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W 
      131.51        61.05       162.08        50.89        37.25       148.18 
TCGA-ER-A1A1 TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH 
       79.99        23.34        20.15        16.37        31.27        32.05 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A 
      247.04        80.32        46.98        33.21        92.98       174.21 
TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z4 
        4.90       216.92        48.59       228.59       202.65        28.08 
TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF 
        7.79        27.72       357.37        53.52        40.27        15.45 
TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP 
        9.70        32.75        47.38        23.93       101.26        74.73 
TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW 
      133.55        11.41       148.80        53.16        26.56        49.48 
TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 
       27.09        27.02        77.82        66.67        28.73       174.84 
TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV 
       26.73        49.45        77.88         0.20        47.54         0.16 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 
        2.40         9.90         7.23        14.04       120.46       117.93 
TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A26D 
       84.72        10.13        64.44        32.48        39.58 

  MPP7 MUTATED MPP7 WILD-TYPE 
          6.44           0.16 
  MPP7 MUTATED MPP7 WILD-TYPE 
        194.83         357.37 
  MPP7 MUTATED MPP7 WILD-TYPE 
        45.945         48.720 
[1] "6.4 - 194.8 (45.9)" "0.2 - 357.4 (48.7)"
[1] "hr=" "1.1"
D72V3, continuous
                vv
clus             DISTANT METASTASIS PRIMARY TUMOR
  MPP7 MUTATED                    6             1
  MPP7 WILD-TYPE                 29             3
                vv
clus             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  MPP7 MUTATED                                           4                  19
  MPP7 WILD-TYPE                                        54                 151
D72V4, multiclass
                                           clus
vv                                          MPP7 MUTATED MPP7 WILD-TYPE
  DISTANT METASTASIS                                   6             29
  PRIMARY TUMOR                                        1              3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE            4             54
  REGIONAL LYMPH NODE                                 19            151
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  MPP7 MUTATED             0       1       1        1        5        2
  MPP7 WILD-TYPE          10       5      21        9       19       15
                vv
clus             STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  MPP7 MUTATED           0         3         0         2          2          2
  MPP7 WILD-TYPE        10        11         9        29         11         20
                vv
clus             STAGE IIIC STAGE IV
  MPP7 MUTATED            5        3
  MPP7 WILD-TYPE         39        9
D72V5, multiclass
             clus
vv            MPP7 MUTATED MPP7 WILD-TYPE
  I OR II NOS            0             10
  STAGE 0                1              5
  STAGE I                1             21
  STAGE IA               1              9
  STAGE IB               5             19
  STAGE II               2             15
  STAGE IIA              0             10
  STAGE IIB              3             11
  STAGE IIC              0              9
  STAGE III              2             29
  STAGE IIIA             2             11
  STAGE IIIB             2             20
  STAGE IIIC             5             39
  STAGE IV               3              9
[1] 14  2
[1] 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
  MPP7 MUTATED       5  5  9  3
  MPP7 WILD-TYPE    46 53 44 52
D72V6, multiclass
       clus
vv      MPP7 MUTATED MPP7 WILD-TYPE
  T0+T1            5             46
  T2               5             53
  T3               9             44
  T4               3             52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  MPP7 MUTATED    15   7   3   4
  MPP7 WILD-TYPE 123  41  29  29
D72V7, multiclass
    clus
vv   MPP7 MUTATED MPP7 WILD-TYPE
  N0           15            123
  N1            7             41
  N2            3             29
  N3            4             29
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              M0  M1 M1A M1B M1C
  MPP7 MUTATED    26   2   0   0   1
  MPP7 WILD-TYPE 214   2   2   2   4
D72V8, multiclass
     clus
vv    MPP7 MUTATED MPP7 WILD-TYPE
  M0            26            214
  M1             2              2
  M1A            0              2
  M1B            0              2
  M1C            1              4
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V9, binary
                cls
clus              0  1
  MPP7 MUTATED   17  4
  MPP7 WILD-TYPE 85 63
[1] "tbl2"
                cls
clus             [,1] [,2]
  MPP7 MUTATED     17    4
  MPP7 WILD-TYPE   85   63
     clus
vv    MPP7 MUTATED MPP7 WILD-TYPE
  NO            17             85
  YES            4             63
[1] 2 2
[1] FALSE
D72V10, binary
                cls
clus               0   1
  MPP7 MUTATED     6  24
  MPP7 WILD-TYPE  27 211
[1] "tbl2"
                cls
clus             [,1] [,2]
  MPP7 MUTATED      6   24
  MPP7 WILD-TYPE   27  211
     clus
vv    MPP7 MUTATED MPP7 WILD-TYPE
  NO             6             27
  YES           24            211
[1] 2 2
[1] FALSE
D72V11, continuous
D72V12, binary
                cls
clus               0   1
  MPP7 MUTATED     6  24
  MPP7 WILD-TYPE  97 141
[1] "tbl2"
                cls
clus             [,1] [,2]
  MPP7 MUTATED      6   24
  MPP7 WILD-TYPE   97  141
        clus
vv       MPP7 MUTATED MPP7 WILD-TYPE
  FEMALE            6             97
  MALE             24            141
[1] 2 2
[1] FALSE
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MPP7 MUTATED       0                         0    30
  MPP7 WILD-TYPE     3                         1   234
D72V13, multiclass
                           clus
vv                          MPP7 MUTATED MPP7 WILD-TYPE
  ASIAN                                0              3
  BLACK OR AFRICAN AMERICAN            0              1
  WHITE                               30            234
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V14, binary
                cls
clus               0   1
  MPP7 MUTATED     0  29
  MPP7 WILD-TYPE   3 232
[1] "tbl2"
                cls
clus             [,1] [,2]
  MPP7 MUTATED      0   29
  MPP7 WILD-TYPE    3  232
                        clus
vv                       MPP7 MUTATED MPP7 WILD-TYPE
  HISPANIC OR LATINO                0              3
  NOT HISPANIC OR LATINO           29            232
[1] 2 2
[1] FALSE

Clustering(73) Variable = IFNGR2 MUTATION ANALYSIS
D73V1, survival
                  sevent
clus2                0   1
  IFNGR2 MUTATED     1   3
  IFNGR2 WILD-TYPE 127 127
  IFNGR2 MUTATED IFNGR2 WILD-TYPE 
               4              254 
  IFNGR2 MUTATED IFNGR2 WILD-TYPE 
               3              127 
$`IFNGR2 MUTATED`
TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-EE-A180 TCGA-EE-A29E 
       85.32         8.38         8.12        38.63 

$`IFNGR2 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.47         8.52       111.09        32.42        70.16       110.79 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J9 
       28.08        22.55        45.83        81.24        10.29        21.14 
TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JG 
       88.50        68.22        69.90        11.41        30.87         7.50 
TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP 
       36.16         6.31        92.42        56.19        64.44        45.11 
TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC 
      114.67        15.25        46.98        46.32        82.29        61.38 
TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU 
       13.32        24.00         6.31         9.34       103.59        26.37 
TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K 
        5.39        80.22        42.71        15.09        41.10        17.72 
TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR 
        8.84        20.48        13.94        52.01        47.87         1.55 
TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA 
        6.97        23.11         4.01         2.89         9.90        11.31 
TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 
       13.22        48.79        35.80        51.12        10.03        39.19 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA 
       13.68         9.99        44.52        36.69        25.15         4.93 
TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 
       22.36         6.64        19.36         7.00        17.56        14.83 
TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EE-A17X 
       13.15         0.20         0.00         0.00        13.22        11.57 
TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 
       10.55         6.31         1.12         1.35        12.20         5.13 
TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I 
        4.31        36.07         4.34         5.13         9.21         1.18 
TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29H 
        7.99         9.90        37.97        11.15         8.55         4.41 
TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R 
        1.08        27.12         9.50        12.03         8.09         8.84 
TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 
        9.99         2.43         8.68         8.09        11.31        49.22 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD 
       23.90         9.67         8.94        39.39        34.29        17.98 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
       34.92        47.21        30.08        19.43        16.01        35.54 
TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS 
       28.31        33.83        30.84         5.42         1.15        13.02 
TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 
       34.98        36.33         8.84        98.27         2.70         6.18 
TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI 
       47.51         9.53        29.46        44.25         7.96        14.56 
TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP 
       63.42       111.78       111.91        56.02        25.08        26.99 
TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA 
       21.60        29.65        27.16        23.05         5.56       124.31 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG 
      122.73        25.84         3.68        30.15        13.81        15.95 
TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 
       12.72         3.22        22.92        21.60        21.60        16.14 
TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 
       22.22        27.35         0.46        13.94        33.60        31.40 
TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B 
       18.61        12.95        38.40         5.72        76.41        25.18 
TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H 
        3.78         3.52        11.90        11.11       114.15        34.88 
TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q 
        4.21        13.45        28.60        42.84        34.68         9.57 
TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE 
       36.07        17.72        78.44        11.80         1.87         1.51 
TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV 
       13.08        12.62        11.74         9.04         6.58        22.49 
TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX 
        1.71        18.41        85.74         4.90        64.47         3.45 
TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA 
       11.01        23.80        14.24        15.52         7.33         7.30 
TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG 
        3.39        20.38         8.22        19.53        11.08         7.17 
TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ 
       30.87        12.92        12.89        47.38        52.08         8.65 
TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY 
        8.81        49.15        40.64         8.68        27.39         0.82 
TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 
        5.23        53.85         7.36        28.73        14.20        10.78 
TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU 
        5.98         6.41         2.27         0.20         0.99         0.13 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 
        0.16         0.43         9.90         7.23        12.85        24.85 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
       31.33        84.72        10.13        16.24        15.42        12.16 
TCGA-GN-A26D TCGA-QB-A6FS 
       14.70         5.79 

  IFNGR2 MUTATED IFNGR2 WILD-TYPE 
            8.12             0.00 
  IFNGR2 MUTATED IFNGR2 WILD-TYPE 
           85.32           124.31 
  IFNGR2 MUTATED IFNGR2 WILD-TYPE 
          23.505           14.765 
[1] "8.1 - 85.3 (23.5)"  "0.0 - 124.3 (14.8)"
[1] "hr=" "1.2"
D73V2, survival
                  sevent
clus2                0   1
  IFNGR2 MUTATED     1   3
  IFNGR2 WILD-TYPE 131 128
  IFNGR2 MUTATED IFNGR2 WILD-TYPE 
               4              259 
  IFNGR2 MUTATED IFNGR2 WILD-TYPE 
               3              128 
$`IFNGR2 MUTATED`
TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-EE-A180 TCGA-EE-A29E 
      103.10        65.49        94.98        39.62 

$`IFNGR2 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.57        16.67       112.04       112.57        71.80       133.25 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J9 
       28.08        31.59        90.90        95.74        43.43        23.77 
TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JG 
      115.53       168.00        69.90        11.87        48.76       113.52 
TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP 
       42.08        12.10       171.58        56.19        66.08        45.11 
TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC 
      130.72        58.06        46.98        46.32       166.52        86.93 
TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU 
       60.23        24.53        13.87         9.34       103.59        39.75 
TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K 
       21.47       161.85        43.69        40.14       131.90        18.38 
TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR 
       10.03        51.68        15.06       135.75       137.92       166.19 
TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX 
        7.43       125.19       151.53        54.67         3.65         6.41 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1HV 
       11.34         3.25         9.90        25.18        66.25        48.89 
TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 
       36.03       117.21        20.38       194.83       176.55        35.93 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC 
      107.34        61.18        53.92        65.92        23.44        68.09 
TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R 
       28.60        10.49       215.44        15.68        13.87        10.16 
TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y 
       45.11        35.01         3.55        52.01        29.82        27.22 
TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 
        8.65        33.73        14.70        26.89        68.15         4.96 
TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A 
      109.64       151.27        78.87       168.26        13.55        63.35 
TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L 
       80.61        47.84        13.97        72.07        32.19         2.60 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S 
       44.35        18.61        56.42        37.35        14.47        55.92 
TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 
       25.87       171.55        17.92        46.82       102.90        24.43 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE 
       39.29        58.75        47.54        67.43       314.56       135.95 
TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM 
      208.04        48.72        89.33        54.74        79.66        75.48 
TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT 
       90.97       101.95        13.91        14.30        55.59        44.88 
TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC 
       94.82        21.67       129.27        28.83        19.76        61.51 
TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ 
       47.28       103.27       103.20        16.96       204.66        96.23 
TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ 
      144.76       203.05       167.90        47.54       248.65        43.23 
TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB 
      103.56       136.47        41.59        53.26       124.31       122.73 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH 
       25.84         3.68        54.51        13.81        23.47       138.81 
TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA 
      172.18       127.20        36.95        64.08        34.32        53.19 
TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 
       27.35        33.40       101.79       148.08        31.40        35.44 
TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C 
       13.94        50.76         9.17        77.75        98.40        48.89 
TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J 
       12.59        13.02        26.37       268.93       152.35         6.44 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S 
      131.51        61.05        44.05       162.08        50.89        37.25 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF 
      148.18        79.99        43.82        23.34        20.15        16.37 
TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL 
       31.27        32.05       247.04        80.32        46.98        33.21 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY 
       92.98       174.21         4.90       216.92        48.59       228.59 
TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB 
      202.65        20.91        28.08         7.79        27.72        48.85 
TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH 
      357.37        53.52        40.27        15.45         9.70        32.75 
TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR 
       47.38        23.93       101.26        74.73       133.55        11.41 
TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ 
      148.80        53.16        26.56        49.48        27.09        27.02 
TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB 
       77.82        66.67        28.73       174.84        12.43        26.73 
TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV 
       49.45        77.88         0.20        22.92        47.54         0.16 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 
        2.40         9.90         7.23        14.04       120.46       117.93 
TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D 
       84.72        10.13        64.44        62.79        32.48        39.58 
TCGA-QB-A6FS 
        6.67 

  IFNGR2 MUTATED IFNGR2 WILD-TYPE 
           39.62             0.16 
  IFNGR2 MUTATED IFNGR2 WILD-TYPE 
          103.10           357.37 
  IFNGR2 MUTATED IFNGR2 WILD-TYPE 
          80.235           47.840 
[1] "39.6 - 103.1 (80.2)" "0.2 - 357.4 (47.8)" 
[1] "hr=" "1.4"
D73V3, continuous
                  vv
clus               DISTANT METASTASIS PRIMARY TUMOR
  IFNGR2 MUTATED                    1             0
  IFNGR2 WILD-TYPE                 34             4
                  vv
clus               REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  IFNGR2 MUTATED                                           0
  IFNGR2 WILD-TYPE                                        58
                  vv
clus               REGIONAL LYMPH NODE
  IFNGR2 MUTATED                     3
  IFNGR2 WILD-TYPE                 167
D73V4, multiclass
                                           clus
vv                                          IFNGR2 MUTATED IFNGR2 WILD-TYPE
  DISTANT METASTASIS                                     1               34
  PRIMARY TUMOR                                          0                4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE              0               58
  REGIONAL LYMPH NODE                                    3              167
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  IFNGR2 MUTATED             0       0       0        0        1        0
  IFNGR2 WILD-TYPE          10       6      22       10       23       17
                  vv
clus               STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  IFNGR2 MUTATED           0         0         0         1          0
  IFNGR2 WILD-TYPE        10        14         9        30         13
                  vv
clus               STAGE IIIB STAGE IIIC STAGE IV
  IFNGR2 MUTATED            1          1        0
  IFNGR2 WILD-TYPE         21         43       12
D73V5, multiclass
             clus
vv            IFNGR2 MUTATED IFNGR2 WILD-TYPE
  I OR II NOS              0               10
  STAGE 0                  0                6
  STAGE I                  0               22
  STAGE IA                 0               10
  STAGE IB                 1               23
  STAGE II                 0               17
  STAGE IIA                0               10
  STAGE IIB                0               14
  STAGE IIC                0                9
  STAGE III                1               30
  STAGE IIIA               0               13
  STAGE IIIB               1               21
  STAGE IIIC               1               43
  STAGE IV                 0               12
[1] 14  2
[1] 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
  IFNGR2 MUTATED       0  1  2  1
  IFNGR2 WILD-TYPE    51 57 51 54
D73V6, multiclass
       clus
vv      IFNGR2 MUTATED IFNGR2 WILD-TYPE
  T0+T1              0               51
  T2                 1               57
  T3                 2               51
  T4                 1               54
[1] 4 2
[1] TRUE
[1] "dimension 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
  IFNGR2 MUTATED     2   2   0   0
  IFNGR2 WILD-TYPE 136  46  32  33
D73V7, multiclass
    clus
vv   IFNGR2 MUTATED IFNGR2 WILD-TYPE
  N0              2              136
  N1              2               46
  N2              0               32
  N3              0               33
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                M0  M1 M1A M1B M1C
  IFNGR2 MUTATED     4   0   0   0   0
  IFNGR2 WILD-TYPE 236   4   2   2   5
D73V8, multiclass
     clus
vv    IFNGR2 MUTATED IFNGR2 WILD-TYPE
  M0               4              236
  M1               0                4
  M1A              0                2
  M1B              0                2
  M1C              0                5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D73V9, binary
                  cls
clus                0  1
  IFNGR2 MUTATED    3  1
  IFNGR2 WILD-TYPE 99 66
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IFNGR2 MUTATED      3    1
  IFNGR2 WILD-TYPE   99   66
     clus
vv    IFNGR2 MUTATED IFNGR2 WILD-TYPE
  NO               3               99
  YES              1               66
[1] 2 2
[1] FALSE
D73V10, binary
                  cls
clus                 0   1
  IFNGR2 MUTATED     0   4
  IFNGR2 WILD-TYPE  33 231
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IFNGR2 MUTATED      0    4
  IFNGR2 WILD-TYPE   33  231
     clus
vv    IFNGR2 MUTATED IFNGR2 WILD-TYPE
  NO               0               33
  YES              4              231
[1] 2 2
[1] FALSE
D73V11, continuous
D73V12, binary
                  cls
clus                 0   1
  IFNGR2 MUTATED     0   4
  IFNGR2 WILD-TYPE 103 161
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IFNGR2 MUTATED      0    4
  IFNGR2 WILD-TYPE  103  161
        clus
vv       IFNGR2 MUTATED IFNGR2 WILD-TYPE
  FEMALE              0              103
  MALE                4              161
[1] 2 2
[1] FALSE
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  IFNGR2 MUTATED       0                         0     4
  IFNGR2 WILD-TYPE     3                         1   260
D73V13, multiclass
                           clus
vv                          IFNGR2 MUTATED IFNGR2 WILD-TYPE
  ASIAN                                  0                3
  BLACK OR AFRICAN AMERICAN              0                1
  WHITE                                  4              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"
D73V14, binary
                  cls
clus                 0   1
  IFNGR2 MUTATED     0   4
  IFNGR2 WILD-TYPE   3 257
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IFNGR2 MUTATED      0    4
  IFNGR2 WILD-TYPE    3  257
                        clus
vv                       IFNGR2 MUTATED IFNGR2 WILD-TYPE
  HISPANIC OR LATINO                  0                3
  NOT HISPANIC OR LATINO              4              257
[1] 2 2
[1] FALSE

Clustering(74) Variable = ASNSD1 MUTATION ANALYSIS
D74V1, survival
                  sevent
clus2                0   1
  ASNSD1 MUTATED     3   2
  ASNSD1 WILD-TYPE 125 128
  ASNSD1 MUTATED ASNSD1 WILD-TYPE 
               5              253 
  ASNSD1 MUTATED ASNSD1 WILD-TYPE 
               2              128 
$`ASNSD1 MUTATED`
TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D9-A6E9 TCGA-EE-A182 TCGA-EE-A2MC 
       46.32        82.29         9.90         1.35        47.51 

$`ASNSD1 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.47         8.52       111.09        32.42        70.16       110.79 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       28.08        22.55        45.83        81.24        10.29        85.32 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
        8.38        21.14        88.50        68.22        69.90        11.41 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       30.87         7.50        36.16         6.31        92.42        56.19 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3CC 
       64.44        45.11       114.67        15.25        46.98        61.38 
TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU 
       13.32        24.00         6.31         9.34       103.59        26.37 
TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K 
        5.39        80.22        42.71        15.09        41.10        17.72 
TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR 
        8.84        20.48        13.94        52.01        47.87         1.55 
TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6EA TCGA-D9-A6EC 
        6.97        23.11         4.01         2.89        11.31        13.22 
TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 
       48.79        35.80        51.12        10.03        39.19        13.68 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB 
        9.99        44.52        36.69        25.15         4.93        22.36 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q 
        6.64        19.36         7.00        17.56        14.83        13.15 
TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y 
        0.20         0.00         0.00        13.22        11.57        10.55 
TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 
        6.31         8.12         1.12        12.20         5.13         4.31 
TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A 
       36.07         4.34         5.13         9.21         1.18         7.99 
TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H 
        9.90        37.97        11.15        38.63         8.55         4.41 
TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R 
        1.08        27.12         9.50        12.03         8.09         8.84 
TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 
        9.99         2.43         8.68         8.09        11.31        49.22 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD 
       23.90         9.67         8.94        39.39        34.29        17.98 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
       34.92        47.21        30.08        19.43        16.01        35.54 
TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS 
       28.31        33.83        30.84         5.42         1.15        13.02 
TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 
       34.98        36.33         8.84        98.27         2.70         6.18 
TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ 
        9.53        29.46        44.25         7.96        14.56        63.42 
TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ 
      111.78       111.91        56.02        25.08        26.99        21.60 
TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB 
       29.65        27.16        23.05         5.56       124.31       122.73 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH 
       25.84         3.68        30.15        13.81        15.95        12.72 
TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA 
        3.22        22.92        21.60        21.60        16.14        22.22 
TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 
       27.35         0.46        13.94        33.60        31.40        18.61 
TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C 
       12.95        38.40         5.72        76.41        25.18         3.78 
TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J 
        3.52        11.90        11.11       114.15        34.88         4.21 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S 
       13.45        28.60        42.84        34.68         9.57        36.07 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF 
       17.72        78.44        11.80         1.87         1.51        13.08 
TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL 
       12.62        11.74         9.04         6.58        22.49         1.71 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY 
       18.41        85.74         4.90        64.47         3.45        11.01 
TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB 
       23.80        14.24        15.52         7.33         7.30         3.39 
TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH 
       20.38         8.22        19.53        11.08         7.17        30.87 
TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR 
       12.92        12.89        47.38        52.08         8.65         8.81 
TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ 
       49.15        40.64         8.68        27.39         0.82         5.23 
TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB 
       53.85         7.36        28.73        14.20        10.78         5.98 
TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV 
        6.41         2.27         0.20         0.99         0.13         0.16 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 
        0.43         9.90         7.23        12.85        24.85        31.33 
TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D 
       84.72        10.13        16.24        15.42        12.16        14.70 
TCGA-QB-A6FS 
        5.79 

  ASNSD1 MUTATED ASNSD1 WILD-TYPE 
            1.35             0.00 
  ASNSD1 MUTATED ASNSD1 WILD-TYPE 
           82.29           124.31 
  ASNSD1 MUTATED ASNSD1 WILD-TYPE 
           46.32            14.70 
[1] "1.4 - 82.3 (46.3)"  "0.0 - 124.3 (14.7)"
[1] "hr=" "1.6"
D74V2, survival
                  sevent
clus2                0   1
  ASNSD1 MUTATED     4   2
  ASNSD1 WILD-TYPE 128 129
  ASNSD1 MUTATED ASNSD1 WILD-TYPE 
               6              257 
  ASNSD1 MUTATED ASNSD1 WILD-TYPE 
               2              129 
$`ASNSD1 MUTATED`
TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D9-A148 TCGA-D9-A6E9 TCGA-EE-A182 TCGA-EE-A2MC 
       46.32       166.52       151.53         9.90        14.70        61.51 

$`ASNSD1 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.57        16.67       112.04       112.57        71.80       133.25 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       28.08        31.59        90.90        95.74        43.43       103.10 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
       65.49        23.77       115.53       168.00        69.90        11.87 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       48.76       113.52        42.08        12.10       171.58        56.19 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3CC 
       66.08        45.11       130.72        58.06        46.98        86.93 
TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU 
       60.23        24.53        13.87         9.34       103.59        39.75 
TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K 
       21.47       161.85        43.69        40.14       131.90        18.38 
TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR 
       10.03        51.68        15.06       135.75       137.92       166.19 
TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 
        7.43       125.19        54.67         3.65         6.41        11.34 
TCGA-D9-A3Z3 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY 
        3.25        25.18        66.25        48.89        36.03       117.21 
TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 
       20.38       194.83       176.55        35.93       107.34        61.18 
TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 
       53.92        65.92        23.44        68.09        28.60        10.49 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH 
      215.44        15.68        13.87        10.16        45.11        35.01 
TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 
        3.55        52.01        29.82        27.22         8.65        94.98 
TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C 
       33.73        26.89        68.15         4.96       109.64       151.27 
TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C 
       78.87       168.26        13.55        63.35        80.61        47.84 
TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M 
       13.97        39.62        72.07        32.19         2.60        44.35 
TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V 
       18.61        56.42        37.35        14.47        55.92        25.87 
TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 
      171.55        17.92        46.82       102.90        24.43        39.29 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH 
       58.75        47.54        67.43       314.56       135.95       208.04 
TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN 
       48.72        89.33        54.74        79.66        75.48        90.97 
TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU 
      101.95        13.91        14.30        55.59        44.88        94.82 
TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MD TCGA-EE-A2ME 
       21.67       129.27        28.83        19.76        47.28       103.27 
TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML 
      103.20        16.96       204.66        96.23       144.76       203.05 
TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS 
      167.90        47.54       248.65        43.23       103.56       136.47 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD 
       41.59        53.26       124.31       122.73        25.84         3.68 
TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 
       54.51        13.81        23.47       138.81       172.18       127.20 
TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE 
       36.95        64.08        34.32        53.19        27.35        33.40 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 
      101.79       148.08        31.40        35.44        13.94        50.76 
TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E 
        9.17        77.75        98.40        48.89        12.59        13.02 
TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M 
       26.37       268.93       152.35         6.44       131.51        61.05 
TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 
       44.05       162.08        50.89        37.25       148.18        79.99 
TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH 
       43.82        23.34        20.15        16.37        31.27        32.05 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A 
      247.04        80.32        46.98        33.21        92.98       174.21 
TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
        4.90       216.92        48.59       228.59       202.65        20.91 
TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD 
       28.08         7.79        27.72        48.85       357.37        53.52 
TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK 
       40.27        15.45         9.70        32.75        47.38        23.93 
TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT 
      101.26        74.73       133.55        11.41       148.80        53.16 
TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 
       26.56        49.48        27.09        27.02        77.82        66.67 
TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD 
       28.73       174.84        12.43        26.73        49.45        77.88 
TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
        0.20        22.92        47.54         0.16         2.40         9.90 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 
        7.23        14.04       120.46       117.93        84.72        10.13 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS 
       64.44        62.79        32.48        39.58         6.67 

  ASNSD1 MUTATED ASNSD1 WILD-TYPE 
            9.90             0.16 
  ASNSD1 MUTATED ASNSD1 WILD-TYPE 
          166.52           357.37 
  ASNSD1 MUTATED ASNSD1 WILD-TYPE 
          53.915           48.590 
[1] "9.9 - 166.5 (53.9)" "0.2 - 357.4 (48.6)"
[1] "hr=" "1.5"
D74V3, continuous
                  vv
clus               DISTANT METASTASIS PRIMARY TUMOR
  ASNSD1 MUTATED                    2             1
  ASNSD1 WILD-TYPE                 33             3
                  vv
clus               REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  ASNSD1 MUTATED                                           1
  ASNSD1 WILD-TYPE                                        57
                  vv
clus               REGIONAL LYMPH NODE
  ASNSD1 MUTATED                     3
  ASNSD1 WILD-TYPE                 167
D74V4, multiclass
                                           clus
vv                                          ASNSD1 MUTATED ASNSD1 WILD-TYPE
  DISTANT METASTASIS                                     2               33
  PRIMARY TUMOR                                          1                3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE              1               57
  REGIONAL LYMPH NODE                                    3              167
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  ASNSD1 MUTATED             2       0       1        0        0        0
  ASNSD1 WILD-TYPE           8       6      21       10       24       17
                  vv
clus               STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  ASNSD1 MUTATED           0         0         0         0          1
  ASNSD1 WILD-TYPE        10        14         9        31         12
                  vv
clus               STAGE IIIB STAGE IIIC STAGE IV
  ASNSD1 MUTATED            0          2        0
  ASNSD1 WILD-TYPE         22         42       12
D74V5, multiclass
             clus
vv            ASNSD1 MUTATED ASNSD1 WILD-TYPE
  I OR II NOS              2                8
  STAGE 0                  0                6
  STAGE I                  1               21
  STAGE IA                 0               10
  STAGE IB                 0               24
  STAGE II                 0               17
  STAGE IIA                0               10
  STAGE IIB                0               14
  STAGE IIC                0                9
  STAGE III                0               31
  STAGE IIIA               1               12
  STAGE IIIB               0               22
  STAGE IIIC               2               42
  STAGE IV                 0               12
[1] 14  2
[1] 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
  ASNSD1 MUTATED       0  3  1  1
  ASNSD1 WILD-TYPE    51 55 52 54
D74V6, multiclass
       clus
vv      ASNSD1 MUTATED ASNSD1 WILD-TYPE
  T0+T1              0               51
  T2                 3               55
  T3                 1               52
  T4                 1               54
[1] 4 2
[1] TRUE
[1] "dimension 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
  ASNSD1 MUTATED     3   2   0   2
  ASNSD1 WILD-TYPE 135  46  32  31
D74V7, multiclass
    clus
vv   ASNSD1 MUTATED ASNSD1 WILD-TYPE
  N0              3              135
  N1              2               46
  N2              0               32
  N3              2               31
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                M0  M1 M1A M1B M1C
  ASNSD1 MUTATED     6   0   0   1   0
  ASNSD1 WILD-TYPE 234   4   2   1   5
D74V8, multiclass
     clus
vv    ASNSD1 MUTATED ASNSD1 WILD-TYPE
  M0               6              234
  M1               0                4
  M1A              0                2
  M1B              1                1
  M1C              0                5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D74V9, binary
                  cls
clus                0  1
  ASNSD1 MUTATED    3  1
  ASNSD1 WILD-TYPE 99 66
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ASNSD1 MUTATED      3    1
  ASNSD1 WILD-TYPE   99   66
     clus
vv    ASNSD1 MUTATED ASNSD1 WILD-TYPE
  NO               3               99
  YES              1               66
[1] 2 2
[1] FALSE
D74V10, binary
                  cls
clus                 0   1
  ASNSD1 MUTATED     0   7
  ASNSD1 WILD-TYPE  33 228
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ASNSD1 MUTATED      0    7
  ASNSD1 WILD-TYPE   33  228
     clus
vv    ASNSD1 MUTATED ASNSD1 WILD-TYPE
  NO               0               33
  YES              7              228
[1] 2 2
[1] FALSE
D74V11, continuous
D74V12, binary
                  cls
clus                 0   1
  ASNSD1 MUTATED     4   3
  ASNSD1 WILD-TYPE  99 162
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ASNSD1 MUTATED      4    3
  ASNSD1 WILD-TYPE   99  162
        clus
vv       ASNSD1 MUTATED ASNSD1 WILD-TYPE
  FEMALE              4               99
  MALE                3              162
[1] 2 2
[1] FALSE
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ASNSD1 MUTATED       0                         0     7
  ASNSD1 WILD-TYPE     3                         1   257
D74V13, multiclass
                           clus
vv                          ASNSD1 MUTATED ASNSD1 WILD-TYPE
  ASIAN                                  0                3
  BLACK OR AFRICAN AMERICAN              0                1
  WHITE                                  7              257
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D74V14, binary
                  cls
clus                 0   1
  ASNSD1 MUTATED     0   7
  ASNSD1 WILD-TYPE   3 254
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ASNSD1 MUTATED      0    7
  ASNSD1 WILD-TYPE    3  254
                        clus
vv                       ASNSD1 MUTATED ASNSD1 WILD-TYPE
  HISPANIC OR LATINO                  0                3
  NOT HISPANIC OR LATINO              7              254
[1] 2 2
[1] FALSE

Clustering(75) Variable = RB1 MUTATION ANALYSIS
D75V1, survival
               sevent
clus2             0   1
  RB1 MUTATED     5   3
  RB1 WILD-TYPE 123 127
  RB1 MUTATED RB1 WILD-TYPE 
            8           250 
  RB1 MUTATED RB1 WILD-TYPE 
            3           127 
$`RB1 MUTATED`
TCGA-D3-A1Q7 TCGA-D3-A1QB TCGA-EE-A29B TCGA-EE-A2MT TCGA-EE-A3J5 TCGA-FS-A1Z0 
      110.79        81.24         9.90        23.05        21.60        23.80 
TCGA-FW-A3TU TCGA-GN-A267 
        0.13        16.24 

$`RB1 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q8 
       16.47         8.52       111.09        32.42        70.16        28.08 
TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 
       22.55        45.83        10.29        85.32         8.38        21.14 
TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JG 
       88.50        68.22        69.90        11.41        30.87         7.50 
TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP 
       36.16         6.31        92.42        56.19        64.44        45.11 
TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC 
      114.67        15.25        46.98        46.32        82.29        61.38 
TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU 
       13.32        24.00         6.31         9.34       103.59        26.37 
TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K 
        5.39        80.22        42.71        15.09        41.10        17.72 
TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR 
        8.84        20.48        13.94        52.01        47.87         1.55 
TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA 
        6.97        23.11         4.01         2.89         9.90        11.31 
TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 
       13.22        48.79        35.80        51.12        10.03        39.19 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA 
       13.68         9.99        44.52        36.69        25.15         4.93 
TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 
       22.36         6.64        19.36         7.00        17.56        14.83 
TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EE-A17X 
       13.15         0.20         0.00         0.00        13.22        11.57 
TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 
       10.55         6.31         8.12         1.12         1.35        12.20 
TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H 
        5.13         4.31        36.07         4.34         5.13         9.21 
TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G 
        1.18         7.99        37.97        11.15        38.63         8.55 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
        4.41         1.08        27.12         9.50        12.03         8.09 
TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 
        8.84         9.99         2.43         8.68         8.09        11.31 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC 
       49.22        23.90         9.67         8.94        39.39        34.29 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK 
       17.98        34.92        47.21        30.08        19.43        16.01 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR 
       35.54        28.31        33.83        30.84         5.42         1.15 
TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 
       13.02        34.98        36.33         8.84        98.27         2.70 
TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH 
        6.18        47.51         9.53        29.46        44.25         7.96 
TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN 
       14.56        63.42       111.78       111.91        56.02        25.08 
TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3AA 
       26.99        21.60        29.65        27.16         5.56       124.31 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG 
      122.73        25.84         3.68        30.15        13.81        15.95 
TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA 
       12.72         3.22        22.92        21.60        16.14        22.22 
TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 
       27.35         0.46        13.94        33.60        31.40        18.61 
TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C 
       12.95        38.40         5.72        76.41        25.18         3.78 
TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J 
        3.52        11.90        11.11       114.15        34.88         4.21 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S 
       13.45        28.60        42.84        34.68         9.57        36.07 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF 
       17.72        78.44        11.80         1.87         1.51        13.08 
TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL 
       12.62        11.74         9.04         6.58        22.49         1.71 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY 
       18.41        85.74         4.90        64.47         3.45        11.01 
TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC 
       14.24        15.52         7.33         7.30         3.39        20.38 
TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ 
        8.22        19.53        11.08         7.17        30.87        12.92 
TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS 
       12.89        47.38        52.08         8.65         8.81        49.15 
TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 
       40.64         8.68        27.39         0.82         5.23        53.85 
TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC 
        7.36        28.73        14.20        10.78         5.98         6.41 
TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
        2.27         0.20         0.99         0.16         0.43         9.90 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 
        7.23        12.85        24.85        31.33        84.72        10.13 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS 
       15.42        12.16        14.70         5.79 

  RB1 MUTATED RB1 WILD-TYPE 
         0.13          0.00 
  RB1 MUTATED RB1 WILD-TYPE 
       110.79        124.31 
  RB1 MUTATED RB1 WILD-TYPE 
       22.325        14.400 
[1] "0.1 - 110.8 (22.3)" "0.0 - 124.3 (14.4)"
[1] "hr=" "1.7"
D75V2, survival
               sevent
clus2             0   1
  RB1 MUTATED     5   3
  RB1 WILD-TYPE 127 128
  RB1 MUTATED RB1 WILD-TYPE 
            8           255 
  RB1 MUTATED RB1 WILD-TYPE 
            3           128 
$`RB1 MUTATED`
TCGA-D3-A1Q7 TCGA-D3-A1QB TCGA-EE-A29B TCGA-EE-A2MT TCGA-EE-A3J5 TCGA-FS-A1Z0 
      133.25        95.74        80.61        41.59        36.95       202.65 
TCGA-FW-A3TU TCGA-GN-A267 
       47.54        64.44 

$`RB1 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q8 
       16.57        16.67       112.04       112.57        71.80        28.08 
TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 
       31.59        90.90        43.43       103.10        65.49        23.77 
TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JG 
      115.53       168.00        69.90        11.87        48.76       113.52 
TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP 
       42.08        12.10       171.58        56.19        66.08        45.11 
TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC 
      130.72        58.06        46.98        46.32       166.52        86.93 
TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU 
       60.23        24.53        13.87         9.34       103.59        39.75 
TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K 
       21.47       161.85        43.69        40.14       131.90        18.38 
TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR 
       10.03        51.68        15.06       135.75       137.92       166.19 
TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX 
        7.43       125.19       151.53        54.67         3.65         6.41 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1HV 
       11.34         3.25         9.90        25.18        66.25        48.89 
TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 
       36.03       117.21        20.38       194.83       176.55        35.93 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC 
      107.34        61.18        53.92        65.92        23.44        68.09 
TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R 
       28.60        10.49       215.44        15.68        13.87        10.16 
TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y 
       45.11        35.01         3.55        52.01        29.82        27.22 
TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 
        8.65        94.98        33.73        14.70        26.89        68.15 
TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I 
        4.96       109.64       151.27        78.87       168.26        13.55 
TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H 
       63.35        47.84        13.97        39.62        72.07        32.19 
TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R 
        2.60        44.35        18.61        56.42        37.35        14.47 
TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 
       55.92        25.87       171.55        17.92        46.82       102.90 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD 
       24.43        39.29        58.75        47.54        67.43       314.56 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
      135.95       208.04        48.72        89.33        54.74        79.66 
TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS 
       75.48        90.97       101.95        13.91        14.30        55.59 
TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 
       44.88        94.82        21.67       129.27        28.83        19.76 
TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI 
       61.51        47.28       103.27       103.20        16.96       204.66 
TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP 
       96.23       144.76       203.05       167.90        47.54       248.65 
TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB 
       43.23       103.56       136.47        53.26       124.31       122.73 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH 
       25.84         3.68        54.51        13.81        23.47       138.81 
TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JD 
      172.18       127.20        64.08        34.32        53.19        27.35 
TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 
       33.40       101.79       148.08        31.40        35.44        13.94 
TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D 
       50.76         9.17        77.75        98.40        48.89        12.59 
TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L 
       13.02        26.37       268.93       152.35         6.44       131.51 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W 
       61.05        44.05       162.08        50.89        37.25       148.18 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG 
       79.99        43.82        23.34        20.15        16.37        31.27 
TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN 
       32.05       247.04        80.32        46.98        33.21        92.98 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z3 
      174.21         4.90       216.92        48.59       228.59        20.91 
TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD 
       28.08         7.79        27.72        48.85       357.37        53.52 
TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK 
       40.27        15.45         9.70        32.75        47.38        23.93 
TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT 
      101.26        74.73       133.55        11.41       148.80        53.16 
TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 
       26.56        49.48        27.09        27.02        77.82        66.67 
TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD 
       28.73       174.84        12.43        26.73        49.45        77.88 
TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
        0.20        22.92         0.16         2.40         9.90         7.23 
TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A268 
       14.04       120.46       117.93        84.72        10.13        62.79 
TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS 
       32.48        39.58         6.67 

  RB1 MUTATED RB1 WILD-TYPE 
        36.95          0.16 
  RB1 MUTATED RB1 WILD-TYPE 
       202.65        357.37 
  RB1 MUTATED RB1 WILD-TYPE 
       72.525        47.840 
[1] "37.0 - 202.7 (72.5)" "0.2 - 357.4 (47.8)" 
[1] "hr=" "1.7"
D75V3, continuous
               vv
clus            DISTANT METASTASIS PRIMARY TUMOR
  RB1 MUTATED                    3             0
  RB1 WILD-TYPE                 32             4
               vv
clus            REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  RB1 MUTATED                                           2                   4
  RB1 WILD-TYPE                                        56                 166
D75V4, multiclass
                                           clus
vv                                          RB1 MUTATED RB1 WILD-TYPE
  DISTANT METASTASIS                                  3            32
  PRIMARY TUMOR                                       0             4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE           2            56
  REGIONAL LYMPH NODE                                 4           166
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  RB1 MUTATED             0       1       0        1        2        0
  RB1 WILD-TYPE          10       5      22        9       22       17
               vv
clus            STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  RB1 MUTATED           0         1         0         2          1          0
  RB1 WILD-TYPE        10        13         9        29         12         22
               vv
clus            STAGE IIIC STAGE IV
  RB1 MUTATED            0        0
  RB1 WILD-TYPE         44       12
D75V5, multiclass
             clus
vv            RB1 MUTATED RB1 WILD-TYPE
  I OR II NOS           0            10
  STAGE 0               1             5
  STAGE I               0            22
  STAGE IA              1             9
  STAGE IB              2            22
  STAGE II              0            17
  STAGE IIA             0            10
  STAGE IIB             1            13
  STAGE IIC             0             9
  STAGE III             2            29
  STAGE IIIA            1            12
  STAGE IIIB            0            22
  STAGE IIIC            0            44
  STAGE IV              0            12
[1] 14  2
[1] 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       3  1  1  2
  RB1 WILD-TYPE    48 57 52 53
D75V6, multiclass
       clus
vv      RB1 MUTATED RB1 WILD-TYPE
  T0+T1           3            48
  T2              1            57
  T3              1            52
  T4              2            53
[1] 4 2
[1] TRUE
[1] "dimension 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     5   2   1   0
  RB1 WILD-TYPE 133  46  31  33
D75V7, multiclass
    clus
vv   RB1 MUTATED RB1 WILD-TYPE
  N0           5           133
  N1           2            46
  N2           1            31
  N3           0            33
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             M0  M1 M1A M1B M1C
  RB1 MUTATED     8   0   0   0   0
  RB1 WILD-TYPE 232   4   2   2   5
D75V8, multiclass
     clus
vv    RB1 MUTATED RB1 WILD-TYPE
  M0            8           232
  M1            0             4
  M1A           0             2
  M1B           0             2
  M1C           0             5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D75V9, binary
               cls
clus             0  1
  RB1 MUTATED    5  1
  RB1 WILD-TYPE 97 66
[1] "tbl2"
               cls
clus            [,1] [,2]
  RB1 MUTATED      5    1
  RB1 WILD-TYPE   97   66
     clus
vv    RB1 MUTATED RB1 WILD-TYPE
  NO            5            97
  YES           1            66
[1] 2 2
[1] FALSE
D75V10, binary
               cls
clus              0   1
  RB1 MUTATED     1   8
  RB1 WILD-TYPE  32 227
[1] "tbl2"
               cls
clus            [,1] [,2]
  RB1 MUTATED      1    8
  RB1 WILD-TYPE   32  227
     clus
vv    RB1 MUTATED RB1 WILD-TYPE
  NO            1            32
  YES           8           227
[1] 2 2
[1] FALSE
D75V11, continuous
D75V12, binary
               cls
clus              0   1
  RB1 MUTATED     4   5
  RB1 WILD-TYPE  99 160
[1] "tbl2"
               cls
clus            [,1] [,2]
  RB1 MUTATED      4    5
  RB1 WILD-TYPE   99  160
        clus
vv       RB1 MUTATED RB1 WILD-TYPE
  FEMALE           4            99
  MALE             5           160
[1] 2 2
[1] FALSE
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RB1 MUTATED       0                         0     9
  RB1 WILD-TYPE     3                         1   255
D75V13, multiclass
                           clus
vv                          RB1 MUTATED RB1 WILD-TYPE
  ASIAN                               0             3
  BLACK OR AFRICAN AMERICAN           0             1
  WHITE                               9           255
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D75V14, binary
               cls
clus              0   1
  RB1 MUTATED     0   9
  RB1 WILD-TYPE   3 252
[1] "tbl2"
               cls
clus            [,1] [,2]
  RB1 MUTATED      0    9
  RB1 WILD-TYPE    3  252
                        clus
vv                       RB1 MUTATED RB1 WILD-TYPE
  HISPANIC OR LATINO               0             3
  NOT HISPANIC OR LATINO           9           252
[1] 2 2
[1] FALSE

Clustering(76) Variable = CCK MUTATION ANALYSIS
D76V1, survival
               sevent
clus2             0   1
  CCK MUTATED     5   0
  CCK WILD-TYPE 123 130
  CCK MUTATED CCK WILD-TYPE 
            5           253 
  CCK MUTATED CCK WILD-TYPE 
            0           130 
$`CCK MUTATED`
TCGA-EE-A29E TCGA-EE-A29R TCGA-EE-A2GJ TCGA-FS-A1ZT TCGA-GN-A265 
       38.63         8.84        19.43        40.64        84.72 

$`CCK WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.47         8.52       111.09        32.42        70.16       110.79 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       28.08        22.55        45.83        81.24        10.29        85.32 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
        8.38        21.14        88.50        68.22        69.90        11.41 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       30.87         7.50        36.16         6.31        92.42        56.19 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 
       64.44        45.11       114.67        15.25        46.98        46.32 
TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO 
       82.29        61.38        13.32        24.00         6.31         9.34 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H 
      103.59        26.37         5.39        80.22        42.71        15.09 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN 
       41.10        17.72         8.84        20.48        13.94        52.01 
TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 
       47.87         1.55         6.97        23.11         4.01         2.89 
TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY 
        9.90        11.31        13.22        48.79        35.80        51.12 
TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 
       10.03        39.19        13.68         9.99        44.52        36.69 
TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 
       25.15         4.93        22.36         6.64        19.36         7.00 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH 
       17.56        14.83        13.15         0.20         0.00         0.00 
TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 
       13.22        11.57        10.55         6.31         8.12         1.12 
TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C 
        1.35        12.20         5.13         4.31        36.07         4.34 
TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C 
        5.13         9.21         1.18         7.99         9.90        37.97 
TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N 
       11.15         8.55         4.41         1.08        27.12         9.50 
TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X 
       12.03         8.09         9.99         2.43         8.68         8.09 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB 
       11.31        49.22        23.90         9.67         8.94        39.39 
TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GK 
       34.29        17.98        34.92        47.21        30.08        16.01 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR 
       35.54        28.31        33.83        30.84         5.42         1.15 
TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 
       13.02        34.98        36.33         8.84        98.27         2.70 
TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH 
        6.18        47.51         9.53        29.46        44.25         7.96 
TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN 
       14.56        63.42       111.78       111.91        56.02        25.08 
TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU 
       26.99        21.60        29.65        27.16        23.05         5.56 
TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF 
      124.31       122.73        25.84         3.68        30.15        13.81 
TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 
       15.95        12.72         3.22        22.92        21.60        21.60 
TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI 
       16.14        22.22        27.35         0.46        13.94        33.60 
TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A 
       31.40        18.61        12.95        38.40         5.72        76.41 
TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G 
       25.18         3.78         3.52        11.90        11.11       114.15 
TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P 
       34.88         4.21        13.45        28.60        42.84        34.68 
TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
        9.57        36.07        17.72        78.44        11.80         1.87 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET 
        1.51        13.08        12.62        11.74         9.04         6.58 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW 
       22.49         1.71        18.41        85.74         4.90        64.47 
TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 
        3.45        11.01        23.80        14.24        15.52         7.33 
TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF 
        7.30         3.39        20.38         8.22        19.53        11.08 
TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP 
        7.17        30.87        12.92        12.89        47.38        52.08 
TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY 
        8.65         8.81        49.15         8.68        27.39         0.82 
TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 
        5.23        53.85         7.36        28.73        14.20        10.78 
TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU 
        5.98         6.41         2.27         0.20         0.99         0.13 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 
        0.16         0.43         9.90         7.23        12.85        24.85 
TCGA-GN-A264 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D 
       31.33        10.13        16.24        15.42        12.16        14.70 
TCGA-QB-A6FS 
        5.79 

  CCK MUTATED CCK WILD-TYPE 
         8.84          0.00 
  CCK MUTATED CCK WILD-TYPE 
        84.72        124.31 
  CCK MUTATED CCK WILD-TYPE 
        38.63         14.56 
[1] "8.8 - 84.7 (38.6)"  "0.0 - 124.3 (14.6)"
[1] "hr="     "2.5e+07"
D76V2, survival
               sevent
clus2             0   1
  CCK MUTATED     5   0
  CCK WILD-TYPE 127 131
  CCK MUTATED CCK WILD-TYPE 
            5           258 
  CCK MUTATED CCK WILD-TYPE 
            0           131 
$`CCK MUTATED`
TCGA-EE-A29E TCGA-EE-A29R TCGA-EE-A2GJ TCGA-FS-A1ZT TCGA-GN-A265 
       39.62        14.47        89.33        53.16        84.72 

$`CCK WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.57        16.67       112.04       112.57        71.80       133.25 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       28.08        31.59        90.90        95.74        43.43       103.10 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
       65.49        23.77       115.53       168.00        69.90        11.87 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       48.76       113.52        42.08        12.10       171.58        56.19 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 
       66.08        45.11       130.72        58.06        46.98        46.32 
TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO 
      166.52        86.93        60.23        24.53        13.87         9.34 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H 
      103.59        39.75        21.47       161.85        43.69        40.14 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN 
      131.90        18.38        10.03        51.68        15.06       135.75 
TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 
      137.92       166.19         7.43       125.19       151.53        54.67 
TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA 
        3.65         6.41        11.34         3.25         9.90        25.18 
TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 
       66.25        48.89        36.03       117.21        20.38       194.83 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA 
      176.55        35.93       107.34        61.18        53.92        65.92 
TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 
       23.44        68.09        28.60        10.49       215.44        15.68 
TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN 
       13.87        10.16        45.11        35.01         3.55        52.01 
TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 
       29.82        27.22         8.65        94.98        33.73        14.70 
TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F 
       26.89        68.15         4.96       109.64       151.27        78.87 
TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D 
      168.26        13.55        63.35        80.61        47.84        13.97 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P 
       72.07        32.19         2.60        44.35        18.61        56.42 
TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 
       37.35        55.92        25.87       171.55        17.92        46.82 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC 
      102.90        24.43        39.29        58.75        47.54        67.43 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GK TCGA-EE-A2GL 
      314.56       135.95       208.04        48.72        54.74        79.66 
TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS 
       75.48        90.97       101.95        13.91        14.30        55.59 
TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 
       44.88        94.82        21.67       129.27        28.83        19.76 
TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI 
       61.51        47.28       103.27       103.20        16.96       204.66 
TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP 
       96.23       144.76       203.05       167.90        47.54       248.65 
TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA 
       43.23       103.56       136.47        41.59        53.26       124.31 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG 
      122.73        25.84         3.68        54.51        13.81        23.47 
TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 
      138.81       172.18       127.20        36.95        64.08        34.32 
TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 
       53.19        27.35        33.40       101.79       148.08        31.40 
TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B 
       35.44        13.94        50.76         9.17        77.75        98.40 
TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H 
       48.89        12.59        13.02        26.37       268.93       152.35 
TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q 
        6.44       131.51        61.05        44.05       162.08        50.89 
TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE 
       37.25       148.18        79.99        43.82        23.34        20.15 
TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV 
       16.37        31.27        32.05       247.04        80.32        46.98 
TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX 
       33.21        92.98       174.21         4.90       216.92        48.59 
TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA 
      228.59       202.65        20.91        28.08         7.79        27.72 
TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG 
       48.85       357.37        53.52        40.27        15.45         9.70 
TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ 
       32.75        47.38        23.93       101.26        74.73       133.55 
TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ 
       11.41       148.80        26.56        49.48        27.09        27.02 
TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB 
       77.82        66.67        28.73       174.84        12.43        26.73 
TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV 
       49.45        77.88         0.20        22.92        47.54         0.16 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 
        2.40         9.90         7.23        14.04       120.46       117.93 
TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS 
       10.13        64.44        62.79        32.48        39.58         6.67 

  CCK MUTATED CCK WILD-TYPE 
        14.47          0.16 
  CCK MUTATED CCK WILD-TYPE 
        89.33        357.37 
  CCK MUTATED CCK WILD-TYPE 
       53.160        48.215 
[1] "14.5 - 89.3 (53.2)" "0.2 - 357.4 (48.2)"
[1] "hr="     "9200000"
D76V3, continuous
               vv
clus            DISTANT METASTASIS PRIMARY TUMOR
  CCK MUTATED                    1             0
  CCK WILD-TYPE                 34             4
               vv
clus            REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  CCK MUTATED                                           0                   4
  CCK WILD-TYPE                                        58                 166
D76V4, multiclass
                                           clus
vv                                          CCK MUTATED CCK WILD-TYPE
  DISTANT METASTASIS                                  1            34
  PRIMARY TUMOR                                       0             4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE           0            58
  REGIONAL LYMPH NODE                                 4           166
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  CCK MUTATED             0       0       0        1        0        0
  CCK WILD-TYPE          10       6      22        9       24       17
               vv
clus            STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  CCK MUTATED           0         0         0         1          0          1
  CCK WILD-TYPE        10        14         9        30         13         21
               vv
clus            STAGE IIIC STAGE IV
  CCK MUTATED            1        0
  CCK WILD-TYPE         43       12
D76V5, multiclass
             clus
vv            CCK MUTATED CCK WILD-TYPE
  I OR II NOS           0            10
  STAGE 0               0             6
  STAGE I               0            22
  STAGE IA              1             9
  STAGE IB              0            24
  STAGE II              0            17
  STAGE IIA             0            10
  STAGE IIB             0            14
  STAGE IIC             0             9
  STAGE III             1            30
  STAGE IIIA            0            13
  STAGE IIIB            1            21
  STAGE IIIC            1            43
  STAGE IV              0            12
[1] 14  2
[1] 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
  CCK MUTATED       1  1  2  0
  CCK WILD-TYPE    50 57 51 55
D76V6, multiclass
       clus
vv      CCK MUTATED CCK WILD-TYPE
  T0+T1           1            50
  T2              1            57
  T3              2            51
  T4              0            55
[1] 4 2
[1] TRUE
[1] "dimension 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
  CCK MUTATED     1   3   0   0
  CCK WILD-TYPE 137  45  32  33
D76V7, multiclass
    clus
vv   CCK MUTATED CCK WILD-TYPE
  N0           1           137
  N1           3            45
  N2           0            32
  N3           0            33
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             M0  M1 M1A M1B M1C
  CCK MUTATED     4   0   0   0   0
  CCK WILD-TYPE 236   4   2   2   5
D76V8, multiclass
     clus
vv    CCK MUTATED CCK WILD-TYPE
  M0            4           236
  M1            0             4
  M1A           0             2
  M1B           0             2
  M1C           0             5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D76V9, binary
               cls
clus              0   1
  CCK MUTATED     2   1
  CCK WILD-TYPE 100  66
[1] "tbl2"
               cls
clus            [,1] [,2]
  CCK MUTATED      2    1
  CCK WILD-TYPE  100   66
     clus
vv    CCK MUTATED CCK WILD-TYPE
  NO            2           100
  YES           1            66
[1] 2 2
[1] FALSE
D76V10, binary
               cls
clus              0   1
  CCK MUTATED     1   4
  CCK WILD-TYPE  32 231
[1] "tbl2"
               cls
clus            [,1] [,2]
  CCK MUTATED      1    4
  CCK WILD-TYPE   32  231
     clus
vv    CCK MUTATED CCK WILD-TYPE
  NO            1            32
  YES           4           231
[1] 2 2
[1] FALSE
D76V11, continuous
D76V12, binary
               cls
clus              0   1
  CCK MUTATED     1   4
  CCK WILD-TYPE 102 161
[1] "tbl2"
               cls
clus            [,1] [,2]
  CCK MUTATED      1    4
  CCK WILD-TYPE  102  161
        clus
vv       CCK MUTATED CCK WILD-TYPE
  FEMALE           1           102
  MALE             4           161
[1] 2 2
[1] FALSE
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CCK MUTATED       0                         0     5
  CCK WILD-TYPE     3                         1   259
D76V13, multiclass
                           clus
vv                          CCK MUTATED CCK WILD-TYPE
  ASIAN                               0             3
  BLACK OR AFRICAN AMERICAN           0             1
  WHITE                               5           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"
D76V14, binary
               cls
clus              0   1
  CCK MUTATED     0   5
  CCK WILD-TYPE   3 256
[1] "tbl2"
               cls
clus            [,1] [,2]
  CCK MUTATED      0    5
  CCK WILD-TYPE    3  256
                        clus
vv                       CCK MUTATED CCK WILD-TYPE
  HISPANIC OR LATINO               0             3
  NOT HISPANIC OR LATINO           5           256
[1] 2 2
[1] FALSE

Clustering(77) Variable = ZNF780B MUTATION ANALYSIS
D77V1, survival
                   sevent
clus2                 0   1
  ZNF780B MUTATED     7   2
  ZNF780B WILD-TYPE 121 128
  ZNF780B MUTATED ZNF780B WILD-TYPE 
                9               249 
  ZNF780B MUTATED ZNF780B WILD-TYPE 
                2               128 
$`ZNF780B MUTATED`
TCGA-EE-A29C TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2MD TCGA-EE-A2MR TCGA-EE-A3AE 
       37.97        34.29        17.98         9.53        29.65        30.15 
TCGA-EE-A3AG TCGA-ER-A2NF TCGA-FW-A3R5 
       15.95        13.08         0.99 

$`ZNF780B WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.47         8.52       111.09        32.42        70.16       110.79 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       28.08        22.55        45.83        81.24        10.29        85.32 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
        8.38        21.14        88.50        68.22        69.90        11.41 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       30.87         7.50        36.16         6.31        92.42        56.19 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 
       64.44        45.11       114.67        15.25        46.98        46.32 
TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO 
       82.29        61.38        13.32        24.00         6.31         9.34 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H 
      103.59        26.37         5.39        80.22        42.71        15.09 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN 
       41.10        17.72         8.84        20.48        13.94        52.01 
TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 
       47.87         1.55         6.97        23.11         4.01         2.89 
TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY 
        9.90        11.31        13.22        48.79        35.80        51.12 
TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 
       10.03        39.19        13.68         9.99        44.52        36.69 
TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 
       25.15         4.93        22.36         6.64        19.36         7.00 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH 
       17.56        14.83        13.15         0.20         0.00         0.00 
TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 
       13.22        11.57        10.55         6.31         8.12         1.12 
TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C 
        1.35        12.20         5.13         4.31        36.07         4.34 
TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29D 
        5.13         9.21         1.18         7.99         9.90        11.15 
TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N 
       38.63         8.55         4.41         1.08        27.12         9.50 
TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W 
       12.03         8.09         8.84         9.99         2.43         8.68 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 
        8.09        11.31        49.22        23.90         9.67         8.94 
TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK 
       39.39        34.92        47.21        30.08        19.43        16.01 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR 
       35.54        28.31        33.83        30.84         5.42         1.15 
TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 
       13.02        34.98        36.33         8.84        98.27         2.70 
TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI 
        6.18        47.51        29.46        44.25         7.96        14.56 
TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP 
       63.42       111.78       111.91        56.02        25.08        26.99 
TCGA-EE-A2MQ TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB 
       21.60        27.16        23.05         5.56       124.31       122.73 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 
       25.84         3.68        13.81        12.72         3.22        22.92 
TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE 
       21.60        21.60        16.14        22.22        27.35         0.46 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 
       13.94        33.60        31.40        18.61        12.95        38.40 
TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E 
        5.72        76.41        25.18         3.78         3.52        11.90 
TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M 
       11.11       114.15        34.88         4.21        13.45        28.60 
TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 
       42.84        34.68         9.57        36.07        17.72        78.44 
TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES 
       11.80         1.87         1.51        12.62        11.74         9.04 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
        6.58        22.49         1.71        18.41        85.74         4.90 
TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 
       64.47         3.45        11.01        23.80        14.24        15.52 
TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE 
        7.33         7.30         3.39        20.38         8.22        19.53 
TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM 
       11.08         7.17        30.87        12.92        12.89        47.38 
TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU 
       52.08         8.65         8.81        49.15        40.64         8.68 
TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 
       27.39         0.82         5.23        53.85         7.36        28.73 
TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 
       14.20        10.78         5.98         6.41         2.27         0.20 
TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 
        0.13         0.16         0.43         9.90         7.23        12.85 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 
       24.85        31.33        84.72        10.13        16.24        15.42 
TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS 
       12.16        14.70         5.79 

  ZNF780B MUTATED ZNF780B WILD-TYPE 
             0.99              0.00 
  ZNF780B MUTATED ZNF780B WILD-TYPE 
            37.97            124.31 
  ZNF780B MUTATED ZNF780B WILD-TYPE 
            17.98             14.56 
[1] "1.0 - 38.0 (18.0)"  "0.0 - 124.3 (14.6)"
[1] "hr=" "2.4"
D77V2, survival
                   sevent
clus2                 0   1
  ZNF780B MUTATED     7   2
  ZNF780B WILD-TYPE 125 129
  ZNF780B MUTATED ZNF780B WILD-TYPE 
                9               254 
  ZNF780B MUTATED ZNF780B WILD-TYPE 
                2               129 
$`ZNF780B MUTATED`
TCGA-EE-A29C TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2MD TCGA-EE-A2MR TCGA-EE-A3AE 
       47.84        67.43       314.56        47.28       103.56        54.51 
TCGA-EE-A3AG TCGA-ER-A2NF TCGA-FW-A3R5 
       23.47        16.37        22.92 

$`ZNF780B WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.57        16.67       112.04       112.57        71.80       133.25 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       28.08        31.59        90.90        95.74        43.43       103.10 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
       65.49        23.77       115.53       168.00        69.90        11.87 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       48.76       113.52        42.08        12.10       171.58        56.19 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 
       66.08        45.11       130.72        58.06        46.98        46.32 
TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO 
      166.52        86.93        60.23        24.53        13.87         9.34 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H 
      103.59        39.75        21.47       161.85        43.69        40.14 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN 
      131.90        18.38        10.03        51.68        15.06       135.75 
TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 
      137.92       166.19         7.43       125.19       151.53        54.67 
TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA 
        3.65         6.41        11.34         3.25         9.90        25.18 
TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 
       66.25        48.89        36.03       117.21        20.38       194.83 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA 
      176.55        35.93       107.34        61.18        53.92        65.92 
TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 
       23.44        68.09        28.60        10.49       215.44        15.68 
TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN 
       13.87        10.16        45.11        35.01         3.55        52.01 
TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 
       29.82        27.22         8.65        94.98        33.73        14.70 
TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F 
       26.89        68.15         4.96       109.64       151.27        78.87 
TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29D TCGA-EE-A29E 
      168.26        13.55        63.35        80.61        13.97        39.62 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P 
       72.07        32.19         2.60        44.35        18.61        56.42 
TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X 
       37.35        14.47        55.92        25.87       171.55        17.92 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB 
       46.82       102.90        24.43        39.29        58.75        47.54 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
      135.95       208.04        48.72        89.33        54.74        79.66 
TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS 
       75.48        90.97       101.95        13.91        14.30        55.59 
TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 
       44.88        94.82        21.67       129.27        28.83        19.76 
TCGA-EE-A2MC TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ 
       61.51       103.27       103.20        16.96       204.66        96.23 
TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ 
      144.76       203.05       167.90        47.54       248.65        43.23 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC 
      136.47        41.59        53.26       124.31       122.73        25.84 
TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 
        3.68        13.81       138.81       172.18       127.20        36.95 
TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH 
       64.08        34.32        53.19        27.35        33.40       101.79 
TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 
      148.08        31.40        35.44        13.94        50.76         9.17 
TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F 
       77.75        98.40        48.89        12.59        13.02        26.37 
TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N 
      268.93       152.35         6.44       131.51        61.05        44.05 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
      162.08        50.89        37.25       148.18        79.99        43.82 
TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET 
       23.34        20.15        31.27        32.05       247.04        80.32 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW 
       46.98        33.21        92.98       174.21         4.90       216.92 
TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 
       48.59       228.59       202.65        20.91        28.08         7.79 
TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF 
       27.72        48.85       357.37        53.52        40.27        15.45 
TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP 
        9.70        32.75        47.38        23.93       101.26        74.73 
TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW 
      133.55        11.41       148.80        53.16        26.56        49.48 
TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 
       27.09        27.02        77.82        66.67        28.73       174.84 
TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU 
       12.43        26.73        49.45        77.88         0.20        47.54 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 
        0.16         2.40         9.90         7.23        14.04       120.46 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
      117.93        84.72        10.13        64.44        62.79        32.48 
TCGA-GN-A26D TCGA-QB-A6FS 
       39.58         6.67 

  ZNF780B MUTATED ZNF780B WILD-TYPE 
            16.37              0.16 
  ZNF780B MUTATED ZNF780B WILD-TYPE 
           314.56            357.37 
  ZNF780B MUTATED ZNF780B WILD-TYPE 
           47.840            48.655 
[1] "16.4 - 314.6 (47.8)" "0.2 - 357.4 (48.7)" 
[1] "hr=" "2.6"
D77V3, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  ZNF780B MUTATED                    0             1
  ZNF780B WILD-TYPE                 35             3
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  ZNF780B MUTATED                                           2
  ZNF780B WILD-TYPE                                        56
                   vv
clus                REGIONAL LYMPH NODE
  ZNF780B MUTATED                     6
  ZNF780B WILD-TYPE                 164
D77V4, multiclass
                                           clus
vv                                          ZNF780B MUTATED ZNF780B WILD-TYPE
  DISTANT METASTASIS                                      0                35
  PRIMARY TUMOR                                           1                 3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE               2                56
  REGIONAL LYMPH NODE                                     6               164
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  ZNF780B MUTATED             0       0       1        1        1        1
  ZNF780B WILD-TYPE          10       6      21        9       23       16
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  ZNF780B MUTATED           0         2         0         2          0
  ZNF780B WILD-TYPE        10        12         9        29         13
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  ZNF780B MUTATED            0          1        0
  ZNF780B WILD-TYPE         22         43       12
D77V5, multiclass
             clus
vv            ZNF780B MUTATED ZNF780B WILD-TYPE
  I OR II NOS               0                10
  STAGE 0                   0                 6
  STAGE I                   1                21
  STAGE IA                  1                 9
  STAGE IB                  1                23
  STAGE II                  1                16
  STAGE IIA                 0                10
  STAGE IIB                 2                12
  STAGE IIC                 0                 9
  STAGE III                 2                29
  STAGE IIIA                0                13
  STAGE IIIB                0                22
  STAGE IIIC                1                43
  STAGE IV                  0                12
[1] 14  2
[1] 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
  ZNF780B MUTATED       2  2  2  2
  ZNF780B WILD-TYPE    49 56 51 53
D77V6, multiclass
       clus
vv      ZNF780B MUTATED ZNF780B WILD-TYPE
  T0+T1               2                49
  T2                  2                56
  T3                  2                51
  T4                  2                53
[1] 4 2
[1] TRUE
[1] "dimension 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
  ZNF780B MUTATED     6   0   2   1
  ZNF780B WILD-TYPE 132  48  30  32
D77V7, multiclass
    clus
vv   ZNF780B MUTATED ZNF780B WILD-TYPE
  N0               6               132
  N1               0                48
  N2               2                30
  N3               1                32
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1 M1A M1B M1C
  ZNF780B MUTATED     9   0   0   0   0
  ZNF780B WILD-TYPE 231   4   2   2   5
D77V8, multiclass
     clus
vv    ZNF780B MUTATED ZNF780B WILD-TYPE
  M0                9               231
  M1                0                 4
  M1A               0                 2
  M1B               0                 2
  M1C               0                 5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D77V9, binary
                   cls
clus                 0  1
  ZNF780B MUTATED    3  4
  ZNF780B WILD-TYPE 99 63
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZNF780B MUTATED      3    4
  ZNF780B WILD-TYPE   99   63
     clus
vv    ZNF780B MUTATED ZNF780B WILD-TYPE
  NO                3                99
  YES               4                63
[1] 2 2
[1] FALSE
D77V10, binary
                   cls
clus                  0   1
  ZNF780B MUTATED     1   8
  ZNF780B WILD-TYPE  32 227
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZNF780B MUTATED      1    8
  ZNF780B WILD-TYPE   32  227
     clus
vv    ZNF780B MUTATED ZNF780B WILD-TYPE
  NO                1                32
  YES               8               227
[1] 2 2
[1] FALSE
D77V11, continuous
D77V12, binary
                   cls
clus                  0   1
  ZNF780B MUTATED     2   7
  ZNF780B WILD-TYPE 101 158
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZNF780B MUTATED      2    7
  ZNF780B WILD-TYPE  101  158
        clus
vv       ZNF780B MUTATED ZNF780B WILD-TYPE
  FEMALE               2               101
  MALE                 7               158
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ZNF780B MUTATED       0                         0     9
  ZNF780B WILD-TYPE     3                         1   255
D77V13, multiclass
                           clus
vv                          ZNF780B MUTATED ZNF780B WILD-TYPE
  ASIAN                                   0                 3
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                   9               255
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D77V14, binary
                   cls
clus                  0   1
  ZNF780B MUTATED     0   9
  ZNF780B WILD-TYPE   3 252
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZNF780B MUTATED      0    9
  ZNF780B WILD-TYPE    3  252
                        clus
vv                       ZNF780B MUTATED ZNF780B WILD-TYPE
  HISPANIC OR LATINO                   0                 3
  NOT HISPANIC OR LATINO               9               252
[1] 2 2
[1] FALSE

Clustering(78) Variable = ATP5F1 MUTATION ANALYSIS
D78V1, survival
                  sevent
clus2                0   1
  ATP5F1 MUTATED     4   3
  ATP5F1 WILD-TYPE 124 127
  ATP5F1 MUTATED ATP5F1 WILD-TYPE 
               7              251 
  ATP5F1 MUTATED ATP5F1 WILD-TYPE 
               3              127 
$`ATP5F1 MUTATED`
TCGA-EE-A29L TCGA-EE-A2GI TCGA-EE-A2GP TCGA-EE-A2GT TCGA-EE-A2M5 TCGA-EE-A3AE 
        1.08        30.08         5.42        34.98         8.84        30.15 
TCGA-FW-A3R5 
        0.99 

$`ATP5F1 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.47         8.52       111.09        32.42        70.16       110.79 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       28.08        22.55        45.83        81.24        10.29        85.32 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
        8.38        21.14        88.50        68.22        69.90        11.41 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       30.87         7.50        36.16         6.31        92.42        56.19 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 
       64.44        45.11       114.67        15.25        46.98        46.32 
TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO 
       82.29        61.38        13.32        24.00         6.31         9.34 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H 
      103.59        26.37         5.39        80.22        42.71        15.09 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN 
       41.10        17.72         8.84        20.48        13.94        52.01 
TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 
       47.87         1.55         6.97        23.11         4.01         2.89 
TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY 
        9.90        11.31        13.22        48.79        35.80        51.12 
TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 
       10.03        39.19        13.68         9.99        44.52        36.69 
TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 
       25.15         4.93        22.36         6.64        19.36         7.00 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH 
       17.56        14.83        13.15         0.20         0.00         0.00 
TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 
       13.22        11.57        10.55         6.31         8.12         1.12 
TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C 
        1.35        12.20         5.13         4.31        36.07         4.34 
TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C 
        5.13         9.21         1.18         7.99         9.90        37.97 
TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29N 
       11.15        38.63         8.55         4.41        27.12         9.50 
TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W 
       12.03         8.09         8.84         9.99         2.43         8.68 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 
        8.09        11.31        49.22        23.90         9.67         8.94 
TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ 
       39.39        34.29        17.98        34.92        47.21        19.43 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GR 
       16.01        35.54        28.31        33.83        30.84         1.15 
TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC 
       13.02        36.33        98.27         2.70         6.18        47.51 
TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ 
        9.53        29.46        44.25         7.96        14.56        63.42 
TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ 
      111.78       111.91        56.02        25.08        26.99        21.60 
TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB 
       29.65        27.16        23.05         5.56       124.31       122.73 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 
       25.84         3.68        13.81        15.95        12.72         3.22 
TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JD 
       22.92        21.60        21.60        16.14        22.22        27.35 
TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 
        0.46        13.94        33.60        31.40        18.61        12.95 
TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D 
       38.40         5.72        76.41        25.18         3.78         3.52 
TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L 
       11.90        11.11       114.15        34.88         4.21        13.45 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W 
       28.60        42.84        34.68         9.57        36.07        17.72 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG 
       78.44        11.80         1.87         1.51        13.08        12.62 
TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN 
       11.74         9.04         6.58        22.49         1.71        18.41 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 
       85.74         4.90        64.47         3.45        11.01        23.80 
TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC 
       14.24        15.52         7.33         7.30         3.39        20.38 
TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ 
        8.22        19.53        11.08         7.17        30.87        12.92 
TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS 
       12.89        47.38        52.08         8.65         8.81        49.15 
TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 
       40.64         8.68        27.39         0.82         5.23        53.85 
TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC 
        7.36        28.73        14.20        10.78         5.98         6.41 
TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
        2.27         0.20         0.13         0.16         0.43         9.90 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 
        7.23        12.85        24.85        31.33        84.72        10.13 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS 
       16.24        15.42        12.16        14.70         5.79 

  ATP5F1 MUTATED ATP5F1 WILD-TYPE 
            0.99             0.00 
  ATP5F1 MUTATED ATP5F1 WILD-TYPE 
           34.98           124.31 
  ATP5F1 MUTATED ATP5F1 WILD-TYPE 
            8.84            14.83 
[1] "1.0 - 35.0 (8.8)"   "0.0 - 124.3 (14.8)"
[1] "hr=" "1.2"
D78V2, survival
                  sevent
clus2                0   1
  ATP5F1 MUTATED     4   3
  ATP5F1 WILD-TYPE 128 128
  ATP5F1 MUTATED ATP5F1 WILD-TYPE 
               7              256 
  ATP5F1 MUTATED ATP5F1 WILD-TYPE 
               3              128 
$`ATP5F1 MUTATED`
TCGA-EE-A29L TCGA-EE-A2GI TCGA-EE-A2GP TCGA-EE-A2GT TCGA-EE-A2M5 TCGA-EE-A3AE 
        2.60        48.72        13.91        44.88        21.67        54.51 
TCGA-FW-A3R5 
       22.92 

$`ATP5F1 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.57        16.67       112.04       112.57        71.80       133.25 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       28.08        31.59        90.90        95.74        43.43       103.10 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
       65.49        23.77       115.53       168.00        69.90        11.87 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       48.76       113.52        42.08        12.10       171.58        56.19 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 
       66.08        45.11       130.72        58.06        46.98        46.32 
TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO 
      166.52        86.93        60.23        24.53        13.87         9.34 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H 
      103.59        39.75        21.47       161.85        43.69        40.14 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN 
      131.90        18.38        10.03        51.68        15.06       135.75 
TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 
      137.92       166.19         7.43       125.19       151.53        54.67 
TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA 
        3.65         6.41        11.34         3.25         9.90        25.18 
TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 
       66.25        48.89        36.03       117.21        20.38       194.83 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA 
      176.55        35.93       107.34        61.18        53.92        65.92 
TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 
       23.44        68.09        28.60        10.49       215.44        15.68 
TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN 
       13.87        10.16        45.11        35.01         3.55        52.01 
TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 
       29.82        27.22         8.65        94.98        33.73        14.70 
TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F 
       26.89        68.15         4.96       109.64       151.27        78.87 
TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D 
      168.26        13.55        63.35        80.61        47.84        13.97 
TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P 
       39.62        72.07        32.19        44.35        18.61        56.42 
TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X 
       37.35        14.47        55.92        25.87       171.55        17.92 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB 
       46.82       102.90        24.43        39.29        58.75        47.54 
TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK 
       67.43       314.56       135.95       208.04        89.33        54.74 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GR TCGA-EE-A2GS 
       79.66        75.48        90.97       101.95        14.30        55.59 
TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD 
       94.82       129.27        28.83        19.76        61.51        47.28 
TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK 
      103.27       103.20        16.96       204.66        96.23       144.76 
TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR 
      203.05       167.90        47.54       248.65        43.23       103.56 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC 
      136.47        41.59        53.26       124.31       122.73        25.84 
TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 
        3.68        13.81        23.47       138.81       172.18       127.20 
TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE 
       36.95        64.08        34.32        53.19        27.35        33.40 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 
      101.79       148.08        31.40        35.44        13.94        50.76 
TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E 
        9.17        77.75        98.40        48.89        12.59        13.02 
TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M 
       26.37       268.93       152.35         6.44       131.51        61.05 
TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 
       44.05       162.08        50.89        37.25       148.18        79.99 
TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH 
       43.82        23.34        20.15        16.37        31.27        32.05 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A 
      247.04        80.32        46.98        33.21        92.98       174.21 
TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
        4.90       216.92        48.59       228.59       202.65        20.91 
TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD 
       28.08         7.79        27.72        48.85       357.37        53.52 
TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK 
       40.27        15.45         9.70        32.75        47.38        23.93 
TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT 
      101.26        74.73       133.55        11.41       148.80        53.16 
TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 
       26.56        49.48        27.09        27.02        77.82        66.67 
TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD 
       28.73       174.84        12.43        26.73        49.45        77.88 
TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
        0.20        47.54         0.16         2.40         9.90         7.23 
TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 
       14.04       120.46       117.93        84.72        10.13        64.44 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS 
       62.79        32.48        39.58         6.67 

  ATP5F1 MUTATED ATP5F1 WILD-TYPE 
            2.60             0.16 
  ATP5F1 MUTATED ATP5F1 WILD-TYPE 
           54.51           357.37 
  ATP5F1 MUTATED ATP5F1 WILD-TYPE 
          22.920           48.805 
[1] "2.6 - 54.5 (22.9)"  "0.2 - 357.4 (48.8)"
[1] "hr=" "1.9"
D78V3, continuous
                  vv
clus               DISTANT METASTASIS PRIMARY TUMOR
  ATP5F1 MUTATED                    0             0
  ATP5F1 WILD-TYPE                 35             4
                  vv
clus               REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  ATP5F1 MUTATED                                           1
  ATP5F1 WILD-TYPE                                        57
                  vv
clus               REGIONAL LYMPH NODE
  ATP5F1 MUTATED                     6
  ATP5F1 WILD-TYPE                 164
D78V4, multiclass
                                           clus
vv                                          ATP5F1 MUTATED ATP5F1 WILD-TYPE
  DISTANT METASTASIS                                     0               35
  PRIMARY TUMOR                                          0                4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE              1               57
  REGIONAL LYMPH NODE                                    6              164
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  ATP5F1 MUTATED             0       0       1        2        0        0
  ATP5F1 WILD-TYPE          10       6      21        8       24       17
                  vv
clus               STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  ATP5F1 MUTATED           1         0         0         1          0
  ATP5F1 WILD-TYPE         9        14         9        30         13
                  vv
clus               STAGE IIIB STAGE IIIC STAGE IV
  ATP5F1 MUTATED            1          1        0
  ATP5F1 WILD-TYPE         21         43       12
D78V5, multiclass
             clus
vv            ATP5F1 MUTATED ATP5F1 WILD-TYPE
  I OR II NOS              0               10
  STAGE 0                  0                6
  STAGE I                  1               21
  STAGE IA                 2                8
  STAGE IB                 0               24
  STAGE II                 0               17
  STAGE IIA                1                9
  STAGE IIB                0               14
  STAGE IIC                0                9
  STAGE III                1               30
  STAGE IIIA               0               13
  STAGE IIIB               1               21
  STAGE IIIC               1               43
  STAGE IV                 0               12
[1] 14  2
[1] 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
  ATP5F1 MUTATED       2  1  1  2
  ATP5F1 WILD-TYPE    49 57 52 53
D78V6, multiclass
       clus
vv      ATP5F1 MUTATED ATP5F1 WILD-TYPE
  T0+T1              2               49
  T2                 1               57
  T3                 1               52
  T4                 2               53
[1] 4 2
[1] TRUE
[1] "dimension 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
  ATP5F1 MUTATED     4   1   1   1
  ATP5F1 WILD-TYPE 134  47  31  32
D78V7, multiclass
    clus
vv   ATP5F1 MUTATED ATP5F1 WILD-TYPE
  N0              4              134
  N1              1               47
  N2              1               31
  N3              1               32
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                M0  M1 M1A M1B M1C
  ATP5F1 MUTATED     7   0   0   0   0
  ATP5F1 WILD-TYPE 233   4   2   2   5
D78V8, multiclass
     clus
vv    ATP5F1 MUTATED ATP5F1 WILD-TYPE
  M0               7              233
  M1               0                4
  M1A              0                2
  M1B              0                2
  M1C              0                5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D78V9, binary
                  cls
clus                0  1
  ATP5F1 MUTATED    4  2
  ATP5F1 WILD-TYPE 98 65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP5F1 MUTATED      4    2
  ATP5F1 WILD-TYPE   98   65
     clus
vv    ATP5F1 MUTATED ATP5F1 WILD-TYPE
  NO               4               98
  YES              2               65
[1] 2 2
[1] FALSE
D78V10, binary
                  cls
clus                 0   1
  ATP5F1 MUTATED     0   7
  ATP5F1 WILD-TYPE  33 228
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP5F1 MUTATED      0    7
  ATP5F1 WILD-TYPE   33  228
     clus
vv    ATP5F1 MUTATED ATP5F1 WILD-TYPE
  NO               0               33
  YES              7              228
[1] 2 2
[1] FALSE
D78V11, continuous
D78V12, binary
                  cls
clus                 0   1
  ATP5F1 MUTATED     1   6
  ATP5F1 WILD-TYPE 102 159
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP5F1 MUTATED      1    6
  ATP5F1 WILD-TYPE  102  159
        clus
vv       ATP5F1 MUTATED ATP5F1 WILD-TYPE
  FEMALE              1              102
  MALE                6              159
[1] 2 2
[1] FALSE
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ATP5F1 MUTATED       0                         0     7
  ATP5F1 WILD-TYPE     3                         1   257
D78V13, multiclass
                           clus
vv                          ATP5F1 MUTATED ATP5F1 WILD-TYPE
  ASIAN                                  0                3
  BLACK OR AFRICAN AMERICAN              0                1
  WHITE                                  7              257
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D78V14, binary
                  cls
clus                 0   1
  ATP5F1 MUTATED     0   7
  ATP5F1 WILD-TYPE   3 254
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP5F1 MUTATED      0    7
  ATP5F1 WILD-TYPE    3  254
                        clus
vv                       ATP5F1 MUTATED ATP5F1 WILD-TYPE
  HISPANIC OR LATINO                  0                3
  NOT HISPANIC OR LATINO              7              254
[1] 2 2
[1] FALSE

Clustering(79) Variable = LOC728819 MUTATION ANALYSIS
D79V1, survival
                     sevent
clus2                   0   1
  LOC728819 MUTATED     4   3
  LOC728819 WILD-TYPE 124 127
  LOC728819 MUTATED LOC728819 WILD-TYPE 
                  7                 251 
  LOC728819 MUTATED LOC728819 WILD-TYPE 
                  3                 127 
$`LOC728819 MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A2J6 TCGA-D3-A2JC TCGA-DA-A1I7 TCGA-EE-A3AA TCGA-ER-A19P 
       16.47        10.29        69.90        36.69       124.31        34.68 
TCGA-FW-A3R5 
        0.99 

$`LOC728819 WILD-TYPE`
TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
        8.52       111.09        32.42        70.16       110.79        28.08 
TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 
       22.55        45.83        81.24        85.32         8.38        21.14 
TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH 
       88.50        68.22        11.41        30.87         7.50        36.16 
TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ 
        6.31        92.42        56.19        64.44        45.11       114.67 
TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE 
       15.25        46.98        46.32        82.29        61.38        13.32 
TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV 
       24.00         6.31         9.34       103.59        26.37         5.39 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N 
       80.22        42.71        15.09        41.10        17.72         8.84 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS 
       20.48        13.94        52.01        47.87         1.55         6.97 
TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC 
       23.11         4.01         2.89         9.90        11.31        13.22 
TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 
       48.79        35.80        51.12        10.03        39.19        13.68 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC 
        9.99        44.52        25.15         4.93        22.36         6.64 
TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R 
       19.36         7.00        17.56        14.83        13.15         0.20 
TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z 
        0.00         0.00        13.22        11.57        10.55         6.31 
TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 
        8.12         1.12         1.35        12.20         5.13         4.31 
TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A 
       36.07         4.34         5.13         9.21         1.18         7.99 
TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H 
        9.90        37.97        11.15        38.63         8.55         4.41 
TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R 
        1.08        27.12         9.50        12.03         8.09         8.84 
TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 
        9.99         2.43         8.68         8.09        11.31        49.22 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD 
       23.90         9.67         8.94        39.39        34.29        17.98 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
       34.92        47.21        30.08        19.43        16.01        35.54 
TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS 
       28.31        33.83        30.84         5.42         1.15        13.02 
TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 
       34.98        36.33         8.84        98.27         2.70         6.18 
TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI 
       47.51         9.53        29.46        44.25         7.96        14.56 
TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP 
       63.42       111.78       111.91        56.02        25.08        26.99 
TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AB 
       21.60        29.65        27.16        23.05         5.56       122.73 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH 
       25.84         3.68        30.15        13.81        15.95        12.72 
TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA 
        3.22        22.92        21.60        21.60        16.14        22.22 
TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 
       27.35         0.46        13.94        33.60        31.40        18.61 
TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C 
       12.95        38.40         5.72        76.41        25.18         3.78 
TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J 
        3.52        11.90        11.11       114.15        34.88         4.21 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W 
       13.45        28.60        42.84         9.57        36.07        17.72 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG 
       78.44        11.80         1.87         1.51        13.08        12.62 
TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN 
       11.74         9.04         6.58        22.49         1.71        18.41 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 
       85.74         4.90        64.47         3.45        11.01        23.80 
TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC 
       14.24        15.52         7.33         7.30         3.39        20.38 
TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ 
        8.22        19.53        11.08         7.17        30.87        12.92 
TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS 
       12.89        47.38        52.08         8.65         8.81        49.15 
TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 
       40.64         8.68        27.39         0.82         5.23        53.85 
TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC 
        7.36        28.73        14.20        10.78         5.98         6.41 
TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
        2.27         0.20         0.13         0.16         0.43         9.90 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 
        7.23        12.85        24.85        31.33        84.72        10.13 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS 
       16.24        15.42        12.16        14.70         5.79 

  LOC728819 MUTATED LOC728819 WILD-TYPE 
               0.99                0.00 
  LOC728819 MUTATED LOC728819 WILD-TYPE 
             124.31              122.73 
  LOC728819 MUTATED LOC728819 WILD-TYPE 
              34.68               14.56 
[1] "1.0 - 124.3 (34.7)" "0.0 - 122.7 (14.6)"
[1] "hr=" "1.7"
D79V2, survival
                     sevent
clus2                   0   1
  LOC728819 MUTATED     4   3
  LOC728819 WILD-TYPE 128 128
  LOC728819 MUTATED LOC728819 WILD-TYPE 
                  7                 256 
  LOC728819 MUTATED LOC728819 WILD-TYPE 
                  3                 128 
$`LOC728819 MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A2J6 TCGA-D3-A2JC TCGA-DA-A1I7 TCGA-EE-A3AA TCGA-ER-A19P 
       16.57        43.43        69.90        61.18       124.31       162.08 
TCGA-FW-A3R5 
       22.92 

$`LOC728819 WILD-TYPE`
TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       16.67       112.04       112.57        71.80       133.25        28.08 
TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 
       31.59        90.90        95.74       103.10        65.49        23.77 
TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH 
      115.53       168.00        11.87        48.76       113.52        42.08 
TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ 
       12.10       171.58        56.19        66.08        45.11       130.72 
TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE 
       58.06        46.98        46.32       166.52        86.93        60.23 
TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV 
       24.53        13.87         9.34       103.59        39.75        21.47 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N 
      161.85        43.69        40.14       131.90        18.38        10.03 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS 
       51.68        15.06       135.75       137.92       166.19         7.43 
TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 
      125.19       151.53        54.67         3.65         6.41        11.34 
TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1HW 
        3.25         9.90        25.18        66.25        48.89        36.03 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 
      117.21        20.38       194.83       176.55        35.93       107.34 
TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 
       53.92        65.92        23.44        68.09        28.60        10.49 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH 
      215.44        15.68        13.87        10.16        45.11        35.01 
TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 
        3.55        52.01        29.82        27.22         8.65        94.98 
TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B 
       33.73        14.70        26.89        68.15         4.96       109.64 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B 
      151.27        78.87       168.26        13.55        63.35        80.61 
TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L 
       47.84        13.97        39.62        72.07        32.19         2.60 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S 
       44.35        18.61        56.42        37.35        14.47        55.92 
TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 
       25.87       171.55        17.92        46.82       102.90        24.43 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE 
       39.29        58.75        47.54        67.43       314.56       135.95 
TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM 
      208.04        48.72        89.33        54.74        79.66        75.48 
TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT 
       90.97       101.95        13.91        14.30        55.59        44.88 
TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC 
       94.82        21.67       129.27        28.83        19.76        61.51 
TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ 
       47.28       103.27       103.20        16.96       204.66        96.23 
TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ 
      144.76       203.05       167.90        47.54       248.65        43.23 
TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AC 
      103.56       136.47        41.59        53.26       122.73        25.84 
TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 
        3.68        54.51        13.81        23.47       138.81       172.18 
TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JD 
      127.20        36.95        64.08        34.32        53.19        27.35 
TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 
       33.40       101.79       148.08        31.40        35.44        13.94 
TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D 
       50.76         9.17        77.75        98.40        48.89        12.59 
TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L 
       13.02        26.37       268.93       152.35         6.44       131.51 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 
       61.05        44.05        50.89        37.25       148.18        79.99 
TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH 
       43.82        23.34        20.15        16.37        31.27        32.05 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A 
      247.04        80.32        46.98        33.21        92.98       174.21 
TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
        4.90       216.92        48.59       228.59       202.65        20.91 
TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD 
       28.08         7.79        27.72        48.85       357.37        53.52 
TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK 
       40.27        15.45         9.70        32.75        47.38        23.93 
TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT 
      101.26        74.73       133.55        11.41       148.80        53.16 
TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 
       26.56        49.48        27.09        27.02        77.82        66.67 
TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD 
       28.73       174.84        12.43        26.73        49.45        77.88 
TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
        0.20        47.54         0.16         2.40         9.90         7.23 
TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 
       14.04       120.46       117.93        84.72        10.13        64.44 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS 
       62.79        32.48        39.58         6.67 

  LOC728819 MUTATED LOC728819 WILD-TYPE 
              16.57                0.16 
  LOC728819 MUTATED LOC728819 WILD-TYPE 
             162.08              357.37 
  LOC728819 MUTATED LOC728819 WILD-TYPE 
             61.180              48.215 
[1] "16.6 - 162.1 (61.2)" "0.2 - 357.4 (48.2)" 
[1] "hr=" "1.2"
D79V3, continuous
                     vv
clus                  DISTANT METASTASIS PRIMARY TUMOR
  LOC728819 MUTATED                    0             0
  LOC728819 WILD-TYPE                 35             4
                     vv
clus                  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  LOC728819 MUTATED                                           1
  LOC728819 WILD-TYPE                                        57
                     vv
clus                  REGIONAL LYMPH NODE
  LOC728819 MUTATED                     6
  LOC728819 WILD-TYPE                 164
D79V4, multiclass
                                           clus
vv                                          LOC728819 MUTATED
  DISTANT METASTASIS                                        0
  PRIMARY TUMOR                                             0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                 1
  REGIONAL LYMPH NODE                                       6
                                           clus
vv                                          LOC728819 WILD-TYPE
  DISTANT METASTASIS                                         35
  PRIMARY TUMOR                                               4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                  57
  REGIONAL LYMPH NODE                                       164
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                     vv
clus                  I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  LOC728819 MUTATED             0       0       0        0        0        0
  LOC728819 WILD-TYPE          10       6      22       10       24       17
                     vv
clus                  STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  LOC728819 MUTATED           0         1         0         3          0
  LOC728819 WILD-TYPE        10        13         9        28         13
                     vv
clus                  STAGE IIIB STAGE IIIC STAGE IV
  LOC728819 MUTATED            1          1        0
  LOC728819 WILD-TYPE         21         43       12
D79V5, multiclass
             clus
vv            LOC728819 MUTATED LOC728819 WILD-TYPE
  I OR II NOS                 0                  10
  STAGE 0                     0                   6
  STAGE I                     0                  22
  STAGE IA                    0                  10
  STAGE IB                    0                  24
  STAGE II                    0                  17
  STAGE IIA                   0                  10
  STAGE IIB                   1                  13
  STAGE IIC                   0                   9
  STAGE III                   3                  28
  STAGE IIIA                  0                  13
  STAGE IIIB                  1                  21
  STAGE IIIC                  1                  43
  STAGE IV                    0                  12
[1] 14  2
[1] 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
  LOC728819 MUTATED       4  0  1  0
  LOC728819 WILD-TYPE    47 58 52 55
D79V6, multiclass
       clus
vv      LOC728819 MUTATED LOC728819 WILD-TYPE
  T0+T1                 4                  47
  T2                    0                  58
  T3                    1                  52
  T4                    0                  55
[1] 4 2
[1] TRUE
[1] "dimension 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
  LOC728819 MUTATED     2   1   3   1
  LOC728819 WILD-TYPE 136  47  29  32
D79V7, multiclass
    clus
vv   LOC728819 MUTATED LOC728819 WILD-TYPE
  N0                 2                 136
  N1                 1                  47
  N2                 3                  29
  N3                 1                  32
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                     vv
clus                   M0  M1 M1A M1B M1C
  LOC728819 MUTATED     7   0   0   0   0
  LOC728819 WILD-TYPE 233   4   2   2   5
D79V8, multiclass
     clus
vv    LOC728819 MUTATED LOC728819 WILD-TYPE
  M0                  7                 233
  M1                  0                   4
  M1A                 0                   2
  M1B                 0                   2
  M1C                 0                   5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D79V9, binary
                     cls
clus                    0   1
  LOC728819 MUTATED     1   1
  LOC728819 WILD-TYPE 101  66
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  LOC728819 MUTATED      1    1
  LOC728819 WILD-TYPE  101   66
     clus
vv    LOC728819 MUTATED LOC728819 WILD-TYPE
  NO                  1                 101
  YES                 1                  66
[1] 2 2
[1] FALSE
D79V10, binary
                     cls
clus                    0   1
  LOC728819 MUTATED     3   4
  LOC728819 WILD-TYPE  30 231
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  LOC728819 MUTATED      3    4
  LOC728819 WILD-TYPE   30  231
     clus
vv    LOC728819 MUTATED LOC728819 WILD-TYPE
  NO                  3                  30
  YES                 4                 231
[1] 2 2
[1] FALSE
D79V11, continuous
[1] "Remove cluster labels:" "LOC728819 MUTATED"     
clus
  LOC728819 MUTATED LOC728819 WILD-TYPE 
                  2                 198 
         TCGA-D3-A1Q3          TCGA-D3-A1Q4          TCGA-D3-A1Q6 
"LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" 
         TCGA-D3-A1Q7          TCGA-D3-A1Q9          TCGA-D3-A1QA 
"LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" 
         TCGA-D3-A2J7          TCGA-D3-A2J8          TCGA-D3-A2J9 
"LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" 
         TCGA-D3-A2JA          TCGA-D3-A2JD          TCGA-D3-A2JF 
"LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" 
         TCGA-D3-A2JG          TCGA-D3-A2JH          TCGA-D3-A2JK 
"LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" 
         TCGA-D3-A3BZ          TCGA-D3-A3C6          TCGA-D3-A3CB 
"LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" 
         TCGA-D3-A3CC          TCGA-D3-A3CF          TCGA-D3-A3ML 
"LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" 
         TCGA-D3-A3MU          TCGA-D3-A3MV          TCGA-D3-A51E 
"LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" 
         TCGA-D3-A51F          TCGA-D3-A51G          TCGA-D3-A51H 
"LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" 
         TCGA-D3-A51K          TCGA-D3-A51R          TCGA-D3-A51T 
"LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" 
         TCGA-D3-A5GN          TCGA-D3-A5GO          TCGA-D3-A5GR 
"LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" 
         TCGA-D3-A5GS          TCGA-D3-A5GU          TCGA-D9-A3Z1 
"LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" 
         TCGA-D9-A3Z3          TCGA-D9-A6E9          TCGA-D9-A6EA 
"LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" 
         TCGA-D9-A6EC          TCGA-DA-A1HW          TCGA-DA-A1HY 
"LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" 
         TCGA-DA-A1I0          TCGA-DA-A1I4          TCGA-DA-A1I5 
"LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" 
         TCGA-DA-A1I8          TCGA-DA-A1IA          TCGA-DA-A1IB 
"LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" 
         TCGA-DA-A1IC          TCGA-DA-A3F2          TCGA-DA-A3F5 
"LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" 
         TCGA-DA-A3F8          TCGA-EB-A5SH          TCGA-EB-A5UL 
"LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" 
         TCGA-EB-A5UN          TCGA-EE-A17X          TCGA-EE-A17Y 
"LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" 
         TCGA-EE-A17Z          TCGA-EE-A180          TCGA-EE-A181 
"LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" 
         TCGA-EE-A182          TCGA-EE-A184          TCGA-EE-A185 
"LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" 
         TCGA-EE-A20B          TCGA-EE-A20F          TCGA-EE-A20H 
"LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" 
         TCGA-EE-A29A          TCGA-EE-A29B          TCGA-EE-A29C 
"LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" 
         TCGA-EE-A29D          TCGA-EE-A29E          TCGA-EE-A29G 
"LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" 
         TCGA-EE-A29H          TCGA-EE-A29L          TCGA-EE-A29M 
"LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" 
         TCGA-EE-A29P          TCGA-EE-A29Q          TCGA-EE-A29R 
"LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" 
         TCGA-EE-A29S          TCGA-EE-A29V          TCGA-EE-A29W 
"LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" 
         TCGA-EE-A29X          TCGA-EE-A2A0          TCGA-EE-A2A1 
"LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" 
         TCGA-EE-A2A2          TCGA-EE-A2A5          TCGA-EE-A2A6 
"LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" 
         TCGA-EE-A2GB          TCGA-EE-A2GC          TCGA-EE-A2GD 
"LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" 
         TCGA-EE-A2GE          TCGA-EE-A2GH          TCGA-EE-A2GI 
"LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" 
         TCGA-EE-A2GJ          TCGA-EE-A2GK          TCGA-EE-A2GL 
"LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" 
         TCGA-EE-A2GM          TCGA-EE-A2GN          TCGA-EE-A2GO 
"LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" 
         TCGA-EE-A2GP          TCGA-EE-A2GR          TCGA-EE-A2GS 
"LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" 
         TCGA-EE-A2GT          TCGA-EE-A2GU          TCGA-EE-A2M5 
"LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" 
         TCGA-EE-A2M6          TCGA-EE-A2M7          TCGA-EE-A2M8 
"LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" 
         TCGA-EE-A2MC          TCGA-EE-A2MD          TCGA-EE-A2ME 
"LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" 
         TCGA-EE-A2MG          TCGA-EE-A2MH          TCGA-EE-A2MI 
"LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" 
         TCGA-EE-A2MJ          TCGA-EE-A2MK          TCGA-EE-A2ML 
"LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" 
         TCGA-EE-A2MM          TCGA-EE-A2MN          TCGA-EE-A2MP 
"LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" 
         TCGA-EE-A2MQ          TCGA-EE-A2MR          TCGA-EE-A2MS 
"LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" 
         TCGA-EE-A2MT          TCGA-EE-A2MU          TCGA-EE-A3AE 
"LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" 
         TCGA-EE-A3AH          TCGA-EE-A3J3          TCGA-EE-A3J4 
"LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" 
         TCGA-EE-A3J5          TCGA-EE-A3J7          TCGA-EE-A3J8 
"LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" 
         TCGA-EE-A3JA          TCGA-EE-A3JE          TCGA-EE-A3JH 
"LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" 
         TCGA-EE-A3JI          TCGA-ER-A197          TCGA-ER-A198 
"LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" 
         TCGA-ER-A199          TCGA-ER-A19C          TCGA-ER-A19D 
"LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" 
         TCGA-ER-A19E          TCGA-ER-A19F          TCGA-ER-A19G 
"LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" 
         TCGA-ER-A19H          TCGA-ER-A19M          TCGA-ER-A19Q 
"LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" 
         TCGA-ER-A19W          TCGA-ER-A2NC          TCGA-ER-A2ND 
"LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" 
         TCGA-ER-A2NF          TCGA-ER-A2NG          TCGA-ER-A2NH 
"LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" 
         TCGA-ER-A3ET          TCGA-ER-A3EV          TCGA-ER-A3PL 
"LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" 
         TCGA-FR-A3YN          TCGA-FR-A44A          TCGA-FS-A1YW 
"LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" 
         TCGA-FS-A1YX          TCGA-FS-A1YY          TCGA-FS-A1Z0 
"LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" 
         TCGA-FS-A1Z4          TCGA-FS-A1Z7          TCGA-FS-A1ZA 
"LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" 
         TCGA-FS-A1ZB          TCGA-FS-A1ZD          TCGA-FS-A1ZE 
"LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" 
         TCGA-FS-A1ZF          TCGA-FS-A1ZG          TCGA-FS-A1ZH 
"LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" 
         TCGA-FS-A1ZJ          TCGA-FS-A1ZK          TCGA-FS-A1ZM 
"LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" 
         TCGA-FS-A1ZP          TCGA-FS-A1ZR          TCGA-FS-A1ZS 
"LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" 
         TCGA-FS-A1ZT          TCGA-FS-A1ZU          TCGA-FS-A1ZW 
"LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" 
         TCGA-FS-A1ZY          TCGA-FS-A1ZZ          TCGA-FS-A4F0 
"LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" 
         TCGA-FS-A4F4          TCGA-FS-A4F5          TCGA-FS-A4F8 
"LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" 
         TCGA-FS-A4F9          TCGA-FS-A4FB          TCGA-FS-A4FC 
"LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" 
         TCGA-FS-A4FD          TCGA-FW-A3TV          TCGA-GF-A6C8 
"LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" 
         TCGA-GN-A262          TCGA-GN-A264          TCGA-GN-A267 
"LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" 
         TCGA-GN-A268          TCGA-GN-A26A          TCGA-GN-A26D 
"LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" 
D79V12, binary
                     cls
clus                    0   1
  LOC728819 MUTATED     3   4
  LOC728819 WILD-TYPE 100 161
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  LOC728819 MUTATED      3    4
  LOC728819 WILD-TYPE  100  161
        clus
vv       LOC728819 MUTATED LOC728819 WILD-TYPE
  FEMALE                 3                 100
  MALE                   4                 161
[1] 2 2
[1] FALSE
                     vv
clus                  ASIAN BLACK OR AFRICAN AMERICAN WHITE
  LOC728819 MUTATED       0                         0     7
  LOC728819 WILD-TYPE     3                         1   257
D79V13, multiclass
                           clus
vv                          LOC728819 MUTATED LOC728819 WILD-TYPE
  ASIAN                                     0                   3
  BLACK OR AFRICAN AMERICAN                 0                   1
  WHITE                                     7                 257
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D79V14, binary
                     cls
clus                    0   1
  LOC728819 MUTATED     0   7
  LOC728819 WILD-TYPE   3 254
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  LOC728819 MUTATED      0    7
  LOC728819 WILD-TYPE    3  254
                        clus
vv                       LOC728819 MUTATED LOC728819 WILD-TYPE
  HISPANIC OR LATINO                     0                   3
  NOT HISPANIC OR LATINO                 7                 254
[1] 2 2
[1] FALSE

Clustering(80) Variable = LACRT MUTATION ANALYSIS
D80V1, survival
                 sevent
clus2               0   1
  LACRT MUTATED     6   2
  LACRT WILD-TYPE 122 128
  LACRT MUTATED LACRT WILD-TYPE 
              8             250 
  LACRT MUTATED LACRT WILD-TYPE 
              2             128 
$`LACRT MUTATED`
TCGA-D3-A2JN TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GO TCGA-EE-A29M TCGA-EE-A2GR 
       56.19        20.48        13.94        47.87        27.12         1.15 
TCGA-FW-A3R5 TCGA-GN-A266 
        0.99        10.13 

$`LACRT WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.47         8.52       111.09        32.42        70.16       110.79 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       28.08        22.55        45.83        81.24        10.29        85.32 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
        8.38        21.14        88.50        68.22        69.90        11.41 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JO 
       30.87         7.50        36.16         6.31        92.42        64.44 
TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB 
       45.11       114.67        15.25        46.98        46.32        82.29 
TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR 
       61.38        13.32        24.00         6.31         9.34       103.59 
TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J 
       26.37         5.39        80.22        42.71        15.09        41.10 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU 
       17.72         8.84        52.01         1.55         6.97        23.11 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1HV 
        4.01         2.89         9.90        11.31        13.22        48.79 
TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 
       35.80        51.12        10.03        39.19        13.68         9.99 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC 
       44.52        36.69        25.15         4.93        22.36         6.64 
TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R 
       19.36         7.00        17.56        14.83        13.15         0.20 
TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z 
        0.00         0.00        13.22        11.57        10.55         6.31 
TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 
        8.12         1.12         1.35        12.20         5.13         4.31 
TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A 
       36.07         4.34         5.13         9.21         1.18         7.99 
TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H 
        9.90        37.97        11.15        38.63         8.55         4.41 
TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S 
        1.08         9.50        12.03         8.09         8.84         9.99 
TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 
        2.43         8.68         8.09        11.31        49.22        23.90 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE 
        9.67         8.94        39.39        34.29        17.98        34.92 
TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM 
       47.21        30.08        19.43        16.01        35.54        28.31 
TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU 
       33.83        30.84         5.42        13.02        34.98        36.33 
TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD 
        8.84        98.27         2.70         6.18        47.51         9.53 
TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK 
       29.46        44.25         7.96        14.56        63.42       111.78 
TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR 
      111.91        56.02        25.08        26.99        21.60        29.65 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC 
       27.16        23.05         5.56       124.31       122.73        25.84 
TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 
        3.68        30.15        13.81        15.95        12.72         3.22 
TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JD 
       22.92        21.60        21.60        16.14        22.22        27.35 
TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 
        0.46        13.94        33.60        31.40        18.61        12.95 
TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D 
       38.40         5.72        76.41        25.18         3.78         3.52 
TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L 
       11.90        11.11       114.15        34.88         4.21        13.45 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W 
       28.60        42.84        34.68         9.57        36.07        17.72 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG 
       78.44        11.80         1.87         1.51        13.08        12.62 
TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN 
       11.74         9.04         6.58        22.49         1.71        18.41 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 
       85.74         4.90        64.47         3.45        11.01        23.80 
TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC 
       14.24        15.52         7.33         7.30         3.39        20.38 
TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ 
        8.22        19.53        11.08         7.17        30.87        12.92 
TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS 
       12.89        47.38        52.08         8.65         8.81        49.15 
TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 
       40.64         8.68        27.39         0.82         5.23        53.85 
TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC 
        7.36        28.73        14.20        10.78         5.98         6.41 
TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
        2.27         0.20         0.13         0.16         0.43         9.90 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 
        7.23        12.85        24.85        31.33        84.72        16.24 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS 
       15.42        12.16        14.70         5.79 

  LACRT MUTATED LACRT WILD-TYPE 
           0.99            0.00 
  LACRT MUTATED LACRT WILD-TYPE 
          56.19          124.31 
  LACRT MUTATED LACRT WILD-TYPE 
         17.210          14.765 
[1] "1.0 - 56.2 (17.2)"  "0.0 - 124.3 (14.8)"
[1] "hr=" "1.9"
D80V2, survival
                 sevent
clus2               0   1
  LACRT MUTATED     6   2
  LACRT WILD-TYPE 126 129
  LACRT MUTATED LACRT WILD-TYPE 
              8             255 
  LACRT MUTATED LACRT WILD-TYPE 
              2             129 
$`LACRT MUTATED`
TCGA-D3-A2JN TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GO TCGA-EE-A29M TCGA-EE-A2GR 
       56.19        51.68        15.06       137.92        44.35        14.30 
TCGA-FW-A3R5 TCGA-GN-A266 
       22.92        10.13 

$`LACRT WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.57        16.67       112.04       112.57        71.80       133.25 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       28.08        31.59        90.90        95.74        43.43       103.10 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
       65.49        23.77       115.53       168.00        69.90        11.87 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JO 
       48.76       113.52        42.08        12.10       171.58        66.08 
TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB 
       45.11       130.72        58.06        46.98        46.32       166.52 
TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR 
       86.93        60.23        24.53        13.87         9.34       103.59 
TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J 
       39.75        21.47       161.85        43.69        40.14       131.90 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU 
       18.38        10.03       135.75       166.19         7.43       125.19 
TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 
      151.53        54.67         3.65         6.41        11.34         3.25 
TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY 
        9.90        25.18        66.25        48.89        36.03       117.21 
TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 
       20.38       194.83       176.55        35.93       107.34        61.18 
TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 
       53.92        65.92        23.44        68.09        28.60        10.49 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH 
      215.44        15.68        13.87        10.16        45.11        35.01 
TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 
        3.55        52.01        29.82        27.22         8.65        94.98 
TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B 
       33.73        14.70        26.89        68.15         4.96       109.64 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B 
      151.27        78.87       168.26        13.55        63.35        80.61 
TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L 
       47.84        13.97        39.62        72.07        32.19         2.60 
TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V 
       18.61        56.42        37.35        14.47        55.92        25.87 
TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 
      171.55        17.92        46.82       102.90        24.43        39.29 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH 
       58.75        47.54        67.43       314.56       135.95       208.04 
TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN 
       48.72        89.33        54.74        79.66        75.48        90.97 
TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 
      101.95        13.91        55.59        44.88        94.82        21.67 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME 
      129.27        28.83        19.76        61.51        47.28       103.27 
TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML 
      103.20        16.96       204.66        96.23       144.76       203.05 
TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS 
      167.90        47.54       248.65        43.23       103.56       136.47 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD 
       41.59        53.26       124.31       122.73        25.84         3.68 
TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 
       54.51        13.81        23.47       138.81       172.18       127.20 
TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE 
       36.95        64.08        34.32        53.19        27.35        33.40 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 
      101.79       148.08        31.40        35.44        13.94        50.76 
TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E 
        9.17        77.75        98.40        48.89        12.59        13.02 
TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M 
       26.37       268.93       152.35         6.44       131.51        61.05 
TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 
       44.05       162.08        50.89        37.25       148.18        79.99 
TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH 
       43.82        23.34        20.15        16.37        31.27        32.05 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A 
      247.04        80.32        46.98        33.21        92.98       174.21 
TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
        4.90       216.92        48.59       228.59       202.65        20.91 
TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD 
       28.08         7.79        27.72        48.85       357.37        53.52 
TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK 
       40.27        15.45         9.70        32.75        47.38        23.93 
TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT 
      101.26        74.73       133.55        11.41       148.80        53.16 
TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 
       26.56        49.48        27.09        27.02        77.82        66.67 
TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD 
       28.73       174.84        12.43        26.73        49.45        77.88 
TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
        0.20        47.54         0.16         2.40         9.90         7.23 
TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 
       14.04       120.46       117.93        84.72        64.44        62.79 
TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS 
       32.48        39.58         6.67 

  LACRT MUTATED LACRT WILD-TYPE 
          10.13            0.16 
  LACRT MUTATED LACRT WILD-TYPE 
         137.92          357.37 
  LACRT MUTATED LACRT WILD-TYPE 
         33.635          48.720 
[1] "10.1 - 137.9 (33.6)" "0.2 - 357.4 (48.7)" 
[1] "hr=" "1.3"
D80V3, continuous
                 vv
clus              DISTANT METASTASIS PRIMARY TUMOR
  LACRT MUTATED                    2             0
  LACRT WILD-TYPE                 33             4
                 vv
clus              REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  LACRT MUTATED                                           2                   5
  LACRT WILD-TYPE                                        56                 165
D80V4, multiclass
                                           clus
vv                                          LACRT MUTATED LACRT WILD-TYPE
  DISTANT METASTASIS                                    2              33
  PRIMARY TUMOR                                         0               4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE             2              56
  REGIONAL LYMPH NODE                                   5             165
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  LACRT MUTATED             1       0       0        0        1        2
  LACRT WILD-TYPE           9       6      22       10       23       15
                 vv
clus              STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  LACRT MUTATED           1         0         0         2          0          0
  LACRT WILD-TYPE         9        14         9        29         13         22
                 vv
clus              STAGE IIIC STAGE IV
  LACRT MUTATED            1        0
  LACRT WILD-TYPE         43       12
D80V5, multiclass
             clus
vv            LACRT MUTATED LACRT WILD-TYPE
  I OR II NOS             1               9
  STAGE 0                 0               6
  STAGE I                 0              22
  STAGE IA                0              10
  STAGE IB                1              23
  STAGE II                2              15
  STAGE IIA               1               9
  STAGE IIB               0              14
  STAGE IIC               0               9
  STAGE III               2              29
  STAGE IIIA              0              13
  STAGE IIIB              0              22
  STAGE IIIC              1              43
  STAGE IV                0              12
[1] 14  2
[1] 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
  LACRT MUTATED       1  2  1  3
  LACRT WILD-TYPE    50 56 52 52
D80V6, multiclass
       clus
vv      LACRT MUTATED LACRT WILD-TYPE
  T0+T1             1              50
  T2                2              56
  T3                1              52
  T4                3              52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  LACRT MUTATED     5   2   1   0
  LACRT WILD-TYPE 133  46  31  33
D80V7, multiclass
    clus
vv   LACRT MUTATED LACRT WILD-TYPE
  N0             5             133
  N1             2              46
  N2             1              31
  N3             0              33
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               M0  M1 M1A M1B M1C
  LACRT MUTATED     8   0   0   0   0
  LACRT WILD-TYPE 232   4   2   2   5
D80V8, multiclass
     clus
vv    LACRT MUTATED LACRT WILD-TYPE
  M0              8             232
  M1              0               4
  M1A             0               2
  M1B             0               2
  M1C             0               5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D80V9, binary
                 cls
clus                0   1
  LACRT MUTATED     2   1
  LACRT WILD-TYPE 100  66
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LACRT MUTATED      2    1
  LACRT WILD-TYPE  100   66
     clus
vv    LACRT MUTATED LACRT WILD-TYPE
  NO              2             100
  YES             1              66
[1] 2 2
[1] FALSE
D80V10, binary
                 cls
clus                0   1
  LACRT MUTATED     2   7
  LACRT WILD-TYPE  31 228
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LACRT MUTATED      2    7
  LACRT WILD-TYPE   31  228
     clus
vv    LACRT MUTATED LACRT WILD-TYPE
  NO              2              31
  YES             7             228
[1] 2 2
[1] FALSE
D80V11, continuous
D80V12, binary
                 cls
clus                0   1
  LACRT MUTATED     4   5
  LACRT WILD-TYPE  99 160
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LACRT MUTATED      4    5
  LACRT WILD-TYPE   99  160
        clus
vv       LACRT MUTATED LACRT WILD-TYPE
  FEMALE             4              99
  MALE               5             160
[1] 2 2
[1] FALSE
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  LACRT MUTATED       0                         0     9
  LACRT WILD-TYPE     3                         1   255
D80V13, multiclass
                           clus
vv                          LACRT MUTATED LACRT WILD-TYPE
  ASIAN                                 0               3
  BLACK OR AFRICAN AMERICAN             0               1
  WHITE                                 9             255
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D80V14, binary
                 cls
clus                0   1
  LACRT MUTATED     0   9
  LACRT WILD-TYPE   3 252
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LACRT MUTATED      0    9
  LACRT WILD-TYPE    3  252
                        clus
vv                       LACRT MUTATED LACRT WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO             9             252
[1] 2 2
[1] FALSE

Clustering(81) Variable = RPGRIP1 MUTATION ANALYSIS
D81V1, survival
                   sevent
clus2                 0   1
  RPGRIP1 MUTATED    14   8
  RPGRIP1 WILD-TYPE 114 122
  RPGRIP1 MUTATED RPGRIP1 WILD-TYPE 
               22               236 
  RPGRIP1 MUTATED RPGRIP1 WILD-TYPE 
                8               122 
$`RPGRIP1 MUTATED`
TCGA-D3-A51T TCGA-D9-A6EC TCGA-DA-A1IC TCGA-DA-A3F8 TCGA-EB-A5UN TCGA-EE-A29D 
       13.94        13.22         6.64        14.83        13.22        11.15 
TCGA-EE-A29E TCGA-EE-A29R TCGA-EE-A2GC TCGA-EE-A2M5 TCGA-EE-A2MI TCGA-EE-A2MR 
       38.63         8.84        34.29         8.84        14.56        29.65 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3J5 TCGA-EE-A3JD TCGA-EE-A3JI TCGA-FS-A1ZP 
       27.16        23.05        21.60        27.35        33.60        52.08 
TCGA-FS-A4F0 TCGA-FS-A4FD TCGA-FW-A3R5 TCGA-GN-A267 
       53.85         2.27         0.99        16.24 

$`RPGRIP1 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.47         8.52       111.09        32.42        70.16       110.79 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       28.08        22.55        45.83        81.24        10.29        85.32 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
        8.38        21.14        88.50        68.22        69.90        11.41 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       30.87         7.50        36.16         6.31        92.42        56.19 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 
       64.44        45.11       114.67        15.25        46.98        46.32 
TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO 
       82.29        61.38        13.32        24.00         6.31         9.34 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H 
      103.59        26.37         5.39        80.22        42.71        15.09 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A5GN TCGA-D3-A5GO 
       41.10        17.72         8.84        20.48        52.01        47.87 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 
        1.55         6.97        23.11         4.01         2.89         9.90 
TCGA-D9-A6EA TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 
       11.31        48.79        35.80        51.12        10.03        39.19 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA 
       13.68         9.99        44.52        36.69        25.15         4.93 
TCGA-DA-A1IB TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-EB-A44Q TCGA-EB-A44R 
       22.36        19.36         7.00        17.56        13.15         0.20 
TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 
        0.00         0.00        11.57        10.55         6.31         8.12 
TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B 
        1.12         1.35        12.20         5.13         4.31        36.07 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B 
        4.34         5.13         9.21         1.18         7.99         9.90 
TCGA-EE-A29C TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N 
       37.97         8.55         4.41         1.08        27.12         9.50 
TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X 
       12.03         8.09         9.99         2.43         8.68         8.09 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB 
       11.31        49.22        23.90         9.67         8.94        39.39 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK 
       17.98        34.92        47.21        30.08        19.43        16.01 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR 
       35.54        28.31        33.83        30.84         5.42         1.15 
TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 
       13.02        34.98        36.33        98.27         2.70         6.18 
TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MJ 
       47.51         9.53        29.46        44.25         7.96        63.42 
TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ 
      111.78       111.91        56.02        25.08        26.99        21.60 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE 
        5.56       124.31       122.73        25.84         3.68        30.15 
TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 
       13.81        15.95        12.72         3.22        22.92        21.60 
TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A195 
       16.14        22.22         0.46        13.94        31.40        18.61 
TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C 
       12.95        38.40         5.72        76.41        25.18         3.78 
TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J 
        3.52        11.90        11.11       114.15        34.88         4.21 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S 
       13.45        28.60        42.84        34.68         9.57        36.07 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF 
       17.72        78.44        11.80         1.87         1.51        13.08 
TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL 
       12.62        11.74         9.04         6.58        22.49         1.71 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY 
       18.41        85.74         4.90        64.47         3.45        11.01 
TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB 
       23.80        14.24        15.52         7.33         7.30         3.39 
TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH 
       20.38         8.22        19.53        11.08         7.17        30.87 
TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS 
       12.92        12.89        47.38         8.65         8.81        49.15 
TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F4 
       40.64         8.68        27.39         0.82         5.23         7.36 
TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FW-A3I3 
       28.73        14.20        10.78         5.98         6.41         0.20 
TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 
        0.13         0.16         0.43         9.90         7.23        12.85 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A268 TCGA-GN-A26A 
       24.85        31.33        84.72        10.13        15.42        12.16 
TCGA-GN-A26D TCGA-QB-A6FS 
       14.70         5.79 

  RPGRIP1 MUTATED RPGRIP1 WILD-TYPE 
             0.99              0.00 
  RPGRIP1 MUTATED RPGRIP1 WILD-TYPE 
            53.85            124.31 
  RPGRIP1 MUTATED RPGRIP1 WILD-TYPE 
           15.535            14.470 
[1] "1.0 - 53.9 (15.5)"  "0.0 - 124.3 (14.5)"
[1] "hr=" "1.4"
D81V2, survival
                   sevent
clus2                 0   1
  RPGRIP1 MUTATED    15   8
  RPGRIP1 WILD-TYPE 117 123
  RPGRIP1 MUTATED RPGRIP1 WILD-TYPE 
               23               240 
  RPGRIP1 MUTATED RPGRIP1 WILD-TYPE 
                8               123 
$`RPGRIP1 MUTATED`
TCGA-D3-A51T TCGA-D9-A1JW TCGA-D9-A6EC TCGA-DA-A1IC TCGA-DA-A3F8 TCGA-EB-A5UN 
       15.06         3.65        66.25        68.09        15.68        52.01 
TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29R TCGA-EE-A2GC TCGA-EE-A2M5 TCGA-EE-A2MI 
       13.97        39.62        14.47        67.43        21.67       204.66 
TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3J5 TCGA-EE-A3JD TCGA-EE-A3JI 
      103.56       136.47        41.59        36.95        27.35       148.08 
TCGA-FS-A1ZP TCGA-FS-A4F0 TCGA-FS-A4FD TCGA-FW-A3R5 TCGA-GN-A267 
       74.73        77.82        77.88        22.92        64.44 

$`RPGRIP1 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.57        16.67       112.04       112.57        71.80       133.25 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       28.08        31.59        90.90        95.74        43.43       103.10 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
       65.49        23.77       115.53       168.00        69.90        11.87 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       48.76       113.52        42.08        12.10       171.58        56.19 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 
       66.08        45.11       130.72        58.06        46.98        46.32 
TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO 
      166.52        86.93        60.23        24.53        13.87         9.34 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H 
      103.59        39.75        21.47       161.85        43.69        40.14 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A5GN TCGA-D3-A5GO 
      131.90        18.38        10.03        51.68       135.75       137.92 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JX 
      166.19         7.43       125.19       151.53        54.67         6.41 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-DA-A1HV TCGA-DA-A1HW 
       11.34         3.25         9.90        25.18        48.89        36.03 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 
      117.21        20.38       194.83       176.55        35.93       107.34 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A3F2 TCGA-DA-A3F3 
       61.18        53.92        65.92        23.44        28.60        10.49 
TCGA-DA-A3F5 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL 
      215.44        13.87        10.16        45.11        35.01         3.55 
TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 
       29.82        27.22         8.65        94.98        33.73        14.70 
TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F 
       26.89        68.15         4.96       109.64       151.27        78.87 
TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29G 
      168.26        13.55        63.35        80.61        47.84        72.07 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
       32.19         2.60        44.35        18.61        56.42        37.35 
TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 
       55.92        25.87       171.55        17.92        46.82       102.90 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE 
       24.43        39.29        58.75        47.54       314.56       135.95 
TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM 
      208.04        48.72        89.33        54.74        79.66        75.48 
TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT 
       90.97       101.95        13.91        14.30        55.59        44.88 
TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD 
       94.82       129.27        28.83        19.76        61.51        47.28 
TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML 
      103.27       103.20        16.96        96.23       144.76       203.05 
TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MU TCGA-EE-A3AA 
      167.90        47.54       248.65        43.23        53.26       124.31 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG 
      122.73        25.84         3.68        54.51        13.81        23.47 
TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA 
      138.81       172.18       127.20        64.08        34.32        53.19 
TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 
       33.40       101.79        31.40        35.44        13.94        50.76 
TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E 
        9.17        77.75        98.40        48.89        12.59        13.02 
TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M 
       26.37       268.93       152.35         6.44       131.51        61.05 
TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 
       44.05       162.08        50.89        37.25       148.18        79.99 
TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH 
       43.82        23.34        20.15        16.37        31.27        32.05 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A 
      247.04        80.32        46.98        33.21        92.98       174.21 
TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
        4.90       216.92        48.59       228.59       202.65        20.91 
TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD 
       28.08         7.79        27.72        48.85       357.37        53.52 
TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK 
       40.27        15.45         9.70        32.75        47.38        23.93 
TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU 
      101.26       133.55        11.41       148.80        53.16        26.56 
TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 
       49.48        27.09        27.02        66.67        28.73       174.84 
TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV 
       12.43        26.73        49.45         0.20        47.54         0.16 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 
        2.40         9.90         7.23        14.04       120.46       117.93 
TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS 
       84.72        10.13        62.79        32.48        39.58         6.67 

  RPGRIP1 MUTATED RPGRIP1 WILD-TYPE 
             3.65              0.16 
  RPGRIP1 MUTATED RPGRIP1 WILD-TYPE 
           204.66            357.37 
  RPGRIP1 MUTATED RPGRIP1 WILD-TYPE 
           52.010            48.215 
[1] "3.6 - 204.7 (52.0)" "0.2 - 357.4 (48.2)"
[1] "hr=" "1.4"
D81V3, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  RPGRIP1 MUTATED                    1             1
  RPGRIP1 WILD-TYPE                 34             3
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  RPGRIP1 MUTATED                                           3
  RPGRIP1 WILD-TYPE                                        55
                   vv
clus                REGIONAL LYMPH NODE
  RPGRIP1 MUTATED                    18
  RPGRIP1 WILD-TYPE                 152
D81V4, multiclass
                                           clus
vv                                          RPGRIP1 MUTATED RPGRIP1 WILD-TYPE
  DISTANT METASTASIS                                      1                34
  PRIMARY TUMOR                                           1                 3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE               3                55
  REGIONAL LYMPH NODE                                    18               152
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  RPGRIP1 MUTATED             0       0       3        0        1        2
  RPGRIP1 WILD-TYPE          10       6      19       10       23       15
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  RPGRIP1 MUTATED           0         3         1         3          2
  RPGRIP1 WILD-TYPE        10        11         8        28         11
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  RPGRIP1 MUTATED            3          4        0
  RPGRIP1 WILD-TYPE         19         40       12
D81V5, multiclass
             clus
vv            RPGRIP1 MUTATED RPGRIP1 WILD-TYPE
  I OR II NOS               0                10
  STAGE 0                   0                 6
  STAGE I                   3                19
  STAGE IA                  0                10
  STAGE IB                  1                23
  STAGE II                  2                15
  STAGE IIA                 0                10
  STAGE IIB                 3                11
  STAGE IIC                 1                 8
  STAGE III                 3                28
  STAGE IIIA                2                11
  STAGE IIIB                3                19
  STAGE IIIC                4                40
  STAGE IV                  0                12
[1] 14  2
[1] 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
  RPGRIP1 MUTATED       1  6  8  6
  RPGRIP1 WILD-TYPE    50 52 45 49
D81V6, multiclass
       clus
vv      RPGRIP1 MUTATED RPGRIP1 WILD-TYPE
  T0+T1               1                50
  T2                  6                52
  T3                  8                45
  T4                  6                49
[1] 4 2
[1] TRUE
[1] "dimension 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
  RPGRIP1 MUTATED     9   7   5   1
  RPGRIP1 WILD-TYPE 129  41  27  32
D81V7, multiclass
    clus
vv   RPGRIP1 MUTATED RPGRIP1 WILD-TYPE
  N0               9               129
  N1               7                41
  N2               5                27
  N3               1                32
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1 M1A M1B M1C
  RPGRIP1 MUTATED    23   0   0   0   0
  RPGRIP1 WILD-TYPE 217   4   2   2   5
D81V8, multiclass
     clus
vv    RPGRIP1 MUTATED RPGRIP1 WILD-TYPE
  M0               23               217
  M1                0                 4
  M1A               0                 2
  M1B               0                 2
  M1C               0                 5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D81V9, binary
                   cls
clus                 0  1
  RPGRIP1 MUTATED   13  5
  RPGRIP1 WILD-TYPE 89 62
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RPGRIP1 MUTATED     13    5
  RPGRIP1 WILD-TYPE   89   62
     clus
vv    RPGRIP1 MUTATED RPGRIP1 WILD-TYPE
  NO               13                89
  YES               5                62
[1] 2 2
[1] FALSE
D81V10, binary
                   cls
clus                  0   1
  RPGRIP1 MUTATED     1  22
  RPGRIP1 WILD-TYPE  32 213
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RPGRIP1 MUTATED      1   22
  RPGRIP1 WILD-TYPE   32  213
     clus
vv    RPGRIP1 MUTATED RPGRIP1 WILD-TYPE
  NO                1                32
  YES              22               213
[1] 2 2
[1] FALSE
D81V11, continuous
D81V12, binary
                   cls
clus                  0   1
  RPGRIP1 MUTATED     4  19
  RPGRIP1 WILD-TYPE  99 146
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RPGRIP1 MUTATED      4   19
  RPGRIP1 WILD-TYPE   99  146
        clus
vv       RPGRIP1 MUTATED RPGRIP1 WILD-TYPE
  FEMALE               4                99
  MALE                19               146
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RPGRIP1 MUTATED       0                         0    23
  RPGRIP1 WILD-TYPE     3                         1   241
D81V13, multiclass
                           clus
vv                          RPGRIP1 MUTATED RPGRIP1 WILD-TYPE
  ASIAN                                   0                 3
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  23               241
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D81V14, binary
                   cls
clus                  0   1
  RPGRIP1 MUTATED     0  23
  RPGRIP1 WILD-TYPE   3 238
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RPGRIP1 MUTATED      0   23
  RPGRIP1 WILD-TYPE    3  238
                        clus
vv                       RPGRIP1 MUTATED RPGRIP1 WILD-TYPE
  HISPANIC OR LATINO                   0                 3
  NOT HISPANIC OR LATINO              23               238
[1] 2 2
[1] FALSE

Clustering(82) Variable = THEMIS MUTATION ANALYSIS
D82V1, survival
                  sevent
clus2                0   1
  THEMIS MUTATED    18  13
  THEMIS WILD-TYPE 110 117
  THEMIS MUTATED THEMIS WILD-TYPE 
              31              227 
  THEMIS MUTATED THEMIS WILD-TYPE 
              13              117 
$`THEMIS MUTATED`
TCGA-D3-A1QA TCGA-D3-A2JL TCGA-D3-A2JO TCGA-D3-A3ML TCGA-D3-A5GO TCGA-DA-A1HV 
       45.83        92.42        64.44         6.31        47.87        48.79 
TCGA-DA-A3F3 TCGA-EE-A17X TCGA-EE-A180 TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29H 
        7.00        11.57         8.12        37.97        11.15         4.41 
TCGA-EE-A29L TCGA-EE-A29Q TCGA-EE-A2GC TCGA-EE-A2GO TCGA-EE-A2M5 TCGA-EE-A2MS 
        1.08         8.09        34.29        30.84         8.84        27.16 
TCGA-EE-A3AE TCGA-EE-A3AH TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3JA TCGA-ER-A193 
       30.15        12.72        21.60        21.60        22.22        31.40 
TCGA-ER-A19A TCGA-ER-A19S TCGA-FS-A1ZA TCGA-FS-A4F9 TCGA-FS-A4FD TCGA-FW-A3R5 
       76.41        36.07         7.30        10.78         2.27         0.99 
TCGA-QB-A6FS 
        5.79 

$`THEMIS WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.47         8.52       111.09        32.42        70.16       110.79 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 
       28.08        22.55        81.24        10.29        85.32         8.38 
TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF 
       21.14        88.50        68.22        69.90        11.41        30.87 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3BZ 
        7.50        36.16         6.31        56.19        45.11       114.67 
TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE 
       15.25        46.98        46.32        82.29        61.38        13.32 
TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E 
       24.00         9.34       103.59        26.37         5.39        80.22 
TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R 
       42.71        15.09        41.10        17.72         8.84        20.48 
TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 
       13.94        52.01         1.55         6.97        23.11         4.01 
TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1HW TCGA-DA-A1HY 
        2.89         9.90        11.31        13.22        35.80        51.12 
TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 
       10.03        39.19        13.68         9.99        44.52        36.69 
TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 
       25.15         4.93        22.36         6.64        19.36        17.56 
TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN 
       14.83        13.15         0.20         0.00         0.00        13.22 
TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 
       10.55         6.31         1.12         1.35        12.20         5.13 
TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I 
        4.31        36.07         4.34         5.13         9.21         1.18 
TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29M TCGA-EE-A29N 
        7.99         9.90        38.63         8.55        27.12         9.50 
TCGA-EE-A29P TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X 
       12.03         8.84         9.99         2.43         8.68         8.09 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB 
       11.31        49.22        23.90         9.67         8.94        39.39 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK 
       17.98        34.92        47.21        30.08        19.43        16.01 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS 
       35.54        28.31        33.83         5.42         1.15        13.02 
TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC 
       34.98        36.33        98.27         2.70         6.18        47.51 
TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ 
        9.53        29.46        44.25         7.96        14.56        63.42 
TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ 
      111.78       111.91        56.02        25.08        26.99        21.60 
TCGA-EE-A2MR TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC 
       29.65        23.05         5.56       124.31       122.73        25.84 
TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J8 
        3.68        13.81        15.95         3.22        22.92        16.14 
TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 
       27.35         0.46        13.94        33.60        18.61        12.95 
TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E 
       38.40         5.72        25.18         3.78         3.52        11.90 
TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M 
       11.11       114.15        34.88         4.21        13.45        28.60 
TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
       42.84        34.68         9.57        17.72        78.44        11.80 
TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES 
        1.87         1.51        13.08        12.62        11.74         9.04 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
        6.58        22.49         1.71        18.41        85.74         4.90 
TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 
       64.47         3.45        11.01        23.80        14.24        15.52 
TCGA-FS-A1Z7 TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF 
        7.33         3.39        20.38         8.22        19.53        11.08 
TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP 
        7.17        30.87        12.92        12.89        47.38        52.08 
TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW 
        8.65         8.81        49.15        40.64         8.68        27.39 
TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 
        0.82         5.23        53.85         7.36        28.73        14.20 
TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY 
        5.98         6.41         0.20         0.13         0.16         0.43 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        9.90         7.23        12.85        24.85        31.33        84.72 
TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D 
       10.13        16.24        15.42        12.16        14.70 

  THEMIS MUTATED THEMIS WILD-TYPE 
            0.99             0.00 
  THEMIS MUTATED THEMIS WILD-TYPE 
           92.42           124.31 
  THEMIS MUTATED THEMIS WILD-TYPE 
            21.6             14.7 
[1] "1.0 - 92.4 (21.6)"  "0.0 - 124.3 (14.7)"
[1] "hr=" "1.2"
D82V2, survival
                  sevent
clus2                0   1
  THEMIS MUTATED    18  13
  THEMIS WILD-TYPE 114 118
  THEMIS MUTATED THEMIS WILD-TYPE 
              31              232 
  THEMIS MUTATED THEMIS WILD-TYPE 
              13              118 
$`THEMIS MUTATED`
TCGA-D3-A1QA TCGA-D3-A2JL TCGA-D3-A2JO TCGA-D3-A3ML TCGA-D3-A5GO TCGA-DA-A1HV 
       90.90       171.58        66.08        13.87       137.92        48.89 
TCGA-DA-A3F3 TCGA-EE-A17X TCGA-EE-A180 TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29H 
       10.49        29.82        94.98        47.84        13.97        32.19 
TCGA-EE-A29L TCGA-EE-A29Q TCGA-EE-A2GC TCGA-EE-A2GO TCGA-EE-A2M5 TCGA-EE-A2MS 
        2.60        37.35        67.43       101.95        21.67       136.47 
TCGA-EE-A3AE TCGA-EE-A3AH TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3JA TCGA-ER-A193 
       54.51       138.81        36.95        64.08        53.19        31.40 
TCGA-ER-A19A TCGA-ER-A19S TCGA-FS-A1ZA TCGA-FS-A4F9 TCGA-FS-A4FD TCGA-FW-A3R5 
       77.75        37.25        27.72        12.43        77.88        22.92 
TCGA-QB-A6FS 
        6.67 

$`THEMIS WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.57        16.67       112.04       112.57        71.80       133.25 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 
       28.08        31.59        95.74        43.43       103.10        65.49 
TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF 
       23.77       115.53       168.00        69.90        11.87        48.76 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3BZ 
      113.52        42.08        12.10        56.19        45.11       130.72 
TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE 
       58.06        46.98        46.32       166.52        86.93        60.23 
TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E 
       24.53         9.34       103.59        39.75        21.47       161.85 
TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R 
       43.69        40.14       131.90        18.38        10.03        51.68 
TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 
       15.06       135.75       166.19         7.43       125.19       151.53 
TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 
       54.67         3.65         6.41        11.34         3.25         9.90 
TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 
       25.18        66.25        36.03       117.21        20.38       194.83 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA 
      176.55        35.93       107.34        61.18        53.92        65.92 
TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q 
       23.44        68.09        28.60       215.44        15.68        13.87 
TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17Y 
       10.16        45.11        35.01         3.55        52.01        27.22 
TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 
        8.65        33.73        14.70        26.89        68.15         4.96 
TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A 
      109.64       151.27        78.87       168.26        13.55        63.35 
TCGA-EE-A29B TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P 
       80.61        39.62        72.07        44.35        18.61        56.42 
TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 
       14.47        55.92        25.87       171.55        17.92        46.82 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD 
      102.90        24.43        39.29        58.75        47.54       314.56 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
      135.95       208.04        48.72        89.33        54.74        79.66 
TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT 
       75.48        90.97        13.91        14.30        55.59        44.88 
TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD 
       94.82       129.27        28.83        19.76        61.51        47.28 
TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK 
      103.27       103.20        16.96       204.66        96.23       144.76 
TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR 
      203.05       167.90        47.54       248.65        43.23       103.56 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD 
       41.59        53.26       124.31       122.73        25.84         3.68 
TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J8 TCGA-EE-A3JD 
       13.81        23.47       172.18       127.20        34.32        27.35 
TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 
       33.40       101.79       148.08        35.44        13.94        50.76 
TCGA-ER-A199 TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F 
        9.17        98.40        48.89        12.59        13.02        26.37 
TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N 
      268.93       152.35         6.44       131.51        61.05        44.05 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
      162.08        50.89       148.18        79.99        43.82        23.34 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET 
       20.15        16.37        31.27        32.05       247.04        80.32 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW 
       46.98        33.21        92.98       174.21         4.90       216.92 
TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 
       48.59       228.59       202.65        20.91        28.08         7.79 
TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG 
       48.85       357.37        53.52        40.27        15.45         9.70 
TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ 
       32.75        47.38        23.93       101.26        74.73       133.55 
TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY 
       11.41       148.80        53.16        26.56        49.48        27.09 
TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4FB 
       27.02        77.82        66.67        28.73       174.84        26.73 
TCGA-FS-A4FC TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
       49.45         0.20        47.54         0.16         2.40         9.90 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 
        7.23        14.04       120.46       117.93        84.72        10.13 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D 
       64.44        62.79        32.48        39.58 

  THEMIS MUTATED THEMIS WILD-TYPE 
            2.60             0.16 
  THEMIS MUTATED THEMIS WILD-TYPE 
          171.58           357.37 
  THEMIS MUTATED THEMIS WILD-TYPE 
          47.840           48.655 
[1] "2.6 - 171.6 (47.8)" "0.2 - 357.4 (48.7)"
[1] "hr=" "1"  
D82V3, continuous
                  vv
clus               DISTANT METASTASIS PRIMARY TUMOR
  THEMIS MUTATED                    3             0
  THEMIS WILD-TYPE                 32             4
                  vv
clus               REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  THEMIS MUTATED                                           7
  THEMIS WILD-TYPE                                        51
                  vv
clus               REGIONAL LYMPH NODE
  THEMIS MUTATED                    22
  THEMIS WILD-TYPE                 148
D82V4, multiclass
                                           clus
vv                                          THEMIS MUTATED THEMIS WILD-TYPE
  DISTANT METASTASIS                                     3               32
  PRIMARY TUMOR                                          0                4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE              7               51
  REGIONAL LYMPH NODE                                   22              148
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  THEMIS MUTATED             1       1       2        3        3        4
  THEMIS WILD-TYPE           9       5      20        7       21       13
                  vv
clus               STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  THEMIS MUTATED           0         3         0         3          1
  THEMIS WILD-TYPE        10        11         9        28         12
                  vv
clus               STAGE IIIB STAGE IIIC STAGE IV
  THEMIS MUTATED            3          6        1
  THEMIS WILD-TYPE         19         38       11
D82V5, multiclass
             clus
vv            THEMIS MUTATED THEMIS WILD-TYPE
  I OR II NOS              1                9
  STAGE 0                  1                5
  STAGE I                  2               20
  STAGE IA                 3                7
  STAGE IB                 3               21
  STAGE II                 4               13
  STAGE IIA                0               10
  STAGE IIB                3               11
  STAGE IIC                0                9
  STAGE III                3               28
  STAGE IIIA               1               12
  STAGE IIIB               3               19
  STAGE IIIC               6               38
  STAGE IV                 1               11
[1] 14  2
[1] 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
  THEMIS MUTATED       6  6  8  6
  THEMIS WILD-TYPE    45 52 45 49
D82V6, multiclass
       clus
vv      THEMIS MUTATED THEMIS WILD-TYPE
  T0+T1              6               45
  T2                 6               52
  T3                 8               45
  T4                 6               49
[1] 4 2
[1] TRUE
[1] "dimension 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
  THEMIS MUTATED    19   2   5   5
  THEMIS WILD-TYPE 119  46  27  28
D82V7, multiclass
    clus
vv   THEMIS MUTATED THEMIS WILD-TYPE
  N0             19              119
  N1              2               46
  N2              5               27
  N3              5               28
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                M0  M1 M1A M1B M1C
  THEMIS MUTATED    30   1   0   0   0
  THEMIS WILD-TYPE 210   3   2   2   5
D82V8, multiclass
     clus
vv    THEMIS MUTATED THEMIS WILD-TYPE
  M0              30              210
  M1               1                3
  M1A              0                2
  M1B              0                2
  M1C              0                5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D82V9, binary
                  cls
clus                0  1
  THEMIS MUTATED   14  8
  THEMIS WILD-TYPE 88 59
[1] "tbl2"
                  cls
clus               [,1] [,2]
  THEMIS MUTATED     14    8
  THEMIS WILD-TYPE   88   59
     clus
vv    THEMIS MUTATED THEMIS WILD-TYPE
  NO              14               88
  YES              8               59
[1] 2 2
[1] FALSE
D82V10, binary
                  cls
clus                 0   1
  THEMIS MUTATED     5  27
  THEMIS WILD-TYPE  28 208
[1] "tbl2"
                  cls
clus               [,1] [,2]
  THEMIS MUTATED      5   27
  THEMIS WILD-TYPE   28  208
     clus
vv    THEMIS MUTATED THEMIS WILD-TYPE
  NO               5               28
  YES             27              208
[1] 2 2
[1] FALSE
D82V11, continuous
D82V12, binary
                  cls
clus                 0   1
  THEMIS MUTATED     9  23
  THEMIS WILD-TYPE  94 142
[1] "tbl2"
                  cls
clus               [,1] [,2]
  THEMIS MUTATED      9   23
  THEMIS WILD-TYPE   94  142
        clus
vv       THEMIS MUTATED THEMIS WILD-TYPE
  FEMALE              9               94
  MALE               23              142
[1] 2 2
[1] FALSE
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  THEMIS MUTATED       0                         0    32
  THEMIS WILD-TYPE     3                         1   232
D82V13, multiclass
                           clus
vv                          THEMIS MUTATED THEMIS WILD-TYPE
  ASIAN                                  0                3
  BLACK OR AFRICAN AMERICAN              0                1
  WHITE                                 32              232
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D82V14, binary
                  cls
clus                 0   1
  THEMIS MUTATED     0  31
  THEMIS WILD-TYPE   3 230
[1] "tbl2"
                  cls
clus               [,1] [,2]
  THEMIS MUTATED      0   31
  THEMIS WILD-TYPE    3  230
                        clus
vv                       THEMIS MUTATED THEMIS WILD-TYPE
  HISPANIC OR LATINO                  0                3
  NOT HISPANIC OR LATINO             31              230
[1] 2 2
[1] FALSE

Clustering(83) Variable = PTPRT MUTATION ANALYSIS
D83V1, survival
                 sevent
clus2               0   1
  PTPRT MUTATED    44  30
  PTPRT WILD-TYPE  84 100
  PTPRT MUTATED PTPRT WILD-TYPE 
             74             184 
  PTPRT MUTATED PTPRT WILD-TYPE 
             30             100 
$`PTPRT MUTATED`
TCGA-D3-A1Q6 TCGA-D3-A1QA TCGA-D3-A2JF TCGA-D3-A2JH TCGA-D3-A2JN TCGA-D3-A2JO 
       70.16        45.83        30.87        36.16        56.19        64.44 
TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3ML TCGA-D3-A3MR TCGA-D3-A51E 
       45.11        15.25        46.98         6.31       103.59        80.22 
TCGA-D3-A51T TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1I1 TCGA-DA-A1I5 
       13.94        11.31        13.22        48.79        39.19        44.52 
TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-EB-A5UN TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A183 
        7.00        14.83        13.22         8.12         1.12        12.20 
TCGA-EE-A184 TCGA-EE-A20C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29P 
        5.13         4.34        11.15        38.63         4.41        12.03 
TCGA-EE-A29R TCGA-EE-A29V TCGA-EE-A2A1 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GH 
        8.84         2.43        49.22        39.39        34.29        47.21 
TCGA-EE-A2GI TCGA-EE-A2GM TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2M5 
       30.08        28.31         1.15        13.02        34.98         8.84 
TCGA-EE-A2M6 TCGA-EE-A2MD TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MM TCGA-EE-A2MQ 
       98.27         9.53        14.56        63.42        56.02        21.60 
TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3AH 
       29.65        27.16         5.56       124.31        25.84        12.72 
TCGA-EE-A3JA TCGA-EE-A3JD TCGA-ER-A19G TCGA-ER-A2NE TCGA-ER-A2NH TCGA-ER-A3PL 
       22.22        27.35       114.15         1.51        11.74         1.71 
TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZD TCGA-FS-A1ZK TCGA-FS-A1ZQ TCGA-FS-A1ZS 
        7.33         7.30         8.22        12.89         8.65        49.15 
TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4FC TCGA-FW-A3R5 TCGA-GF-A6C8 TCGA-GN-A262 
        5.23        53.85         6.41         0.99        12.85        24.85 
TCGA-GN-A264 TCGA-GN-A266 
       31.33        10.13 

$`PTPRT WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       16.47         8.52       111.09        32.42       110.79        28.08 
TCGA-D3-A1Q9 TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 
       22.55        81.24        10.29        85.32         8.38        21.14 
TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JK 
       88.50        68.22        69.90        11.41         7.50         6.31 
TCGA-D3-A2JL TCGA-D3-A3BZ TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE 
       92.42       114.67        46.32        82.29        61.38        13.32 
TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51F TCGA-D3-A51H 
       24.00         9.34        26.37         5.39        42.71        15.09 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A5GN TCGA-D3-A5GO 
       41.10        17.72         8.84        20.48        52.01        47.87 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 
        1.55         6.97        23.11         4.01         2.89         9.90 
TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I7 
       35.80        51.12        10.03        13.68         9.99        36.69 
TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 
       25.15         4.93        22.36         6.64        19.36        17.56 
TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EE-A17X TCGA-EE-A17Y 
       13.15         0.20         0.00         0.00        11.57        10.55 
TCGA-EE-A17Z TCGA-EE-A182 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H 
        6.31         1.35         4.31        36.07         5.13         9.21 
TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29G TCGA-EE-A29L 
        1.18         7.99         9.90        37.97         8.55         1.08 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29W TCGA-EE-A29X 
       27.12         9.50         8.09         9.99         8.68         8.09 
TCGA-EE-A2A0 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GD TCGA-EE-A2GE 
       11.31        23.90         9.67         8.94        17.98        34.92 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP 
       19.43        16.01        35.54        33.83        30.84         5.42 
TCGA-EE-A2GU TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2ME TCGA-EE-A2MG 
       36.33         2.70         6.18        47.51        29.46        44.25 
TCGA-EE-A2MH TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MT 
        7.96       111.78       111.91        25.08        26.99        23.05 
TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3J3 
      122.73         3.68        30.15        13.81        15.95         3.22 
TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JE TCGA-EE-A3JH 
       22.92        21.60        21.60        16.14         0.46        13.94 
TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 
       33.60        31.40        18.61        12.95        38.40         5.72 
TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F 
       76.41        25.18         3.78         3.52        11.90        11.11 
TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P 
       34.88         4.21        13.45        28.60        42.84        34.68 
TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
        9.57        36.07        17.72        78.44        11.80         1.87 
TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-FR-A3YN 
       13.08        12.62         9.04         6.58        22.49        18.41 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 
       85.74         4.90        64.47         3.45        11.01        23.80 
TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZE TCGA-FS-A1ZF 
       14.24        15.52         3.39        20.38        19.53        11.08 
TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZR 
        7.17        30.87        12.92        47.38        52.08         8.81 
TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A4F4 TCGA-FS-A4F5 
       40.64         8.68        27.39         0.82         7.36        28.73 
TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU 
       14.20        10.78         5.98         2.27         0.20         0.13 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GN-A265 TCGA-GN-A267 
        0.16         0.43         9.90         7.23        84.72        16.24 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS 
       15.42        12.16        14.70         5.79 

  PTPRT MUTATED PTPRT WILD-TYPE 
           0.99            0.00 
  PTPRT MUTATED PTPRT WILD-TYPE 
         124.31          122.73 
  PTPRT MUTATED PTPRT WILD-TYPE 
          15.04           14.47 
[1] "1.0 - 124.3 (15.0)" "0.0 - 122.7 (14.5)"
[1] "hr=" "1.5"
D83V2, survival
                 sevent
clus2               0   1
  PTPRT MUTATED    44  30
  PTPRT WILD-TYPE  88 101
  PTPRT MUTATED PTPRT WILD-TYPE 
             74             189 
  PTPRT MUTATED PTPRT WILD-TYPE 
             30             101 
$`PTPRT MUTATED`
TCGA-D3-A1Q6 TCGA-D3-A1QA TCGA-D3-A2JF TCGA-D3-A2JH TCGA-D3-A2JN TCGA-D3-A2JO 
       71.80        90.90        48.76        42.08        56.19        66.08 
TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3ML TCGA-D3-A3MR TCGA-D3-A51E 
       45.11        58.06        46.98        13.87       103.59       161.85 
TCGA-D3-A51T TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1I1 TCGA-DA-A1I5 
       15.06        25.18        66.25        48.89       194.83       107.34 
TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-EB-A5UN TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A183 
       10.49        15.68        52.01        94.98        33.73        26.89 
TCGA-EE-A184 TCGA-EE-A20C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29P 
       68.15       151.27        13.97        39.62        32.19        56.42 
TCGA-EE-A29R TCGA-EE-A29V TCGA-EE-A2A1 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GH 
       14.47        25.87       102.90        47.54        67.43       208.04 
TCGA-EE-A2GI TCGA-EE-A2GM TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2M5 
       48.72        75.48        14.30        55.59        44.88        21.67 
TCGA-EE-A2M6 TCGA-EE-A2MD TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MM TCGA-EE-A2MQ 
      129.27        47.28       204.66        96.23       167.90        43.23 
TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3AH 
      103.56       136.47        53.26       124.31        25.84       138.81 
TCGA-EE-A3JA TCGA-EE-A3JD TCGA-ER-A19G TCGA-ER-A2NE TCGA-ER-A2NH TCGA-ER-A3PL 
       53.19        27.35       268.93        20.15        32.05        33.21 
TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZD TCGA-FS-A1ZK TCGA-FS-A1ZQ TCGA-FS-A1ZS 
        7.79        27.72        53.52        23.93       133.55       148.80 
TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4FC TCGA-FW-A3R5 TCGA-GF-A6C8 TCGA-GN-A262 
       27.02        77.82        49.45        22.92        14.04       120.46 
TCGA-GN-A264 TCGA-GN-A266 
      117.93        10.13 

$`PTPRT WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       16.57        16.67       112.04       112.57       133.25        28.08 
TCGA-D3-A1Q9 TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 
       31.59        95.74        43.43       103.10        65.49        23.77 
TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JK 
      115.53       168.00        69.90        11.87       113.52        12.10 
TCGA-D3-A2JL TCGA-D3-A3BZ TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE 
      171.58       130.72        46.32       166.52        86.93        60.23 
TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51F TCGA-D3-A51H 
       24.53         9.34        39.75        21.47        43.69        40.14 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A5GN TCGA-D3-A5GO 
      131.90        18.38        10.03        51.68       135.75       137.92 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW 
      166.19         7.43       125.19       151.53        54.67         3.65 
TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-DA-A1HW TCGA-DA-A1HY 
        6.41        11.34         3.25         9.90        36.03       117.21 
TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA 
       20.38       176.55        35.93        61.18        53.92        65.92 
TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-EB-A44Q TCGA-EB-A44R 
       23.44        68.09        28.60       215.44        13.87        10.16 
TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z 
       45.11        35.01         3.55        29.82        27.22         8.65 
TCGA-EE-A182 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I 
       14.70         4.96       109.64        78.87       168.26        13.55 
TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29G TCGA-EE-A29L TCGA-EE-A29M 
       63.35        80.61        47.84        72.07         2.60        44.35 
TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 
       18.61        37.35        55.92       171.55        17.92        46.82 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GJ 
       24.43        39.29        58.75       314.56       135.95        89.33 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GU 
       54.74        79.66        90.97       101.95        13.91        94.82 
TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH 
       28.83        19.76        61.51       103.27       103.20        16.96 
TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MT TCGA-EE-A3AB 
      144.76       203.05        47.54       248.65        41.59       122.73 
TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3J3 TCGA-EE-A3J4 
        3.68        54.51        13.81        23.47       172.18       127.20 
TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI 
       36.95        64.08        34.32        33.40       101.79       148.08 
TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A 
       31.40        35.44        13.94        50.76         9.17        77.75 
TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19H 
       98.40        48.89        12.59        13.02        26.37       152.35 
TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q 
        6.44       131.51        61.05        44.05       162.08        50.89 
TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NF 
       37.25       148.18        79.99        43.82        23.34        16.37 
TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-FR-A3YN TCGA-FR-A44A 
       31.27       247.04        80.32        46.98        92.98       174.21 
TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
        4.90       216.92        48.59       228.59       202.65        20.91 
TCGA-FS-A1Z4 TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG 
       28.08        48.85       357.37        40.27        15.45         9.70 
TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZR TCGA-FS-A1ZT 
       32.75        47.38       101.26        74.73        11.41        53.16 
TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 
       26.56        49.48        27.09        66.67        28.73       174.84 
TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV 
       12.43        26.73        77.88         0.20        47.54         0.16 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 
        2.40         9.90         7.23        84.72        64.44        62.79 
TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS 
       32.48        39.58         6.67 

  PTPRT MUTATED PTPRT WILD-TYPE 
           7.79            0.16 
  PTPRT MUTATED PTPRT WILD-TYPE 
         268.93          357.37 
  PTPRT MUTATED PTPRT WILD-TYPE 
          50.73           47.38 
[1] "7.8 - 268.9 (50.7)" "0.2 - 357.4 (47.4)"
[1] "hr=" "1.4"
D83V3, continuous
                 vv
clus              DISTANT METASTASIS PRIMARY TUMOR
  PTPRT MUTATED                   12             2
  PTPRT WILD-TYPE                 23             2
                 vv
clus              REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  PTPRT MUTATED                                          14                  48
  PTPRT WILD-TYPE                                        44                 122
D83V4, multiclass
                                           clus
vv                                          PTPRT MUTATED PTPRT WILD-TYPE
  DISTANT METASTASIS                                   12              23
  PRIMARY TUMOR                                         2               2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE            14              44
  REGIONAL LYMPH NODE                                  48             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              I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  PTPRT MUTATED             4       3       5        4        7        7
  PTPRT WILD-TYPE           6       3      17        6       17       10
                 vv
clus              STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  PTPRT MUTATED           3         5         3        10          3          6
  PTPRT WILD-TYPE         7         9         6        21         10         16
                 vv
clus              STAGE IIIC STAGE IV
  PTPRT MUTATED           10        2
  PTPRT WILD-TYPE         34       10
D83V5, multiclass
             clus
vv            PTPRT MUTATED PTPRT WILD-TYPE
  I OR II NOS             4               6
  STAGE 0                 3               3
  STAGE I                 5              17
  STAGE IA                4               6
  STAGE IB                7              17
  STAGE II                7              10
  STAGE IIA               3               7
  STAGE IIB               5               9
  STAGE IIC               3               6
  STAGE III              10              21
  STAGE IIIA              3              10
  STAGE IIIB              6              16
  STAGE IIIC             10              34
  STAGE IV                2              10
[1] 14  2
[1] 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
  PTPRT MUTATED      16 15 17 15
  PTPRT WILD-TYPE    35 43 36 40
D83V6, multiclass
       clus
vv      PTPRT MUTATED PTPRT WILD-TYPE
  T0+T1            16              35
  T2               15              43
  T3               17              36
  T4               15              40
[1] 4 2
[1] TRUE
[1] "dimension 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
  PTPRT MUTATED   44 13  9  5
  PTPRT WILD-TYPE 94 35 23 28
D83V7, multiclass
    clus
vv   PTPRT MUTATED PTPRT WILD-TYPE
  N0            44              94
  N1            13              35
  N2             9              23
  N3             5              28
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               M0  M1 M1A M1B M1C
  PTPRT MUTATED    71   0   1   0   1
  PTPRT WILD-TYPE 169   4   1   2   4
D83V8, multiclass
     clus
vv    PTPRT MUTATED PTPRT WILD-TYPE
  M0             71             169
  M1              0               4
  M1A             1               1
  M1B             0               2
  M1C             1               4
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D83V9, binary
                 cls
clus               0  1
  PTPRT MUTATED   31 17
  PTPRT WILD-TYPE 71 50
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTPRT MUTATED     31   17
  PTPRT WILD-TYPE   71   50
     clus
vv    PTPRT MUTATED PTPRT WILD-TYPE
  NO             31              71
  YES            17              50
[1] 2 2
[1] FALSE
D83V10, binary
                 cls
clus                0   1
  PTPRT MUTATED    11  65
  PTPRT WILD-TYPE  22 170
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTPRT MUTATED     11   65
  PTPRT WILD-TYPE   22  170
     clus
vv    PTPRT MUTATED PTPRT WILD-TYPE
  NO             11              22
  YES            65             170
[1] 2 2
[1] FALSE
D83V11, continuous
D83V12, binary
                 cls
clus                0   1
  PTPRT MUTATED    25  51
  PTPRT WILD-TYPE  78 114
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTPRT MUTATED     25   51
  PTPRT WILD-TYPE   78  114
        clus
vv       PTPRT MUTATED PTPRT WILD-TYPE
  FEMALE            25              78
  MALE              51             114
[1] 2 2
[1] FALSE
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PTPRT MUTATED       0                         0    76
  PTPRT WILD-TYPE     3                         1   188
D83V13, multiclass
                           clus
vv                          PTPRT MUTATED PTPRT WILD-TYPE
  ASIAN                                 0               3
  BLACK OR AFRICAN AMERICAN             0               1
  WHITE                                76             188
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D83V14, binary
                 cls
clus                0   1
  PTPRT MUTATED     1  75
  PTPRT WILD-TYPE   2 186
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTPRT MUTATED      1   75
  PTPRT WILD-TYPE    2  186
                        clus
vv                       PTPRT MUTATED PTPRT WILD-TYPE
  HISPANIC OR LATINO                 1               2
  NOT HISPANIC OR LATINO            75             186
[1] 2 2
[1] FALSE

Clustering(84) Variable = SELPLG MUTATION ANALYSIS
D84V1, survival
                  sevent
clus2                0   1
  SELPLG MUTATED     5   4
  SELPLG WILD-TYPE 123 126
  SELPLG MUTATED SELPLG WILD-TYPE 
               9              249 
  SELPLG MUTATED SELPLG WILD-TYPE 
               4              126 
$`SELPLG MUTATED`
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A5GO TCGA-EE-A181 TCGA-EE-A29B TCGA-EE-A2A6 
      103.59        26.37        47.87         1.12         9.90         8.94 
TCGA-EE-A2MC TCGA-EE-A3JD TCGA-ER-A19D 
       47.51        27.35         3.52 

$`SELPLG WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.47         8.52       111.09        32.42        70.16       110.79 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       28.08        22.55        45.83        81.24        10.29        85.32 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
        8.38        21.14        88.50        68.22        69.90        11.41 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       30.87         7.50        36.16         6.31        92.42        56.19 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 
       64.44        45.11       114.67        15.25        46.98        46.32 
TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO 
       82.29        61.38        13.32        24.00         6.31         9.34 
TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K 
        5.39        80.22        42.71        15.09        41.10        17.72 
TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS 
        8.84        20.48        13.94        52.01         1.55         6.97 
TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC 
       23.11         4.01         2.89         9.90        11.31        13.22 
TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 
       48.79        35.80        51.12        10.03        39.19        13.68 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB 
        9.99        44.52        36.69        25.15         4.93        22.36 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q 
        6.64        19.36         7.00        17.56        14.83        13.15 
TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y 
        0.20         0.00         0.00        13.22        11.57        10.55 
TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 
        6.31         8.12         1.35        12.20         5.13         4.31 
TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A 
       36.07         4.34         5.13         9.21         1.18         7.99 
TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L 
       37.97        11.15        38.63         8.55         4.41         1.08 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S 
       27.12         9.50        12.03         8.09         8.84         9.99 
TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 
        2.43         8.68         8.09        11.31        49.22        23.90 
TCGA-EE-A2A5 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH 
        9.67        39.39        34.29        17.98        34.92        47.21 
TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN 
       30.08        19.43        16.01        35.54        28.31        33.83 
TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU 
       30.84         5.42         1.15        13.02        34.98        36.33 
TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MD TCGA-EE-A2ME 
        8.84        98.27         2.70         6.18         9.53        29.46 
TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML 
       44.25         7.96        14.56        63.42       111.78       111.91 
TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS 
       56.02        25.08        26.99        21.60        29.65        27.16 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD 
       23.05         5.56       124.31       122.73        25.84         3.68 
TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 
       30.15        13.81        15.95        12.72         3.22        22.92 
TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JE TCGA-EE-A3JH 
       21.60        21.60        16.14        22.22         0.46        13.94 
TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 
       33.60        31.40        18.61        12.95        38.40         5.72 
TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G 
       76.41        25.18         3.78        11.90        11.11       114.15 
TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P 
       34.88         4.21        13.45        28.60        42.84        34.68 
TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
        9.57        36.07        17.72        78.44        11.80         1.87 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET 
        1.51        13.08        12.62        11.74         9.04         6.58 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW 
       22.49         1.71        18.41        85.74         4.90        64.47 
TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 
        3.45        11.01        23.80        14.24        15.52         7.33 
TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF 
        7.30         3.39        20.38         8.22        19.53        11.08 
TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP 
        7.17        30.87        12.92        12.89        47.38        52.08 
TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW 
        8.65         8.81        49.15        40.64         8.68        27.39 
TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 
        0.82         5.23        53.85         7.36        28.73        14.20 
TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 
       10.78         5.98         6.41         2.27         0.20         0.99 
TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 
        0.13         0.16         0.43         9.90         7.23        12.85 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 
       24.85        31.33        84.72        10.13        16.24        15.42 
TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS 
       12.16        14.70         5.79 

  SELPLG MUTATED SELPLG WILD-TYPE 
            1.12             0.00 
  SELPLG MUTATED SELPLG WILD-TYPE 
          103.59           124.31 
  SELPLG MUTATED SELPLG WILD-TYPE 
           26.37            14.70 
[1] "1.1 - 103.6 (26.4)" "0.0 - 124.3 (14.7)"
[1] "hr=" "1.2"
D84V2, survival
                  sevent
clus2                0   1
  SELPLG MUTATED     5   4
  SELPLG WILD-TYPE 127 127
  SELPLG MUTATED SELPLG WILD-TYPE 
               9              254 
  SELPLG MUTATED SELPLG WILD-TYPE 
               4              127 
$`SELPLG MUTATED`
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A5GO TCGA-EE-A181 TCGA-EE-A29B TCGA-EE-A2A6 
      103.59        39.75       137.92        33.73        80.61        58.75 
TCGA-EE-A2MC TCGA-EE-A3JD TCGA-ER-A19D 
       61.51        27.35        12.59 

$`SELPLG WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.57        16.67       112.04       112.57        71.80       133.25 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       28.08        31.59        90.90        95.74        43.43       103.10 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
       65.49        23.77       115.53       168.00        69.90        11.87 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       48.76       113.52        42.08        12.10       171.58        56.19 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 
       66.08        45.11       130.72        58.06        46.98        46.32 
TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO 
      166.52        86.93        60.23        24.53        13.87         9.34 
TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K 
       21.47       161.85        43.69        40.14       131.90        18.38 
TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS 
       10.03        51.68        15.06       135.75       166.19         7.43 
TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 
      125.19       151.53        54.67         3.65         6.41        11.34 
TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1HW 
        3.25         9.90        25.18        66.25        48.89        36.03 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 
      117.21        20.38       194.83       176.55        35.93       107.34 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
       61.18        53.92        65.92        23.44        68.09        28.60 
TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG 
       10.49       215.44        15.68        13.87        10.16        45.11 
TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z 
       35.01         3.55        52.01        29.82        27.22         8.65 
TCGA-EE-A180 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B 
       94.98        14.70        26.89        68.15         4.96       109.64 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29C 
      151.27        78.87       168.26        13.55        63.35        47.84 
TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M 
       13.97        39.62        72.07        32.19         2.60        44.35 
TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V 
       18.61        56.42        37.35        14.47        55.92        25.87 
TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 
      171.55        17.92        46.82       102.90        24.43        39.29 
TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI 
       47.54        67.43       314.56       135.95       208.04        48.72 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO 
       89.33        54.74        79.66        75.48        90.97       101.95 
TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 
       13.91        14.30        55.59        44.88        94.82        21.67 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG 
      129.27        28.83        19.76        47.28       103.27       103.20 
TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM 
       16.96       204.66        96.23       144.76       203.05       167.90 
TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT 
       47.54       248.65        43.23       103.56       136.47        41.59 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE 
       53.26       124.31       122.73        25.84         3.68        54.51 
TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 
       13.81        23.47       138.81       172.18       127.20        36.95 
TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI 
       64.08        34.32        53.19        33.40       101.79       148.08 
TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A 
       31.40        35.44        13.94        50.76         9.17        77.75 
TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H 
       98.40        48.89        13.02        26.37       268.93       152.35 
TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q 
        6.44       131.51        61.05        44.05       162.08        50.89 
TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE 
       37.25       148.18        79.99        43.82        23.34        20.15 
TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV 
       16.37        31.27        32.05       247.04        80.32        46.98 
TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX 
       33.21        92.98       174.21         4.90       216.92        48.59 
TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA 
      228.59       202.65        20.91        28.08         7.79        27.72 
TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG 
       48.85       357.37        53.52        40.27        15.45         9.70 
TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ 
       32.75        47.38        23.93       101.26        74.73       133.55 
TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY 
       11.41       148.80        53.16        26.56        49.48        27.09 
TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 
       27.02        77.82        66.67        28.73       174.84        12.43 
TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU 
       26.73        49.45        77.88         0.20        22.92        47.54 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 
        0.16         2.40         9.90         7.23        14.04       120.46 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
      117.93        84.72        10.13        64.44        62.79        32.48 
TCGA-GN-A26D TCGA-QB-A6FS 
       39.58         6.67 

  SELPLG MUTATED SELPLG WILD-TYPE 
           12.59             0.16 
  SELPLG MUTATED SELPLG WILD-TYPE 
          137.92           357.37 
  SELPLG MUTATED SELPLG WILD-TYPE 
          58.750           48.215 
[1] "12.6 - 137.9 (58.8)" "0.2 - 357.4 (48.2)" 
[1] "hr=" "1"  
D84V3, continuous
                  vv
clus               DISTANT METASTASIS PRIMARY TUMOR
  SELPLG MUTATED                    2             0
  SELPLG WILD-TYPE                 33             4
                  vv
clus               REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  SELPLG MUTATED                                           2
  SELPLG WILD-TYPE                                        56
                  vv
clus               REGIONAL LYMPH NODE
  SELPLG MUTATED                     5
  SELPLG WILD-TYPE                 165
D84V4, multiclass
                                           clus
vv                                          SELPLG MUTATED SELPLG WILD-TYPE
  DISTANT METASTASIS                                     2               33
  PRIMARY TUMOR                                          0                4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE              2               56
  REGIONAL LYMPH NODE                                    5              165
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  SELPLG MUTATED             0       0       1        1        1        2
  SELPLG WILD-TYPE          10       6      21        9       23       15
                  vv
clus               STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  SELPLG MUTATED           0         1         0         2          1
  SELPLG WILD-TYPE        10        13         9        29         12
                  vv
clus               STAGE IIIB STAGE IIIC STAGE IV
  SELPLG MUTATED            0          0        0
  SELPLG WILD-TYPE         22         44       12
D84V5, multiclass
             clus
vv            SELPLG MUTATED SELPLG WILD-TYPE
  I OR II NOS              0               10
  STAGE 0                  0                6
  STAGE I                  1               21
  STAGE IA                 1                9
  STAGE IB                 1               23
  STAGE II                 2               15
  STAGE IIA                0               10
  STAGE IIB                1               13
  STAGE IIC                0                9
  STAGE III                2               29
  STAGE IIIA               1               12
  STAGE IIIB               0               22
  STAGE IIIC               0               44
  STAGE IV                 0               12
[1] 14  2
[1] 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
  SELPLG MUTATED       2  2  3  1
  SELPLG WILD-TYPE    49 56 50 54
D84V6, multiclass
       clus
vv      SELPLG MUTATED SELPLG WILD-TYPE
  T0+T1              2               49
  T2                 2               56
  T3                 3               50
  T4                 1               54
[1] 4 2
[1] TRUE
[1] "dimension 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
  SELPLG MUTATED     6   1   2   0
  SELPLG WILD-TYPE 132  47  30  33
D84V7, multiclass
    clus
vv   SELPLG MUTATED SELPLG WILD-TYPE
  N0              6              132
  N1              1               47
  N2              2               30
  N3              0               33
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                M0  M1 M1A M1B M1C
  SELPLG MUTATED     9   0   0   0   0
  SELPLG WILD-TYPE 231   4   2   2   5
D84V8, multiclass
     clus
vv    SELPLG MUTATED SELPLG WILD-TYPE
  M0               9              231
  M1               0                4
  M1A              0                2
  M1B              0                2
  M1C              0                5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D84V9, binary
                  cls
clus                0  1
  SELPLG MUTATED    4  1
  SELPLG WILD-TYPE 98 66
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SELPLG MUTATED      4    1
  SELPLG WILD-TYPE   98   66
     clus
vv    SELPLG MUTATED SELPLG WILD-TYPE
  NO               4               98
  YES              1               66
[1] 2 2
[1] FALSE
D84V10, binary
                  cls
clus                 0   1
  SELPLG MUTATED     2   7
  SELPLG WILD-TYPE  31 228
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SELPLG MUTATED      2    7
  SELPLG WILD-TYPE   31  228
     clus
vv    SELPLG MUTATED SELPLG WILD-TYPE
  NO               2               31
  YES              7              228
[1] 2 2
[1] FALSE
D84V11, continuous
D84V12, binary
                  cls
clus                 0   1
  SELPLG MUTATED     2   7
  SELPLG WILD-TYPE 101 158
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SELPLG MUTATED      2    7
  SELPLG WILD-TYPE  101  158
        clus
vv       SELPLG MUTATED SELPLG WILD-TYPE
  FEMALE              2              101
  MALE                7              158
[1] 2 2
[1] FALSE
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SELPLG MUTATED       0                         0     9
  SELPLG WILD-TYPE     3                         1   255
D84V13, multiclass
                           clus
vv                          SELPLG MUTATED SELPLG WILD-TYPE
  ASIAN                                  0                3
  BLACK OR AFRICAN AMERICAN              0                1
  WHITE                                  9              255
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D84V14, binary
                  cls
clus                 0   1
  SELPLG MUTATED     0   9
  SELPLG WILD-TYPE   3 252
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SELPLG MUTATED      0    9
  SELPLG WILD-TYPE    3  252
                        clus
vv                       SELPLG MUTATED SELPLG WILD-TYPE
  HISPANIC OR LATINO                  0                3
  NOT HISPANIC OR LATINO              9              252
[1] 2 2
[1] FALSE

Clustering(85) Variable = CSN3 MUTATION ANALYSIS
D85V1, survival
                sevent
clus2              0   1
  CSN3 MUTATED     4   0
  CSN3 WILD-TYPE 124 130
  CSN3 MUTATED CSN3 WILD-TYPE 
             4            254 
  CSN3 MUTATED CSN3 WILD-TYPE 
             0            130 
$`CSN3 MUTATED`
TCGA-D3-A5GN TCGA-EE-A2M6 TCGA-FR-A3YN TCGA-FS-A1ZT 
       52.01        98.27        18.41        40.64 

$`CSN3 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.47         8.52       111.09        32.42        70.16       110.79 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       28.08        22.55        45.83        81.24        10.29        85.32 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
        8.38        21.14        88.50        68.22        69.90        11.41 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       30.87         7.50        36.16         6.31        92.42        56.19 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 
       64.44        45.11       114.67        15.25        46.98        46.32 
TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO 
       82.29        61.38        13.32        24.00         6.31         9.34 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H 
      103.59        26.37         5.39        80.22        42.71        15.09 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GO 
       41.10        17.72         8.84        20.48        13.94        47.87 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 
        1.55         6.97        23.11         4.01         2.89         9.90 
TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 
       11.31        13.22        48.79        35.80        51.12        10.03 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 
       39.19        13.68         9.99        44.52        36.69        25.15 
TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 
        4.93        22.36         6.64        19.36         7.00        17.56 
TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN 
       14.83        13.15         0.20         0.00         0.00        13.22 
TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 
       11.57        10.55         6.31         8.12         1.12         1.35 
TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F 
       12.20         5.13         4.31        36.07         4.34         5.13 
TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D 
        9.21         1.18         7.99         9.90        37.97        11.15 
TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N 
       38.63         8.55         4.41         1.08        27.12         9.50 
TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W 
       12.03         8.09         8.84         9.99         2.43         8.68 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 
        8.09        11.31        49.22        23.90         9.67         8.94 
TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI 
       39.39        34.29        17.98        34.92        47.21        30.08 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO 
       19.43        16.01        35.54        28.31        33.83        30.84 
TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 
        5.42         1.15        13.02        34.98        36.33         8.84 
TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG 
        2.70         6.18        47.51         9.53        29.46        44.25 
TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM 
        7.96        14.56        63.42       111.78       111.91        56.02 
TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT 
       25.08        26.99        21.60        29.65        27.16        23.05 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE 
        5.56       124.31       122.73        25.84         3.68        30.15 
TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 
       13.81        15.95        12.72         3.22        22.92        21.60 
TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH 
       21.60        16.14        22.22        27.35         0.46        13.94 
TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 
       33.60        31.40        18.61        12.95        38.40         5.72 
TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F 
       76.41        25.18         3.78         3.52        11.90        11.11 
TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N 
      114.15        34.88         4.21        13.45        28.60        42.84 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
       34.68         9.57        36.07        17.72        78.44        11.80 
TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES 
        1.87         1.51        13.08        12.62        11.74         9.04 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW 
        6.58        22.49         1.71        85.74         4.90        64.47 
TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 
        3.45        11.01        23.80        14.24        15.52         7.33 
TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF 
        7.30         3.39        20.38         8.22        19.53        11.08 
TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP 
        7.17        30.87        12.92        12.89        47.38        52.08 
TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY 
        8.65         8.81        49.15         8.68        27.39         0.82 
TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 
        5.23        53.85         7.36        28.73        14.20        10.78 
TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU 
        5.98         6.41         2.27         0.20         0.99         0.13 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 
        0.16         0.43         9.90         7.23        12.85        24.85 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
       31.33        84.72        10.13        16.24        15.42        12.16 
TCGA-GN-A26D TCGA-QB-A6FS 
       14.70         5.79 

  CSN3 MUTATED CSN3 WILD-TYPE 
         18.41           0.00 
  CSN3 MUTATED CSN3 WILD-TYPE 
         98.27         124.31 
  CSN3 MUTATED CSN3 WILD-TYPE 
        46.325         14.400 
[1] "18.4 - 98.3 (46.3)" "0.0 - 124.3 (14.4)"
[1] "hr="     "2.5e+07"
D85V2, survival
                sevent
clus2              0   1
  CSN3 MUTATED     4   0
  CSN3 WILD-TYPE 128 131
  CSN3 MUTATED CSN3 WILD-TYPE 
             4            259 
  CSN3 MUTATED CSN3 WILD-TYPE 
             0            131 
$`CSN3 MUTATED`
TCGA-D3-A5GN TCGA-EE-A2M6 TCGA-FR-A3YN TCGA-FS-A1ZT 
      135.75       129.27        92.98        53.16 

$`CSN3 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.57        16.67       112.04       112.57        71.80       133.25 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       28.08        31.59        90.90        95.74        43.43       103.10 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
       65.49        23.77       115.53       168.00        69.90        11.87 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       48.76       113.52        42.08        12.10       171.58        56.19 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 
       66.08        45.11       130.72        58.06        46.98        46.32 
TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO 
      166.52        86.93        60.23        24.53        13.87         9.34 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H 
      103.59        39.75        21.47       161.85        43.69        40.14 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GO 
      131.90        18.38        10.03        51.68        15.06       137.92 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW 
      166.19         7.43       125.19       151.53        54.67         3.65 
TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC 
        6.41        11.34         3.25         9.90        25.18        66.25 
TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 
       48.89        36.03       117.21        20.38       194.83       176.55 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB 
       35.93       107.34        61.18        53.92        65.92        23.44 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q 
       68.09        28.60        10.49       215.44        15.68        13.87 
TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X 
       10.16        45.11        35.01         3.55        52.01        29.82 
TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 
       27.22         8.65        94.98        33.73        14.70        26.89 
TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H 
       68.15         4.96       109.64       151.27        78.87       168.26 
TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E 
       13.55        63.35        80.61        47.84        13.97        39.62 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P 
       72.07        32.19         2.60        44.35        18.61        56.42 
TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X 
       37.35        14.47        55.92        25.87       171.55        17.92 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB 
       46.82       102.90        24.43        39.29        58.75        47.54 
TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ 
       67.43       314.56       135.95       208.04        48.72        89.33 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP 
       54.74        79.66        75.48        90.97       101.95        13.91 
TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M7 
       14.30        55.59        44.88        94.82        21.67        28.83 
TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH 
       19.76        61.51        47.28       103.27       103.20        16.96 
TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN 
      204.66        96.23       144.76       203.05       167.90        47.54 
TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU 
      248.65        43.23       103.56       136.47        41.59        53.26 
TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF 
      124.31       122.73        25.84         3.68        54.51        13.81 
TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 
       23.47       138.81       172.18       127.20        36.95        64.08 
TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI 
       34.32        53.19        27.35        33.40       101.79       148.08 
TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A 
       31.40        35.44        13.94        50.76         9.17        77.75 
TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G 
       98.40        48.89        12.59        13.02        26.37       268.93 
TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P 
      152.35         6.44       131.51        61.05        44.05       162.08 
TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
       50.89        37.25       148.18        79.99        43.82        23.34 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET 
       20.15        16.37        31.27        32.05       247.04        80.32 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX 
       46.98        33.21       174.21         4.90       216.92        48.59 
TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA 
      228.59       202.65        20.91        28.08         7.79        27.72 
TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG 
       48.85       357.37        53.52        40.27        15.45         9.70 
TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ 
       32.75        47.38        23.93       101.26        74.73       133.55 
TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ 
       11.41       148.80        26.56        49.48        27.09        27.02 
TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB 
       77.82        66.67        28.73       174.84        12.43        26.73 
TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV 
       49.45        77.88         0.20        22.92        47.54         0.16 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 
        2.40         9.90         7.23        14.04       120.46       117.93 
TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D 
       84.72        10.13        64.44        62.79        32.48        39.58 
TCGA-QB-A6FS 
        6.67 

  CSN3 MUTATED CSN3 WILD-TYPE 
         53.16           0.16 
  CSN3 MUTATED CSN3 WILD-TYPE 
        135.75         357.37 
  CSN3 MUTATED CSN3 WILD-TYPE 
       111.125         47.540 
[1] "53.2 - 135.8 (111.1)" "0.2 - 357.4 (47.5)"  
[1] "hr="     "9300000"
D85V3, continuous
                vv
clus             DISTANT METASTASIS PRIMARY TUMOR
  CSN3 MUTATED                    1             0
  CSN3 WILD-TYPE                 34             4
                vv
clus             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  CSN3 MUTATED                                           0                   3
  CSN3 WILD-TYPE                                        58                 167
D85V4, multiclass
                                           clus
vv                                          CSN3 MUTATED CSN3 WILD-TYPE
  DISTANT METASTASIS                                   1             34
  PRIMARY TUMOR                                        0              4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE            0             58
  REGIONAL LYMPH NODE                                  3            167
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  CSN3 MUTATED             0       0       2        0        1        0
  CSN3 WILD-TYPE          10       6      20       10       23       17
                vv
clus             STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  CSN3 MUTATED           0         0         0         1          0          0
  CSN3 WILD-TYPE        10        14         9        30         13         22
                vv
clus             STAGE IIIC STAGE IV
  CSN3 MUTATED            0        0
  CSN3 WILD-TYPE         44       12
D85V5, multiclass
             clus
vv            CSN3 MUTATED CSN3 WILD-TYPE
  I OR II NOS            0             10
  STAGE 0                0              6
  STAGE I                2             20
  STAGE IA               0             10
  STAGE IB               1             23
  STAGE II               0             17
  STAGE IIA              0             10
  STAGE IIB              0             14
  STAGE IIC              0              9
  STAGE III              1             30
  STAGE IIIA             0             13
  STAGE IIIB             0             22
  STAGE IIIC             0             44
  STAGE IV               0             12
[1] 14  2
[1] 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
  CSN3 MUTATED       2  2  0  0
  CSN3 WILD-TYPE    49 56 53 55
D85V6, multiclass
       clus
vv      CSN3 MUTATED CSN3 WILD-TYPE
  T0+T1            2             49
  T2               2             56
  T3               0             53
  T4               0             55
[1] 4 2
[1] TRUE
[1] "dimension 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
  CSN3 MUTATED     3   1   0   0
  CSN3 WILD-TYPE 135  47  32  33
D85V7, multiclass
    clus
vv   CSN3 MUTATED CSN3 WILD-TYPE
  N0            3            135
  N1            1             47
  N2            0             32
  N3            0             33
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              M0  M1 M1A M1B M1C
  CSN3 MUTATED     4   0   0   0   0
  CSN3 WILD-TYPE 236   4   2   2   5
D85V8, multiclass
     clus
vv    CSN3 MUTATED CSN3 WILD-TYPE
  M0             4            236
  M1             0              4
  M1A            0              2
  M1B            0              2
  M1C            0              5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D85V9, binary
                cls
clus               0   1
  CSN3 MUTATED     2   0
  CSN3 WILD-TYPE 100  67
[1] "tbl2"
                cls
clus             [,1] [,2]
  CSN3 MUTATED      2    0
  CSN3 WILD-TYPE  100   67
     clus
vv    CSN3 MUTATED CSN3 WILD-TYPE
  NO             2            100
  YES            0             67
[1] 2 2
[1] FALSE
D85V10, binary
                cls
clus               0   1
  CSN3 MUTATED     0   4
  CSN3 WILD-TYPE  33 231
[1] "tbl2"
                cls
clus             [,1] [,2]
  CSN3 MUTATED      0    4
  CSN3 WILD-TYPE   33  231
     clus
vv    CSN3 MUTATED CSN3 WILD-TYPE
  NO             0             33
  YES            4            231
[1] 2 2
[1] FALSE
D85V11, continuous
D85V12, binary
                cls
clus               0   1
  CSN3 MUTATED     1   3
  CSN3 WILD-TYPE 102 162
[1] "tbl2"
                cls
clus             [,1] [,2]
  CSN3 MUTATED      1    3
  CSN3 WILD-TYPE  102  162
        clus
vv       CSN3 MUTATED CSN3 WILD-TYPE
  FEMALE            1            102
  MALE              3            162
[1] 2 2
[1] FALSE
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CSN3 MUTATED       0                         0     4
  CSN3 WILD-TYPE     3                         1   260
D85V13, multiclass
                           clus
vv                          CSN3 MUTATED CSN3 WILD-TYPE
  ASIAN                                0              3
  BLACK OR AFRICAN AMERICAN            0              1
  WHITE                                4            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"
D85V14, binary
                cls
clus               0   1
  CSN3 MUTATED     0   4
  CSN3 WILD-TYPE   3 257
[1] "tbl2"
                cls
clus             [,1] [,2]
  CSN3 MUTATED      0    4
  CSN3 WILD-TYPE    3  257
                        clus
vv                       CSN3 MUTATED CSN3 WILD-TYPE
  HISPANIC OR LATINO                0              3
  NOT HISPANIC OR LATINO            4            257
[1] 2 2
[1] FALSE

Clustering(86) Variable = SLC7A11 MUTATION ANALYSIS
D86V1, survival
                   sevent
clus2                 0   1
  SLC7A11 MUTATED     7   3
  SLC7A11 WILD-TYPE 121 127
  SLC7A11 MUTATED SLC7A11 WILD-TYPE 
               10               248 
  SLC7A11 MUTATED SLC7A11 WILD-TYPE 
                3               127 
$`SLC7A11 MUTATED`
TCGA-D3-A1Q6 TCGA-D9-A6EC TCGA-DA-A1HV TCGA-EE-A2A2 TCGA-EE-A2GC TCGA-EE-A2M7 
       70.16        13.22        48.79        23.90        34.29         2.70 
TCGA-EE-A2MS TCGA-FW-A3R5 TCGA-GN-A266 TCGA-QB-A6FS 
       27.16         0.99        10.13         5.79 

$`SLC7A11 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       16.47         8.52       111.09        32.42       110.79        28.08 
TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 
       22.55        45.83        81.24        10.29        85.32         8.38 
TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF 
       21.14        88.50        68.22        69.90        11.41        30.87 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO 
        7.50        36.16         6.31        92.42        56.19        64.44 
TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB 
       45.11       114.67        15.25        46.98        46.32        82.29 
TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR 
       61.38        13.32        24.00         6.31         9.34       103.59 
TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J 
       26.37         5.39        80.22        42.71        15.09        41.10 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO 
       17.72         8.84        20.48        13.94        52.01        47.87 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 
        1.55         6.97        23.11         4.01         2.89         9.90 
TCGA-D9-A6EA TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 
       11.31        35.80        51.12        10.03        39.19        13.68 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB 
        9.99        44.52        36.69        25.15         4.93        22.36 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q 
        6.64        19.36         7.00        17.56        14.83        13.15 
TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y 
        0.20         0.00         0.00        13.22        11.57        10.55 
TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 
        6.31         8.12         1.12         1.35        12.20         5.13 
TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I 
        4.31        36.07         4.34         5.13         9.21         1.18 
TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G 
        7.99         9.90        37.97        11.15        38.63         8.55 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
        4.41         1.08        27.12         9.50        12.03         8.09 
TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 
        8.84         9.99         2.43         8.68         8.09        11.31 
TCGA-EE-A2A1 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE 
       49.22         9.67         8.94        39.39        17.98        34.92 
TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM 
       47.21        30.08        19.43        16.01        35.54        28.31 
TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT 
       33.83        30.84         5.42         1.15        13.02        34.98 
TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD 
       36.33         8.84        98.27         6.18        47.51         9.53 
TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK 
       29.46        44.25         7.96        14.56        63.42       111.78 
TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR 
      111.91        56.02        25.08        26.99        21.60        29.65 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD 
       23.05         5.56       124.31       122.73        25.84         3.68 
TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 
       30.15        13.81        15.95        12.72         3.22        22.92 
TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE 
       21.60        21.60        16.14        22.22        27.35         0.46 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 
       13.94        33.60        31.40        18.61        12.95        38.40 
TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E 
        5.72        76.41        25.18         3.78         3.52        11.90 
TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M 
       11.11       114.15        34.88         4.21        13.45        28.60 
TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 
       42.84        34.68         9.57        36.07        17.72        78.44 
TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH 
       11.80         1.87         1.51        13.08        12.62        11.74 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A 
        9.04         6.58        22.49         1.71        18.41        85.74 
TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
        4.90        64.47         3.45        11.01        23.80        14.24 
TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD 
       15.52         7.33         7.30         3.39        20.38         8.22 
TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK 
       19.53        11.08         7.17        30.87        12.92        12.89 
TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT 
       47.38        52.08         8.65         8.81        49.15        40.64 
TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 
        8.68        27.39         0.82         5.23        53.85         7.36 
TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD 
       28.73        14.20        10.78         5.98         6.41         2.27 
TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
        0.20         0.13         0.16         0.43         9.90         7.23 
TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 
       12.85        24.85        31.33        84.72        16.24        15.42 
TCGA-GN-A26A TCGA-GN-A26D 
       12.16        14.70 

  SLC7A11 MUTATED SLC7A11 WILD-TYPE 
             0.99              0.00 
  SLC7A11 MUTATED SLC7A11 WILD-TYPE 
            70.16            124.31 
  SLC7A11 MUTATED SLC7A11 WILD-TYPE 
           18.560            14.765 
[1] "1.0 - 70.2 (18.6)"  "0.0 - 124.3 (14.8)"
[1] "hr=" "1.7"
D86V2, survival
                   sevent
clus2                 0   1
  SLC7A11 MUTATED     7   3
  SLC7A11 WILD-TYPE 125 128
  SLC7A11 MUTATED SLC7A11 WILD-TYPE 
               10               253 
  SLC7A11 MUTATED SLC7A11 WILD-TYPE 
                3               128 
$`SLC7A11 MUTATED`
TCGA-D3-A1Q6 TCGA-D9-A6EC TCGA-DA-A1HV TCGA-EE-A2A2 TCGA-EE-A2GC TCGA-EE-A2M7 
       71.80        66.25        48.89        24.43        67.43        28.83 
TCGA-EE-A2MS TCGA-FW-A3R5 TCGA-GN-A266 TCGA-QB-A6FS 
      136.47        22.92        10.13         6.67 

$`SLC7A11 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       16.57        16.67       112.04       112.57       133.25        28.08 
TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 
       31.59        90.90        95.74        43.43       103.10        65.49 
TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF 
       23.77       115.53       168.00        69.90        11.87        48.76 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO 
      113.52        42.08        12.10       171.58        56.19        66.08 
TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB 
       45.11       130.72        58.06        46.98        46.32       166.52 
TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR 
       86.93        60.23        24.53        13.87         9.34       103.59 
TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J 
       39.75        21.47       161.85        43.69        40.14       131.90 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO 
       18.38        10.03        51.68        15.06       135.75       137.92 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW 
      166.19         7.43       125.19       151.53        54.67         3.65 
TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-DA-A1HW 
        6.41        11.34         3.25         9.90        25.18        36.03 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 
      117.21        20.38       194.83       176.55        35.93       107.34 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
       61.18        53.92        65.92        23.44        68.09        28.60 
TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG 
       10.49       215.44        15.68        13.87        10.16        45.11 
TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z 
       35.01         3.55        52.01        29.82        27.22         8.65 
TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 
       94.98        33.73        14.70        26.89        68.15         4.96 
TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A 
      109.64       151.27        78.87       168.26        13.55        63.35 
TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H 
       80.61        47.84        13.97        39.62        72.07        32.19 
TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R 
        2.60        44.35        18.61        56.42        37.35        14.47 
TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 
       55.92        25.87       171.55        17.92        46.82       102.90 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH 
       39.29        58.75        47.54       314.56       135.95       208.04 
TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN 
       48.72        89.33        54.74        79.66        75.48        90.97 
TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU 
      101.95        13.91        14.30        55.59        44.88        94.82 
TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME 
       21.67       129.27        19.76        61.51        47.28       103.27 
TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML 
      103.20        16.96       204.66        96.23       144.76       203.05 
TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MT 
      167.90        47.54       248.65        43.23       103.56        41.59 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE 
       53.26       124.31       122.73        25.84         3.68        54.51 
TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 
       13.81        23.47       138.81       172.18       127.20        36.95 
TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH 
       64.08        34.32        53.19        27.35        33.40       101.79 
TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 
      148.08        31.40        35.44        13.94        50.76         9.17 
TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F 
       77.75        98.40        48.89        12.59        13.02        26.37 
TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N 
      268.93       152.35         6.44       131.51        61.05        44.05 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
      162.08        50.89        37.25       148.18        79.99        43.82 
TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES 
       23.34        20.15        16.37        31.27        32.05       247.04 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
       80.32        46.98        33.21        92.98       174.21         4.90 
TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 
      216.92        48.59       228.59       202.65        20.91        28.08 
TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE 
        7.79        27.72        48.85       357.37        53.52        40.27 
TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM 
       15.45         9.70        32.75        47.38        23.93       101.26 
TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU 
       74.73       133.55        11.41       148.80        53.16        26.56 
TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 
       49.48        27.09        27.02        77.82        66.67        28.73 
TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 
      174.84        12.43        26.73        49.45        77.88         0.20 
TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 
       47.54         0.16         2.40         9.90         7.23        14.04 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
      120.46       117.93        84.72        64.44        62.79        32.48 
TCGA-GN-A26D 
       39.58 

  SLC7A11 MUTATED SLC7A11 WILD-TYPE 
             6.67              0.16 
  SLC7A11 MUTATED SLC7A11 WILD-TYPE 
           136.47            357.37 
  SLC7A11 MUTATED SLC7A11 WILD-TYPE 
            38.86             48.59 
[1] "6.7 - 136.5 (38.9)" "0.2 - 357.4 (48.6)"
[1] "hr=" "1.2"
D86V3, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  SLC7A11 MUTATED                    1             1
  SLC7A11 WILD-TYPE                 34             3
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  SLC7A11 MUTATED                                           2
  SLC7A11 WILD-TYPE                                        56
                   vv
clus                REGIONAL LYMPH NODE
  SLC7A11 MUTATED                     7
  SLC7A11 WILD-TYPE                 163
D86V4, multiclass
                                           clus
vv                                          SLC7A11 MUTATED SLC7A11 WILD-TYPE
  DISTANT METASTASIS                                      1                34
  PRIMARY TUMOR                                           1                 3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE               2                56
  REGIONAL LYMPH NODE                                     7               163
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  SLC7A11 MUTATED             1       0       0        0        0        2
  SLC7A11 WILD-TYPE           9       6      22       10       24       15
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  SLC7A11 MUTATED           0         1         0         2          1
  SLC7A11 WILD-TYPE        10        13         9        29         12
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  SLC7A11 MUTATED            1          2        0
  SLC7A11 WILD-TYPE         21         42       12
D86V5, multiclass
             clus
vv            SLC7A11 MUTATED SLC7A11 WILD-TYPE
  I OR II NOS               1                 9
  STAGE 0                   0                 6
  STAGE I                   0                22
  STAGE IA                  0                10
  STAGE IB                  0                24
  STAGE II                  2                15
  STAGE IIA                 0                10
  STAGE IIB                 1                13
  STAGE IIC                 0                 9
  STAGE III                 2                29
  STAGE IIIA                1                12
  STAGE IIIB                1                21
  STAGE IIIC                2                42
  STAGE IV                  0                12
[1] 14  2
[1] 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
  SLC7A11 MUTATED       2  1  4  2
  SLC7A11 WILD-TYPE    49 57 49 53
D86V6, multiclass
       clus
vv      SLC7A11 MUTATED SLC7A11 WILD-TYPE
  T0+T1               2                49
  T2                  1                57
  T3                  4                49
  T4                  2                53
[1] 4 2
[1] TRUE
[1] "dimension 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
  SLC7A11 MUTATED     4   3   2   1
  SLC7A11 WILD-TYPE 134  45  30  32
D86V7, multiclass
    clus
vv   SLC7A11 MUTATED SLC7A11 WILD-TYPE
  N0               4               134
  N1               3                45
  N2               2                30
  N3               1                32
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1 M1A M1B M1C
  SLC7A11 MUTATED    10   0   0   0   0
  SLC7A11 WILD-TYPE 230   4   2   2   5
D86V8, multiclass
     clus
vv    SLC7A11 MUTATED SLC7A11 WILD-TYPE
  M0               10               230
  M1                0                 4
  M1A               0                 2
  M1B               0                 2
  M1C               0                 5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D86V9, binary
                   cls
clus                  0   1
  SLC7A11 MUTATED     2   2
  SLC7A11 WILD-TYPE 100  65
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC7A11 MUTATED      2    2
  SLC7A11 WILD-TYPE  100   65
     clus
vv    SLC7A11 MUTATED SLC7A11 WILD-TYPE
  NO                2               100
  YES               2                65
[1] 2 2
[1] FALSE
D86V10, binary
                   cls
clus                  0   1
  SLC7A11 MUTATED     3   8
  SLC7A11 WILD-TYPE  30 227
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC7A11 MUTATED      3    8
  SLC7A11 WILD-TYPE   30  227
     clus
vv    SLC7A11 MUTATED SLC7A11 WILD-TYPE
  NO                3                30
  YES               8               227
[1] 2 2
[1] FALSE
D86V11, continuous
D86V12, binary
                   cls
clus                  0   1
  SLC7A11 MUTATED     3   8
  SLC7A11 WILD-TYPE 100 157
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC7A11 MUTATED      3    8
  SLC7A11 WILD-TYPE  100  157
        clus
vv       SLC7A11 MUTATED SLC7A11 WILD-TYPE
  FEMALE               3               100
  MALE                 8               157
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SLC7A11 MUTATED       0                         0    11
  SLC7A11 WILD-TYPE     3                         1   253
D86V13, multiclass
                           clus
vv                          SLC7A11 MUTATED SLC7A11 WILD-TYPE
  ASIAN                                   0                 3
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  11               253
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D86V14, binary
                   cls
clus                  0   1
  SLC7A11 MUTATED     0  11
  SLC7A11 WILD-TYPE   3 250
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC7A11 MUTATED      0   11
  SLC7A11 WILD-TYPE    3  250
                        clus
vv                       SLC7A11 MUTATED SLC7A11 WILD-TYPE
  HISPANIC OR LATINO                   0                 3
  NOT HISPANIC OR LATINO              11               250
[1] 2 2
[1] FALSE

Clustering(87) Variable = SYNE1 MUTATION ANALYSIS
D87V1, survival
                 sevent
clus2              0  1
  SYNE1 MUTATED   35 31
  SYNE1 WILD-TYPE 93 99
  SYNE1 MUTATED SYNE1 WILD-TYPE 
             66             192 
  SYNE1 MUTATED SYNE1 WILD-TYPE 
             31              99 
$`SYNE1 MUTATED`
TCGA-D3-A1Q8 TCGA-D3-A2JA TCGA-D3-A2JD TCGA-D3-A2JK TCGA-D3-A2JO TCGA-D3-A3C8 
       28.08        88.50        11.41         6.31        64.44        46.32 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51K TCGA-D3-A51T TCGA-D9-A3Z1 TCGA-D9-A6EA 
      103.59        26.37        17.72        13.94         4.01        11.31 
TCGA-D9-A6EC TCGA-DA-A1I0 TCGA-DA-A1I7 TCGA-DA-A3F3 TCGA-EB-A5SG TCGA-EE-A180 
       13.22        10.03        36.69         7.00         0.00         8.12 
TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A20C TCGA-EE-A29E TCGA-EE-A29L TCGA-EE-A2A2 
        1.12         1.35         4.34        38.63         1.08        23.90 
TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GM 
       34.29        17.98        47.21        30.08        19.43        28.31 
TCGA-EE-A2GO TCGA-EE-A2GR TCGA-EE-A2M5 TCGA-EE-A2MC TCGA-EE-A2MI TCGA-EE-A2MJ 
       30.84         1.15         8.84        47.51        14.56        63.42 
TCGA-EE-A2MK TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A3AA TCGA-EE-A3AB 
      111.78        21.60        29.65        27.16       124.31       122.73 
TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JI 
       30.15        13.81        15.95        22.22        27.35        33.60 
TCGA-ER-A19H TCGA-ER-A19P TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NG TCGA-ER-A2NH 
       34.88        34.68        17.72        78.44        12.62        11.74 
TCGA-FS-A1Z3 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZK TCGA-FS-A1ZZ 
       14.24         7.30         3.39        20.38        12.89         5.23 
TCGA-FS-A4F4 TCGA-FS-A4FD TCGA-FW-A3R5 TCGA-FW-A3TV TCGA-GN-A265 TCGA-GN-A266 
        7.36         2.27         0.99         0.16        84.72        10.13 

$`SYNE1 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.47         8.52       111.09        32.42        70.16       110.79 
TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 
       22.55        45.83        81.24        10.29        85.32         8.38 
TCGA-D3-A2J9 TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH 
       21.14        68.22        69.90        30.87         7.50        36.16 
TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 
       92.42        56.19        45.11       114.67        15.25        46.98 
TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO 
       82.29        61.38        13.32        24.00         6.31         9.34 
TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51N 
        5.39        80.22        42.71        15.09        41.10         8.84 
TCGA-D3-A51R TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU 
       20.48        52.01        47.87         1.55         6.97        23.11 
TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I1 
        2.89         9.90        48.79        35.80        51.12        39.19 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB 
       13.68         9.99        44.52        25.15         4.93        22.36 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R 
        6.64        19.36        17.56        14.83        13.15         0.20 
TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A183 
        0.00        13.22        11.57        10.55         6.31        12.20 
TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I 
        5.13         4.31        36.07         5.13         9.21         1.18 
TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29H 
        7.99         9.90        37.97        11.15         8.55         4.41 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S 
       27.12         9.50        12.03         8.09         8.84         9.99 
TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A5 
        2.43         8.68         8.09        11.31        49.22         9.67 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GN 
        8.94        39.39        34.92        16.01        35.54        33.83 
TCGA-EE-A2GP TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 
        5.42        13.02        34.98        36.33        98.27         2.70 
TCGA-EE-A2M8 TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2ML 
        6.18         9.53        29.46        44.25         7.96       111.91 
TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AC 
       56.02        25.08        26.99        23.05         5.56        25.84 
TCGA-EE-A3AD TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 
        3.68        12.72         3.22        22.92        21.60        21.60 
TCGA-EE-A3J8 TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 
       16.14         0.46        13.94        31.40        18.61        12.95 
TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D 
       38.40         5.72        76.41        25.18         3.78         3.52 
TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M 
       11.90        11.11       114.15         4.21        13.45        28.60 
TCGA-ER-A19N TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE 
       42.84         9.57        36.07        11.80         1.87         1.51 
TCGA-ER-A2NF TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN 
       13.08         9.04         6.58        22.49         1.71        18.41 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 
       85.74         4.90        64.47         3.45        11.01        23.80 
TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG 
       15.52         7.33         8.22        19.53        11.08         7.17 
TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR 
       30.87        12.92        47.38        52.08         8.65         8.81 
TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A4F0 
       49.15        40.64         8.68        27.39         0.82        53.85 
TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FW-A3I3 
       28.73        14.20        10.78         5.98         6.41         0.20 
TCGA-FW-A3TU TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 
        0.13         0.43         9.90         7.23        12.85        24.85 
TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS 
       31.33        16.24        15.42        12.16        14.70         5.79 

  SYNE1 MUTATED SYNE1 WILD-TYPE 
              0               0 
  SYNE1 MUTATED SYNE1 WILD-TYPE 
         124.31          114.67 
  SYNE1 MUTATED SYNE1 WILD-TYPE 
          17.85           13.81 
[1] "0.0 - 124.3 (17.9)" "0.0 - 114.7 (13.8)"
[1] "hr=" "1.2"
D87V2, survival
                 sevent
clus2               0   1
  SYNE1 MUTATED    36  31
  SYNE1 WILD-TYPE  96 100
  SYNE1 MUTATED SYNE1 WILD-TYPE 
             67             196 
  SYNE1 MUTATED SYNE1 WILD-TYPE 
             31             100 
$`SYNE1 MUTATED`
TCGA-D3-A1Q8 TCGA-D3-A2JA TCGA-D3-A2JD TCGA-D3-A2JK TCGA-D3-A2JO TCGA-D3-A3C8 
       28.08       115.53        11.87        12.10        66.08        46.32 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51K TCGA-D3-A51T TCGA-D9-A148 TCGA-D9-A3Z1 
      103.59        39.75        18.38        15.06       151.53        11.34 
TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1I0 TCGA-DA-A1I7 TCGA-DA-A3F3 TCGA-EB-A5SG 
       25.18        66.25        20.38        61.18        10.49        45.11 
TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A20C TCGA-EE-A29E TCGA-EE-A29L 
       94.98        33.73        14.70       151.27        39.62         2.60 
TCGA-EE-A2A2 TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ 
       24.43        67.43       314.56       208.04        48.72        89.33 
TCGA-EE-A2GM TCGA-EE-A2GO TCGA-EE-A2GR TCGA-EE-A2M5 TCGA-EE-A2MC TCGA-EE-A2MI 
       75.48       101.95        14.30        21.67        61.51       204.66 
TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A3AA 
       96.23       144.76        43.23       103.56       136.47       124.31 
TCGA-EE-A3AB TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3JA TCGA-EE-A3JD 
      122.73        54.51        13.81        23.47        53.19        27.35 
TCGA-EE-A3JI TCGA-ER-A19H TCGA-ER-A19P TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NG 
      148.08       152.35       162.08       148.18        79.99        31.27 
TCGA-ER-A2NH TCGA-FS-A1Z3 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZK 
       32.05        20.91        27.72        48.85       357.37        23.93 
TCGA-FS-A1ZZ TCGA-FS-A4F4 TCGA-FS-A4FD TCGA-FW-A3R5 TCGA-FW-A3TV TCGA-GN-A265 
       27.02        66.67        77.88        22.92         0.16        84.72 
TCGA-GN-A266 
       10.13 

$`SYNE1 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.57        16.67       112.04       112.57        71.80       133.25 
TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 
       31.59        90.90        95.74        43.43       103.10        65.49 
TCGA-D3-A2J9 TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH 
       23.77       168.00        69.90        48.76       113.52        42.08 
TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 
      171.58        56.19        45.11       130.72        58.06        46.98 
TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO 
      166.52        86.93        60.23        24.53        13.87         9.34 
TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51N 
       21.47       161.85        43.69        40.14       131.90        10.03 
TCGA-D3-A51R TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU 
       51.68       135.75       137.92       166.19         7.43       125.19 
TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-DA-A1HV 
       54.67         3.65         6.41         3.25         9.90        48.89 
TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 
       36.03       117.21       194.83       176.55        35.93       107.34 
TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 
       53.92        65.92        23.44        68.09        28.60       215.44 
TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN 
       15.68        13.87        10.16        35.01         3.55        52.01 
TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 
       29.82        27.22         8.65        26.89        68.15         4.96 
TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B 
      109.64        78.87       168.26        13.55        63.35        80.61 
TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29N 
       47.84        13.97        72.07        32.19        44.35        18.61 
TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W 
       56.42        37.35        14.47        55.92        25.87       171.55 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB 
       17.92        46.82       102.90        39.29        58.75        47.54 
TCGA-EE-A2GE TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GS 
      135.95        54.74        79.66        90.97        13.91        55.59 
TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MD 
       44.88        94.82       129.27        28.83        19.76        47.28 
TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN 
      103.27       103.20        16.96       203.05       167.90        47.54 
TCGA-EE-A2MP TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AH 
      248.65        41.59        53.26        25.84         3.68       138.81 
TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JE 
      172.18       127.20        36.95        64.08        34.32        33.40 
TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 
      101.79        31.40        35.44        13.94        50.76         9.17 
TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F 
       77.75        98.40        48.89        12.59        13.02        26.37 
TCGA-ER-A19G TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19Q 
      268.93         6.44       131.51        61.05        44.05        50.89 
TCGA-ER-A19S TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A3ES 
       37.25        43.82        23.34        20.15        16.37       247.04 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
       80.32        46.98        33.21        92.98       174.21         4.90 
TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1Z7 
      216.92        48.59       228.59       202.65        28.08         7.79 
TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ 
       53.52        40.27        15.45         9.70        32.75        47.38 
TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT 
      101.26        74.73       133.55        11.41       148.80        53.16 
TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A4F0 TCGA-FS-A4F5 TCGA-FS-A4F8 
       26.56        49.48        27.09        77.82        28.73       174.84 
TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A5DY 
       12.43        26.73        49.45         0.20        47.54         2.40 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A267 
        9.90         7.23        14.04       120.46       117.93        64.44 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS 
       62.79        32.48        39.58         6.67 

  SYNE1 MUTATED SYNE1 WILD-TYPE 
           0.16            0.20 
  SYNE1 MUTATED SYNE1 WILD-TYPE 
         357.37          268.93 
  SYNE1 MUTATED SYNE1 WILD-TYPE 
          48.85           47.69 
[1] "0.2 - 357.4 (48.9)" "0.2 - 268.9 (47.7)"
[1] "hr=" "1.2"
D87V3, continuous
                 vv
clus              DISTANT METASTASIS PRIMARY TUMOR
  SYNE1 MUTATED                   10             2
  SYNE1 WILD-TYPE                 25             2
                 vv
clus              REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  SYNE1 MUTATED                                          16                  41
  SYNE1 WILD-TYPE                                        42                 129
D87V4, multiclass
                                           clus
vv                                          SYNE1 MUTATED SYNE1 WILD-TYPE
  DISTANT METASTASIS                                   10              25
  PRIMARY TUMOR                                         2               2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE            16              42
  REGIONAL LYMPH NODE                                  41             129
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  SYNE1 MUTATED             2       2       5        3        1        6
  SYNE1 WILD-TYPE           8       4      17        7       23       11
                 vv
clus              STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  SYNE1 MUTATED           1         4         1        10          4          5
  SYNE1 WILD-TYPE         9        10         8        21          9         17
                 vv
clus              STAGE IIIC STAGE IV
  SYNE1 MUTATED           15        3
  SYNE1 WILD-TYPE         29        9
D87V5, multiclass
             clus
vv            SYNE1 MUTATED SYNE1 WILD-TYPE
  I OR II NOS             2               8
  STAGE 0                 2               4
  STAGE I                 5              17
  STAGE IA                3               7
  STAGE IB                1              23
  STAGE II                6              11
  STAGE IIA               1               9
  STAGE IIB               4              10
  STAGE IIC               1               8
  STAGE III              10              21
  STAGE IIIA              4               9
  STAGE IIIB              5              17
  STAGE IIIC             15              29
  STAGE IV                3               9
[1] 14  2
[1] 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
  SYNE1 MUTATED      12 11 11 18
  SYNE1 WILD-TYPE    39 47 42 37
D87V6, multiclass
       clus
vv      SYNE1 MUTATED SYNE1 WILD-TYPE
  T0+T1            12              39
  T2               11              47
  T3               11              42
  T4               18              37
[1] 4 2
[1] TRUE
[1] "dimension 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
  SYNE1 MUTATED    31   9  12  13
  SYNE1 WILD-TYPE 107  39  20  20
D87V7, multiclass
    clus
vv   SYNE1 MUTATED SYNE1 WILD-TYPE
  N0            31             107
  N1             9              39
  N2            12              20
  N3            13              20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               M0  M1 M1A M1B M1C
  SYNE1 MUTATED    61   1   1   2   0
  SYNE1 WILD-TYPE 179   3   1   0   5
D87V8, multiclass
     clus
vv    SYNE1 MUTATED SYNE1 WILD-TYPE
  M0             61             179
  M1              1               3
  M1A             1               1
  M1B             2               0
  M1C             0               5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D87V9, binary
                 cls
clus               0  1
  SYNE1 MUTATED   24 15
  SYNE1 WILD-TYPE 78 52
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SYNE1 MUTATED     24   15
  SYNE1 WILD-TYPE   78   52
     clus
vv    SYNE1 MUTATED SYNE1 WILD-TYPE
  NO             24              78
  YES            15              52
[1] 2 2
[1] FALSE
D87V10, binary
                 cls
clus                0   1
  SYNE1 MUTATED    13  56
  SYNE1 WILD-TYPE  20 179
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SYNE1 MUTATED     13   56
  SYNE1 WILD-TYPE   20  179
     clus
vv    SYNE1 MUTATED SYNE1 WILD-TYPE
  NO             13              20
  YES            56             179
[1] 2 2
[1] FALSE
D87V11, continuous
D87V12, binary
                 cls
clus                0   1
  SYNE1 MUTATED    22  47
  SYNE1 WILD-TYPE  81 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SYNE1 MUTATED     22   47
  SYNE1 WILD-TYPE   81  118
        clus
vv       SYNE1 MUTATED SYNE1 WILD-TYPE
  FEMALE            22              81
  MALE              47             118
[1] 2 2
[1] FALSE
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SYNE1 MUTATED       0                         0    69
  SYNE1 WILD-TYPE     3                         1   195
D87V13, multiclass
                           clus
vv                          SYNE1 MUTATED SYNE1 WILD-TYPE
  ASIAN                                 0               3
  BLACK OR AFRICAN AMERICAN             0               1
  WHITE                                69             195
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D87V14, binary
                 cls
clus                0   1
  SYNE1 MUTATED     2  66
  SYNE1 WILD-TYPE   1 195
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SYNE1 MUTATED      2   66
  SYNE1 WILD-TYPE    1  195
                        clus
vv                       SYNE1 MUTATED SYNE1 WILD-TYPE
  HISPANIC OR LATINO                 2               1
  NOT HISPANIC OR LATINO            66             195
[1] 2 2
[1] FALSE

Clustering(88) Variable = NFASC MUTATION ANALYSIS
D88V1, survival
                 sevent
clus2               0   1
  NFASC MUTATED    10  12
  NFASC WILD-TYPE 118 118
  NFASC MUTATED NFASC WILD-TYPE 
             22             236 
  NFASC MUTATED NFASC WILD-TYPE 
             12             118 
$`NFASC MUTATED`
TCGA-D3-A1Q6 TCGA-D3-A3C7 TCGA-D3-A5GO TCGA-DA-A1HW TCGA-DA-A1I1 TCGA-DA-A1I7 
       70.16        46.98        47.87        35.80        39.19        36.69 
TCGA-EE-A29D TCGA-EE-A2MR TCGA-EE-A3AG TCGA-EE-A3J3 TCGA-EE-A3JD TCGA-ER-A3PL 
       11.15        29.65        15.95         3.22        27.35         1.71 
TCGA-FS-A1YY TCGA-FS-A1ZC TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZZ TCGA-FS-A4FC 
       11.01        20.38        52.08         8.65         5.23         6.41 
TCGA-FW-A3R5 TCGA-GN-A262 TCGA-GN-A265 TCGA-GN-A266 
        0.99        24.85        84.72        10.13 

$`NFASC WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       16.47         8.52       111.09        32.42       110.79        28.08 
TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 
       22.55        45.83        81.24        10.29        85.32         8.38 
TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF 
       21.14        88.50        68.22        69.90        11.41        30.87 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO 
        7.50        36.16         6.31        92.42        56.19        64.44 
TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC 
       45.11       114.67        15.25        46.32        82.29        61.38 
TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU 
       13.32        24.00         6.31         9.34       103.59        26.37 
TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K 
        5.39        80.22        42.71        15.09        41.10        17.72 
TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS 
        8.84        20.48        13.94        52.01         1.55         6.97 
TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC 
       23.11         4.01         2.89         9.90        11.31        13.22 
TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 
       48.79        51.12        10.03        13.68         9.99        44.52 
TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 
       25.15         4.93        22.36         6.64        19.36         7.00 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH 
       17.56        14.83        13.15         0.20         0.00         0.00 
TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 
       13.22        11.57        10.55         6.31         8.12         1.12 
TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C 
        1.35        12.20         5.13         4.31        36.07         4.34 
TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C 
        5.13         9.21         1.18         7.99         9.90        37.97 
TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N 
       38.63         8.55         4.41         1.08        27.12         9.50 
TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W 
       12.03         8.09         8.84         9.99         2.43         8.68 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 
        8.09        11.31        49.22        23.90         9.67         8.94 
TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI 
       39.39        34.29        17.98        34.92        47.21        30.08 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO 
       19.43        16.01        35.54        28.31        33.83        30.84 
TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 
        5.42         1.15        13.02        34.98        36.33         8.84 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME 
       98.27         2.70         6.18        47.51         9.53        29.46 
TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML 
       44.25         7.96        14.56        63.42       111.78       111.91 
TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MS TCGA-EE-A2MT 
       56.02        25.08        26.99        21.60        27.16        23.05 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE 
        5.56       124.31       122.73        25.84         3.68        30.15 
TCGA-EE-A3AF TCGA-EE-A3AH TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 
       13.81        12.72        22.92        21.60        21.60        16.14 
TCGA-EE-A3JA TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 
       22.22         0.46        13.94        33.60        31.40        18.61 
TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C 
       12.95        38.40         5.72        76.41        25.18         3.78 
TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J 
        3.52        11.90        11.11       114.15        34.88         4.21 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S 
       13.45        28.60        42.84        34.68         9.57        36.07 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF 
       17.72        78.44        11.80         1.87         1.51        13.08 
TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-FR-A3YN 
       12.62        11.74         9.04         6.58        22.49        18.41 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1Z0 TCGA-FS-A1Z3 
       85.74         4.90        64.47         3.45        23.80        14.24 
TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZD TCGA-FS-A1ZE 
       15.52         7.33         7.30         3.39         8.22        19.53 
TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM 
       11.08         7.17        30.87        12.92        12.89        47.38 
TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY 
        8.81        49.15        40.64         8.68        27.39         0.82 
TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB 
       53.85         7.36        28.73        14.20        10.78         5.98 
TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
        2.27         0.20         0.13         0.16         0.43         9.90 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
        7.23        12.85        31.33        16.24        15.42        12.16 
TCGA-GN-A26D TCGA-QB-A6FS 
       14.70         5.79 

  NFASC MUTATED NFASC WILD-TYPE 
           0.99            0.00 
  NFASC MUTATED NFASC WILD-TYPE 
          84.72          124.31 
  NFASC MUTATED NFASC WILD-TYPE 
         22.615          14.400 
[1] "1.0 - 84.7 (22.6)"  "0.0 - 124.3 (14.4)"
[1] "hr=" "1"  
D88V2, survival
                 sevent
clus2               0   1
  NFASC MUTATED    10  12
  NFASC WILD-TYPE 122 119
  NFASC MUTATED NFASC WILD-TYPE 
             22             241 
  NFASC MUTATED NFASC WILD-TYPE 
             12             119 
$`NFASC MUTATED`
TCGA-D3-A1Q6 TCGA-D3-A3C7 TCGA-D3-A5GO TCGA-DA-A1HW TCGA-DA-A1I1 TCGA-DA-A1I7 
       71.80        46.98       137.92        36.03       194.83        61.18 
TCGA-EE-A29D TCGA-EE-A2MR TCGA-EE-A3AG TCGA-EE-A3J3 TCGA-EE-A3JD TCGA-ER-A3PL 
       13.97       103.56        23.47       172.18        27.35        33.21 
TCGA-FS-A1YY TCGA-FS-A1ZC TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZZ TCGA-FS-A4FC 
      228.59       357.37        74.73       133.55        27.02        49.45 
TCGA-FW-A3R5 TCGA-GN-A262 TCGA-GN-A265 TCGA-GN-A266 
       22.92       120.46        84.72        10.13 

$`NFASC WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       16.57        16.67       112.04       112.57       133.25        28.08 
TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 
       31.59        90.90        95.74        43.43       103.10        65.49 
TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF 
       23.77       115.53       168.00        69.90        11.87        48.76 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO 
      113.52        42.08        12.10       171.58        56.19        66.08 
TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC 
       45.11       130.72        58.06        46.32       166.52        86.93 
TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU 
       60.23        24.53        13.87         9.34       103.59        39.75 
TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K 
       21.47       161.85        43.69        40.14       131.90        18.38 
TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS 
       10.03        51.68        15.06       135.75       166.19         7.43 
TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 
      125.19       151.53        54.67         3.65         6.41        11.34 
TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1HY 
        3.25         9.90        25.18        66.25        48.89       117.21 
TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I8 TCGA-DA-A1IA 
       20.38       176.55        35.93       107.34        53.92        65.92 
TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 
       23.44        68.09        28.60        10.49       215.44        15.68 
TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN 
       13.87        10.16        45.11        35.01         3.55        52.01 
TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 
       29.82        27.22         8.65        94.98        33.73        14.70 
TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F 
       26.89        68.15         4.96       109.64       151.27        78.87 
TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E 
      168.26        13.55        63.35        80.61        47.84        39.62 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P 
       72.07        32.19         2.60        44.35        18.61        56.42 
TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X 
       37.35        14.47        55.92        25.87       171.55        17.92 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB 
       46.82       102.90        24.43        39.29        58.75        47.54 
TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ 
       67.43       314.56       135.95       208.04        48.72        89.33 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP 
       54.74        79.66        75.48        90.97       101.95        13.91 
TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 
       14.30        55.59        44.88        94.82        21.67       129.27 
TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG 
       28.83        19.76        61.51        47.28       103.27       103.20 
TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM 
       16.96       204.66        96.23       144.76       203.05       167.90 
TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU 
       47.54       248.65        43.23       136.47        41.59        53.26 
TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF 
      124.31       122.73        25.84         3.68        54.51        13.81 
TCGA-EE-A3AH TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA 
      138.81       127.20        36.95        64.08        34.32        53.19 
TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 
       33.40       101.79       148.08        31.40        35.44        13.94 
TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D 
       50.76         9.17        77.75        98.40        48.89        12.59 
TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L 
       13.02        26.37       268.93       152.35         6.44       131.51 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W 
       61.05        44.05       162.08        50.89        37.25       148.18 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG 
       79.99        43.82        23.34        20.15        16.37        31.27 
TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-FR-A3YN TCGA-FR-A44A 
       32.05       247.04        80.32        46.98        92.98       174.21 
TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 
        4.90       216.92        48.59       202.65        20.91        28.08 
TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF 
        7.79        27.72        48.85        53.52        40.27        15.45 
TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZR 
        9.70        32.75        47.38        23.93       101.26        11.41 
TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A4F0 
      148.80        53.16        26.56        49.48        27.09        77.82 
TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FD 
       66.67        28.73       174.84        12.43        26.73        77.88 
TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
        0.20        47.54         0.16         2.40         9.90         7.23 
TCGA-GF-A6C8 TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D 
       14.04       117.93        64.44        62.79        32.48        39.58 
TCGA-QB-A6FS 
        6.67 

  NFASC MUTATED NFASC WILD-TYPE 
          10.13            0.16 
  NFASC MUTATED NFASC WILD-TYPE 
         357.37          314.56 
  NFASC MUTATED NFASC WILD-TYPE 
          66.49           47.54 
[1] "10.1 - 357.4 (66.5)" "0.2 - 314.6 (47.5)" 
[1] "hr=" "1.4"
D88V3, continuous
                 vv
clus              DISTANT METASTASIS PRIMARY TUMOR
  NFASC MUTATED                    5             0
  NFASC WILD-TYPE                 30             4
                 vv
clus              REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  NFASC MUTATED                                           9                   8
  NFASC WILD-TYPE                                        49                 162
D88V4, multiclass
                                           clus
vv                                          NFASC MUTATED NFASC WILD-TYPE
  DISTANT METASTASIS                                    5              30
  PRIMARY TUMOR                                         0               4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE             9              49
  REGIONAL LYMPH NODE                                   8             162
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  NFASC MUTATED             2       0       1        0        1        2
  NFASC WILD-TYPE           8       6      21       10       23       15
                 vv
clus              STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  NFASC MUTATED           2         1         0         5          0          2
  NFASC WILD-TYPE         8        13         9        26         13         20
                 vv
clus              STAGE IIIC STAGE IV
  NFASC MUTATED            2        1
  NFASC WILD-TYPE         42       11
D88V5, multiclass
             clus
vv            NFASC MUTATED NFASC WILD-TYPE
  I OR II NOS             2               8
  STAGE 0                 0               6
  STAGE I                 1              21
  STAGE IA                0              10
  STAGE IB                1              23
  STAGE II                2              15
  STAGE IIA               2               8
  STAGE IIB               1              13
  STAGE IIC               0               9
  STAGE III               5              26
  STAGE IIIA              0              13
  STAGE IIIB              2              20
  STAGE IIIC              2              42
  STAGE IV                1              11
[1] 14  2
[1] 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
  NFASC MUTATED       5  2  6  2
  NFASC WILD-TYPE    46 56 47 53
D88V6, multiclass
       clus
vv      NFASC MUTATED NFASC WILD-TYPE
  T0+T1             5              46
  T2                2              56
  T3                6              47
  T4                2              53
[1] 4 2
[1] TRUE
[1] "dimension 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
  NFASC MUTATED    10   4   4   1
  NFASC WILD-TYPE 128  44  28  32
D88V7, multiclass
    clus
vv   NFASC MUTATED NFASC WILD-TYPE
  N0            10             128
  N1             4              44
  N2             4              28
  N3             1              32
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               M0  M1 M1A M1B M1C
  NFASC MUTATED    18   0   1   0   0
  NFASC WILD-TYPE 222   4   1   2   5
D88V8, multiclass
     clus
vv    NFASC MUTATED NFASC WILD-TYPE
  M0             18             222
  M1              0               4
  M1A             1               1
  M1B             0               2
  M1C             0               5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D88V9, binary
                 cls
clus               0  1
  NFASC MUTATED    4  3
  NFASC WILD-TYPE 98 64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NFASC MUTATED      4    3
  NFASC WILD-TYPE   98   64
     clus
vv    NFASC MUTATED NFASC WILD-TYPE
  NO              4              98
  YES             3              64
[1] 2 2
[1] FALSE
D88V10, binary
                 cls
clus                0   1
  NFASC MUTATED     7  15
  NFASC WILD-TYPE  26 220
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NFASC MUTATED      7   15
  NFASC WILD-TYPE   26  220
     clus
vv    NFASC MUTATED NFASC WILD-TYPE
  NO              7              26
  YES            15             220
[1] 2 2
[1] FALSE
D88V11, continuous
D88V12, binary
                 cls
clus                0   1
  NFASC MUTATED     6  16
  NFASC WILD-TYPE  97 149
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NFASC MUTATED      6   16
  NFASC WILD-TYPE   97  149
        clus
vv       NFASC MUTATED NFASC WILD-TYPE
  FEMALE             6              97
  MALE              16             149
[1] 2 2
[1] FALSE
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  NFASC MUTATED       0                         0    22
  NFASC WILD-TYPE     3                         1   242
D88V13, multiclass
                           clus
vv                          NFASC MUTATED NFASC WILD-TYPE
  ASIAN                                 0               3
  BLACK OR AFRICAN AMERICAN             0               1
  WHITE                                22             242
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D88V14, binary
                 cls
clus                0   1
  NFASC MUTATED     1  21
  NFASC WILD-TYPE   2 240
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NFASC MUTATED      1   21
  NFASC WILD-TYPE    2  240
                        clus
vv                       NFASC MUTATED NFASC WILD-TYPE
  HISPANIC OR LATINO                 1               2
  NOT HISPANIC OR LATINO            21             240
[1] 2 2
[1] FALSE

Clustering(89) Variable = CCDC11 MUTATION ANALYSIS
D89V1, survival
                  sevent
clus2                0   1
  CCDC11 MUTATED     7  10
  CCDC11 WILD-TYPE 121 120
  CCDC11 MUTATED CCDC11 WILD-TYPE 
              17              241 
  CCDC11 MUTATED CCDC11 WILD-TYPE 
              10              120 
$`CCDC11 MUTATED`
TCGA-D3-A1Q5 TCGA-D3-A2JF TCGA-D9-A3Z1 TCGA-DA-A1HV TCGA-EE-A17X TCGA-EE-A181 
       32.42        30.87         4.01        48.79        11.57         1.12 
TCGA-EE-A20C TCGA-EE-A29M TCGA-EE-A2A2 TCGA-EE-A2GC TCGA-EE-A2GI TCGA-EE-A2M6 
        4.34        27.12        23.90        34.29        30.08        98.27 
TCGA-EE-A2MJ TCGA-EE-A3AG TCGA-EE-A3J5 TCGA-FS-A4F5 TCGA-GN-A26A 
       63.42        15.95        21.60        28.73        12.16 

$`CCDC11 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       16.47         8.52       111.09        70.16       110.79        28.08 
TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 
       22.55        45.83        81.24        10.29        85.32         8.38 
TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JG 
       21.14        88.50        68.22        69.90        11.41         7.50 
TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP 
       36.16         6.31        92.42        56.19        64.44        45.11 
TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC 
      114.67        15.25        46.98        46.32        82.29        61.38 
TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU 
       13.32        24.00         6.31         9.34       103.59        26.37 
TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K 
        5.39        80.22        42.71        15.09        41.10        17.72 
TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR 
        8.84        20.48        13.94        52.01        47.87         1.55 
TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC 
        6.97        23.11         2.89         9.90        11.31        13.22 
TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 
       35.80        51.12        10.03        39.19        13.68         9.99 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC 
       44.52        36.69        25.15         4.93        22.36         6.64 
TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R 
       19.36         7.00        17.56        14.83        13.15         0.20 
TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 
        0.00         0.00        13.22        10.55         6.31         8.12 
TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20F 
        1.35        12.20         5.13         4.31        36.07         5.13 
TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D 
        9.21         1.18         7.99         9.90        37.97        11.15 
TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P 
       38.63         8.55         4.41         1.08         9.50        12.03 
TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X 
        8.09         8.84         9.99         2.43         8.68         8.09 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD 
       11.31        49.22         9.67         8.94        39.39        17.98 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM 
       34.92        47.21        19.43        16.01        35.54        28.31 
TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT 
       33.83        30.84         5.42         1.15        13.02        34.98 
TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD 
       36.33         8.84         2.70         6.18        47.51         9.53 
TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2ML 
       29.46        44.25         7.96        14.56       111.78       111.91 
TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS 
       56.02        25.08        26.99        21.60        29.65        27.16 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD 
       23.05         5.56       124.31       122.73        25.84         3.68 
TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 
       30.15        13.81        12.72         3.22        22.92        21.60 
TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI 
       16.14        22.22        27.35         0.46        13.94        33.60 
TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A 
       31.40        18.61        12.95        38.40         5.72        76.41 
TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G 
       25.18         3.78         3.52        11.90        11.11       114.15 
TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P 
       34.88         4.21        13.45        28.60        42.84        34.68 
TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
        9.57        36.07        17.72        78.44        11.80         1.87 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET 
        1.51        13.08        12.62        11.74         9.04         6.58 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW 
       22.49         1.71        18.41        85.74         4.90        64.47 
TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 
        3.45        11.01        23.80        14.24        15.52         7.33 
TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF 
        7.30         3.39        20.38         8.22        19.53        11.08 
TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP 
        7.17        30.87        12.92        12.89        47.38        52.08 
TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW 
        8.65         8.81        49.15        40.64         8.68        27.39 
TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 
        0.82         5.23        53.85         7.36        14.20        10.78 
TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU 
        5.98         6.41         2.27         0.20         0.99         0.13 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 
        0.16         0.43         9.90         7.23        12.85        24.85 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26D 
       31.33        84.72        10.13        16.24        15.42        14.70 
TCGA-QB-A6FS 
        5.79 

  CCDC11 MUTATED CCDC11 WILD-TYPE 
            1.12             0.00 
  CCDC11 MUTATED CCDC11 WILD-TYPE 
           98.27           124.31 
  CCDC11 MUTATED CCDC11 WILD-TYPE 
           27.12            14.20 
[1] "1.1 - 98.3 (27.1)"  "0.0 - 124.3 (14.2)"
[1] "hr=" "1"  
D89V2, survival
                  sevent
clus2                0   1
  CCDC11 MUTATED     7  10
  CCDC11 WILD-TYPE 125 121
  CCDC11 MUTATED CCDC11 WILD-TYPE 
              17              246 
  CCDC11 MUTATED CCDC11 WILD-TYPE 
              10              121 
$`CCDC11 MUTATED`
TCGA-D3-A1Q5 TCGA-D3-A2JF TCGA-D9-A3Z1 TCGA-DA-A1HV TCGA-EE-A17X TCGA-EE-A181 
      112.57        48.76        11.34        48.89        29.82        33.73 
TCGA-EE-A20C TCGA-EE-A29M TCGA-EE-A2A2 TCGA-EE-A2GC TCGA-EE-A2GI TCGA-EE-A2M6 
      151.27        44.35        24.43        67.43        48.72       129.27 
TCGA-EE-A2MJ TCGA-EE-A3AG TCGA-EE-A3J5 TCGA-FS-A4F5 TCGA-GN-A26A 
       96.23        23.47        36.95        28.73        32.48 

$`CCDC11 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       16.57        16.67       112.04        71.80       133.25        28.08 
TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 
       31.59        90.90        95.74        43.43       103.10        65.49 
TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JG 
       23.77       115.53       168.00        69.90        11.87       113.52 
TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP 
       42.08        12.10       171.58        56.19        66.08        45.11 
TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC 
      130.72        58.06        46.98        46.32       166.52        86.93 
TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU 
       60.23        24.53        13.87         9.34       103.59        39.75 
TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K 
       21.47       161.85        43.69        40.14       131.90        18.38 
TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR 
       10.03        51.68        15.06       135.75       137.92       166.19 
TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX 
        7.43       125.19       151.53        54.67         3.65         6.41 
TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1HW TCGA-DA-A1HY 
        3.25         9.90        25.18        66.25        36.03       117.21 
TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 
       20.38       194.83       176.55        35.93       107.34        61.18 
TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 
       53.92        65.92        23.44        68.09        28.60        10.49 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH 
      215.44        15.68        13.87        10.16        45.11        35.01 
TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A182 
        3.55        52.01        27.22         8.65        94.98        14.70 
TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H 
       26.89        68.15         4.96       109.64        78.87       168.26 
TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E 
       13.55        63.35        80.61        47.84        13.97        39.62 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
       72.07        32.19         2.60        18.61        56.42        37.35 
TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 
       14.47        55.92        25.87       171.55        17.92        46.82 
TCGA-EE-A2A1 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE 
      102.90        39.29        58.75        47.54       314.56       135.95 
TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN 
      208.04        89.33        54.74        79.66        75.48        90.97 
TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU 
      101.95        13.91        14.30        55.59        44.88        94.82 
TCGA-EE-A2M5 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME 
       21.67        28.83        19.76        61.51        47.28       103.27 
TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM 
      103.20        16.96       204.66       144.76       203.05       167.90 
TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT 
       47.54       248.65        43.23       103.56       136.47        41.59 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE 
       53.26       124.31       122.73        25.84         3.68        54.51 
TCGA-EE-A3AF TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 
       13.81       138.81       172.18       127.20        64.08        34.32 
TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 
       53.19        27.35        33.40       101.79       148.08        31.40 
TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B 
       35.44        13.94        50.76         9.17        77.75        98.40 
TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H 
       48.89        12.59        13.02        26.37       268.93       152.35 
TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q 
        6.44       131.51        61.05        44.05       162.08        50.89 
TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE 
       37.25       148.18        79.99        43.82        23.34        20.15 
TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV 
       16.37        31.27        32.05       247.04        80.32        46.98 
TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX 
       33.21        92.98       174.21         4.90       216.92        48.59 
TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA 
      228.59       202.65        20.91        28.08         7.79        27.72 
TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG 
       48.85       357.37        53.52        40.27        15.45         9.70 
TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ 
       32.75        47.38        23.93       101.26        74.73       133.55 
TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY 
       11.41       148.80        53.16        26.56        49.48        27.09 
TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB 
       27.02        77.82        66.67       174.84        12.43        26.73 
TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV 
       49.45        77.88         0.20        22.92        47.54         0.16 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 
        2.40         9.90         7.23        14.04       120.46       117.93 
TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26D TCGA-QB-A6FS 
       84.72        10.13        64.44        62.79        39.58         6.67 

  CCDC11 MUTATED CCDC11 WILD-TYPE 
           11.34             0.16 
  CCDC11 MUTATED CCDC11 WILD-TYPE 
          151.27           357.37 
  CCDC11 MUTATED CCDC11 WILD-TYPE 
           44.35            48.72 
[1] "11.3 - 151.3 (44.4)" "0.2 - 357.4 (48.7)" 
[1] "hr=" "1.4"
D89V3, continuous
                  vv
clus               DISTANT METASTASIS PRIMARY TUMOR
  CCDC11 MUTATED                    2             0
  CCDC11 WILD-TYPE                 33             4
                  vv
clus               REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  CCDC11 MUTATED                                           4
  CCDC11 WILD-TYPE                                        54
                  vv
clus               REGIONAL LYMPH NODE
  CCDC11 MUTATED                    11
  CCDC11 WILD-TYPE                 159
D89V4, multiclass
                                           clus
vv                                          CCDC11 MUTATED CCDC11 WILD-TYPE
  DISTANT METASTASIS                                     2               33
  PRIMARY TUMOR                                          0                4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE              4               54
  REGIONAL LYMPH NODE                                   11              159
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  CCDC11 MUTATED             1       1       1        3        2        1
  CCDC11 WILD-TYPE           9       5      21        7       22       16
                  vv
clus               STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  CCDC11 MUTATED           0         1         0         3          1
  CCDC11 WILD-TYPE        10        13         9        28         12
                  vv
clus               STAGE IIIB STAGE IIIC STAGE IV
  CCDC11 MUTATED            1          2        0
  CCDC11 WILD-TYPE         21         42       12
D89V5, multiclass
             clus
vv            CCDC11 MUTATED CCDC11 WILD-TYPE
  I OR II NOS              1                9
  STAGE 0                  1                5
  STAGE I                  1               21
  STAGE IA                 3                7
  STAGE IB                 2               22
  STAGE II                 1               16
  STAGE IIA                0               10
  STAGE IIB                1               13
  STAGE IIC                0                9
  STAGE III                3               28
  STAGE IIIA               1               12
  STAGE IIIB               1               21
  STAGE IIIC               2               42
  STAGE IV                 0               12
[1] 14  2
[1] 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
  CCDC11 MUTATED       6  3  3  3
  CCDC11 WILD-TYPE    45 55 50 52
D89V6, multiclass
       clus
vv      CCDC11 MUTATED CCDC11 WILD-TYPE
  T0+T1              6               45
  T2                 3               55
  T3                 3               50
  T4                 3               52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  CCDC11 MUTATED    11   3   2   1
  CCDC11 WILD-TYPE 127  45  30  32
D89V7, multiclass
    clus
vv   CCDC11 MUTATED CCDC11 WILD-TYPE
  N0             11              127
  N1              3               45
  N2              2               30
  N3              1               32
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                M0  M1 M1A M1B M1C
  CCDC11 MUTATED    17   0   0   0   0
  CCDC11 WILD-TYPE 223   4   2   2   5
D89V8, multiclass
     clus
vv    CCDC11 MUTATED CCDC11 WILD-TYPE
  M0              17              223
  M1               0                4
  M1A              0                2
  M1B              0                2
  M1C              0                5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D89V9, binary
                  cls
clus                0  1
  CCDC11 MUTATED    9  2
  CCDC11 WILD-TYPE 93 65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CCDC11 MUTATED      9    2
  CCDC11 WILD-TYPE   93   65
     clus
vv    CCDC11 MUTATED CCDC11 WILD-TYPE
  NO               9               93
  YES              2               65
[1] 2 2
[1] FALSE
D89V10, binary
                  cls
clus                 0   1
  CCDC11 MUTATED     2  15
  CCDC11 WILD-TYPE  31 220
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CCDC11 MUTATED      2   15
  CCDC11 WILD-TYPE   31  220
     clus
vv    CCDC11 MUTATED CCDC11 WILD-TYPE
  NO               2               31
  YES             15              220
[1] 2 2
[1] FALSE
D89V11, continuous
D89V12, binary
                  cls
clus                 0   1
  CCDC11 MUTATED     5  12
  CCDC11 WILD-TYPE  98 153
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CCDC11 MUTATED      5   12
  CCDC11 WILD-TYPE   98  153
        clus
vv       CCDC11 MUTATED CCDC11 WILD-TYPE
  FEMALE              5               98
  MALE               12              153
[1] 2 2
[1] FALSE
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CCDC11 MUTATED       0                         0    17
  CCDC11 WILD-TYPE     3                         1   247
D89V13, multiclass
                           clus
vv                          CCDC11 MUTATED CCDC11 WILD-TYPE
  ASIAN                                  0                3
  BLACK OR AFRICAN AMERICAN              0                1
  WHITE                                 17              247
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D89V14, binary
                  cls
clus                 0   1
  CCDC11 MUTATED     0  16
  CCDC11 WILD-TYPE   3 245
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CCDC11 MUTATED      0   16
  CCDC11 WILD-TYPE    3  245
                        clus
vv                       CCDC11 MUTATED CCDC11 WILD-TYPE
  HISPANIC OR LATINO                  0                3
  NOT HISPANIC OR LATINO             16              245
[1] 2 2
[1] FALSE

Clustering(90) Variable = IL31RA MUTATION ANALYSIS
D90V1, survival
                  sevent
clus2                0   1
  IL31RA MUTATED    11   5
  IL31RA WILD-TYPE 117 125
  IL31RA MUTATED IL31RA WILD-TYPE 
              16              242 
  IL31RA MUTATED IL31RA WILD-TYPE 
               5              125 
$`IL31RA MUTATED`
TCGA-D3-A2J7 TCGA-D3-A2JF TCGA-D9-A6EC TCGA-EE-A181 TCGA-EE-A29M TCGA-EE-A2GT 
       85.32        30.87        13.22         1.12        27.12        34.98 
TCGA-EE-A2MP TCGA-EE-A2MT TCGA-EE-A3AC TCGA-EE-A3AG TCGA-EE-A3JA TCGA-EE-A3JI 
       26.99        23.05        25.84        15.95        22.22        33.60 
TCGA-FS-A1ZR TCGA-FS-A4F0 TCGA-FW-A3R5 TCGA-QB-A6FS 
        8.81        53.85         0.99         5.79 

$`IL31RA WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.47         8.52       111.09        32.42        70.16       110.79 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J8 
       28.08        22.55        45.83        81.24        10.29         8.38 
TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JG 
       21.14        88.50        68.22        69.90        11.41         7.50 
TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP 
       36.16         6.31        92.42        56.19        64.44        45.11 
TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC 
      114.67        15.25        46.98        46.32        82.29        61.38 
TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU 
       13.32        24.00         6.31         9.34       103.59        26.37 
TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K 
        5.39        80.22        42.71        15.09        41.10        17.72 
TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR 
        8.84        20.48        13.94        52.01        47.87         1.55 
TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA 
        6.97        23.11         4.01         2.89         9.90        11.31 
TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 
       48.79        35.80        51.12        10.03        39.19        13.68 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB 
        9.99        44.52        36.69        25.15         4.93        22.36 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q 
        6.64        19.36         7.00        17.56        14.83        13.15 
TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y 
        0.20         0.00         0.00        13.22        11.57        10.55 
TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 
        6.31         8.12         1.35        12.20         5.13         4.31 
TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A 
       36.07         4.34         5.13         9.21         1.18         7.99 
TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H 
        9.90        37.97        11.15        38.63         8.55         4.41 
TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S 
        1.08         9.50        12.03         8.09         8.84         9.99 
TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 
        2.43         8.68         8.09        11.31        49.22        23.90 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE 
        9.67         8.94        39.39        34.29        17.98        34.92 
TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM 
       47.21        30.08        19.43        16.01        35.54        28.31 
TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU 
       33.83        30.84         5.42         1.15        13.02        36.33 
TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD 
        8.84        98.27         2.70         6.18        47.51         9.53 
TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK 
       29.46        44.25         7.96        14.56        63.42       111.78 
TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS 
      111.91        56.02        25.08        21.60        29.65        27.16 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF 
        5.56       124.31       122.73         3.68        30.15        13.81 
TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 
       12.72         3.22        22.92        21.60        21.60        16.14 
TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 
       27.35         0.46        13.94        31.40        18.61        12.95 
TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D 
       38.40         5.72        76.41        25.18         3.78         3.52 
TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L 
       11.90        11.11       114.15        34.88         4.21        13.45 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W 
       28.60        42.84        34.68         9.57        36.07        17.72 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG 
       78.44        11.80         1.87         1.51        13.08        12.62 
TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN 
       11.74         9.04         6.58        22.49         1.71        18.41 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 
       85.74         4.90        64.47         3.45        11.01        23.80 
TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC 
       14.24        15.52         7.33         7.30         3.39        20.38 
TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ 
        8.22        19.53        11.08         7.17        30.87        12.92 
TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZT 
       12.89        47.38        52.08         8.65        49.15        40.64 
TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F4 TCGA-FS-A4F5 
        8.68        27.39         0.82         5.23         7.36        28.73 
TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 
       14.20        10.78         5.98         6.41         2.27         0.20 
TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 
        0.13         0.16         0.43         9.90         7.23        12.85 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 
       24.85        31.33        84.72        10.13        16.24        15.42 
TCGA-GN-A26A TCGA-GN-A26D 
       12.16        14.70 

  IL31RA MUTATED IL31RA WILD-TYPE 
            0.99             0.00 
  IL31RA MUTATED IL31RA WILD-TYPE 
           85.32           124.31 
  IL31RA MUTATED IL31RA WILD-TYPE 
          24.445           14.220 
[1] "1.0 - 85.3 (24.4)"  "0.0 - 124.3 (14.2)"
[1] "hr=" "1.8"
D90V2, survival
                  sevent
clus2                0   1
  IL31RA MUTATED    11   5
  IL31RA WILD-TYPE 121 126
  IL31RA MUTATED IL31RA WILD-TYPE 
              16              247 
  IL31RA MUTATED IL31RA WILD-TYPE 
               5              126 
$`IL31RA MUTATED`
TCGA-D3-A2J7 TCGA-D3-A2JF TCGA-D9-A6EC TCGA-EE-A181 TCGA-EE-A29M TCGA-EE-A2GT 
      103.10        48.76        66.25        33.73        44.35        44.88 
TCGA-EE-A2MP TCGA-EE-A2MT TCGA-EE-A3AC TCGA-EE-A3AG TCGA-EE-A3JA TCGA-EE-A3JI 
      248.65        41.59        25.84        23.47        53.19       148.08 
TCGA-FS-A1ZR TCGA-FS-A4F0 TCGA-FW-A3R5 TCGA-QB-A6FS 
       11.41        77.82        22.92         6.67 

$`IL31RA WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.57        16.67       112.04       112.57        71.80       133.25 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J8 
       28.08        31.59        90.90        95.74        43.43        65.49 
TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JG 
       23.77       115.53       168.00        69.90        11.87       113.52 
TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP 
       42.08        12.10       171.58        56.19        66.08        45.11 
TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC 
      130.72        58.06        46.98        46.32       166.52        86.93 
TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU 
       60.23        24.53        13.87         9.34       103.59        39.75 
TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K 
       21.47       161.85        43.69        40.14       131.90        18.38 
TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR 
       10.03        51.68        15.06       135.75       137.92       166.19 
TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX 
        7.43       125.19       151.53        54.67         3.65         6.41 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-DA-A1HV TCGA-DA-A1HW 
       11.34         3.25         9.90        25.18        48.89        36.03 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 
      117.21        20.38       194.83       176.55        35.93       107.34 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
       61.18        53.92        65.92        23.44        68.09        28.60 
TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG 
       10.49       215.44        15.68        13.87        10.16        45.11 
TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z 
       35.01         3.55        52.01        29.82        27.22         8.65 
TCGA-EE-A180 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B 
       94.98        14.70        26.89        68.15         4.96       109.64 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B 
      151.27        78.87       168.26        13.55        63.35        80.61 
TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L 
       47.84        13.97        39.62        72.07        32.19         2.60 
TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V 
       18.61        56.42        37.35        14.47        55.92        25.87 
TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 
      171.55        17.92        46.82       102.90        24.43        39.29 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH 
       58.75        47.54        67.43       314.56       135.95       208.04 
TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN 
       48.72        89.33        54.74        79.66        75.48        90.97 
TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M5 
      101.95        13.91        14.30        55.59        94.82        21.67 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME 
      129.27        28.83        19.76        61.51        47.28       103.27 
TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML 
      103.20        16.96       204.66        96.23       144.76       203.05 
TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MU 
      167.90        47.54        43.23       103.56       136.47        53.26 
TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AH 
      124.31       122.73         3.68        54.51        13.81       138.81 
TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JD 
      172.18       127.20        36.95        64.08        34.32        27.35 
TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 
       33.40       101.79        31.40        35.44        13.94        50.76 
TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E 
        9.17        77.75        98.40        48.89        12.59        13.02 
TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M 
       26.37       268.93       152.35         6.44       131.51        61.05 
TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 
       44.05       162.08        50.89        37.25       148.18        79.99 
TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH 
       43.82        23.34        20.15        16.37        31.27        32.05 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A 
      247.04        80.32        46.98        33.21        92.98       174.21 
TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
        4.90       216.92        48.59       228.59       202.65        20.91 
TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD 
       28.08         7.79        27.72        48.85       357.37        53.52 
TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK 
       40.27        15.45         9.70        32.75        47.38        23.93 
TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU 
      101.26        74.73       133.55       148.80        53.16        26.56 
TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 
       49.48        27.09        27.02        66.67        28.73       174.84 
TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU 
       12.43        26.73        49.45        77.88         0.20        47.54 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 
        0.16         2.40         9.90         7.23        14.04       120.46 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
      117.93        84.72        10.13        64.44        62.79        32.48 
TCGA-GN-A26D 
       39.58 

  IL31RA MUTATED IL31RA WILD-TYPE 
            6.67             0.16 
  IL31RA MUTATED IL31RA WILD-TYPE 
          248.65           357.37 
  IL31RA MUTATED IL31RA WILD-TYPE 
          44.615           48.720 
[1] "6.7 - 248.7 (44.6)" "0.2 - 357.4 (48.7)"
[1] "hr=" "1.6"
D90V3, continuous
                  vv
clus               DISTANT METASTASIS PRIMARY TUMOR
  IL31RA MUTATED                    2             1
  IL31RA WILD-TYPE                 33             3
                  vv
clus               REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  IL31RA MUTATED                                           3
  IL31RA WILD-TYPE                                        55
                  vv
clus               REGIONAL LYMPH NODE
  IL31RA MUTATED                    11
  IL31RA WILD-TYPE                 159
D90V4, multiclass
                                           clus
vv                                          IL31RA MUTATED IL31RA WILD-TYPE
  DISTANT METASTASIS                                     2               33
  PRIMARY TUMOR                                          1                3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE              3               55
  REGIONAL LYMPH NODE                                   11              159
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  IL31RA MUTATED             1       0       2        1        3        2
  IL31RA WILD-TYPE           9       6      20        9       21       15
                  vv
clus               STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  IL31RA MUTATED           1         1         0         3          1
  IL31RA WILD-TYPE         9        13         9        28         12
                  vv
clus               STAGE IIIB STAGE IIIC STAGE IV
  IL31RA MUTATED            0          2        0
  IL31RA WILD-TYPE         22         42       12
D90V5, multiclass
             clus
vv            IL31RA MUTATED IL31RA WILD-TYPE
  I OR II NOS              1                9
  STAGE 0                  0                6
  STAGE I                  2               20
  STAGE IA                 1                9
  STAGE IB                 3               21
  STAGE II                 2               15
  STAGE IIA                1                9
  STAGE IIB                1               13
  STAGE IIC                0                9
  STAGE III                3               28
  STAGE IIIA               1               12
  STAGE IIIB               0               22
  STAGE IIIC               2               42
  STAGE IV                 0               12
[1] 14  2
[1] 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
  IL31RA MUTATED       4  7  4  1
  IL31RA WILD-TYPE    47 51 49 54
D90V6, multiclass
       clus
vv      IL31RA MUTATED IL31RA WILD-TYPE
  T0+T1              4               47
  T2                 7               51
  T3                 4               49
  T4                 1               54
[1] 4 2
[1] TRUE
[1] "dimension 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
  IL31RA MUTATED    11   2   3   1
  IL31RA WILD-TYPE 127  46  29  32
D90V7, multiclass
    clus
vv   IL31RA MUTATED IL31RA WILD-TYPE
  N0             11              127
  N1              2               46
  N2              3               29
  N3              1               32
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                M0  M1 M1A M1B M1C
  IL31RA MUTATED    17   0   0   0   0
  IL31RA WILD-TYPE 223   4   2   2   5
D90V8, multiclass
     clus
vv    IL31RA MUTATED IL31RA WILD-TYPE
  M0              17              223
  M1               0                4
  M1A              0                2
  M1B              0                2
  M1C              0                5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D90V9, binary
                  cls
clus                0  1
  IL31RA MUTATED    8  1
  IL31RA WILD-TYPE 94 66
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IL31RA MUTATED      8    1
  IL31RA WILD-TYPE   94   66
     clus
vv    IL31RA MUTATED IL31RA WILD-TYPE
  NO               8               94
  YES              1               66
[1] 2 2
[1] FALSE
D90V10, binary
                  cls
clus                 0   1
  IL31RA MUTATED     3  14
  IL31RA WILD-TYPE  30 221
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IL31RA MUTATED      3   14
  IL31RA WILD-TYPE   30  221
     clus
vv    IL31RA MUTATED IL31RA WILD-TYPE
  NO               3               30
  YES             14              221
[1] 2 2
[1] FALSE
D90V11, continuous
D90V12, binary
                  cls
clus                 0   1
  IL31RA MUTATED     6  11
  IL31RA WILD-TYPE  97 154
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IL31RA MUTATED      6   11
  IL31RA WILD-TYPE   97  154
        clus
vv       IL31RA MUTATED IL31RA WILD-TYPE
  FEMALE              6               97
  MALE               11              154
[1] 2 2
[1] FALSE
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  IL31RA MUTATED       0                         0    17
  IL31RA WILD-TYPE     3                         1   247
D90V13, multiclass
                           clus
vv                          IL31RA MUTATED IL31RA WILD-TYPE
  ASIAN                                  0                3
  BLACK OR AFRICAN AMERICAN              0                1
  WHITE                                 17              247
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D90V14, binary
                  cls
clus                 0   1
  IL31RA MUTATED     0  17
  IL31RA WILD-TYPE   3 244
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IL31RA MUTATED      0   17
  IL31RA WILD-TYPE    3  244
                        clus
vv                       IL31RA MUTATED IL31RA WILD-TYPE
  HISPANIC OR LATINO                  0                3
  NOT HISPANIC OR LATINO             17              244
[1] 2 2
[1] FALSE

Clustering(91) Variable = MLL MUTATION ANALYSIS
D91V1, survival
               sevent
clus2             0   1
  MLL MUTATED    20  16
  MLL WILD-TYPE 108 114
  MLL MUTATED MLL WILD-TYPE 
           36           222 
  MLL MUTATED MLL WILD-TYPE 
           16           114 
$`MLL MUTATED`
TCGA-D3-A1QA TCGA-D3-A3C7 TCGA-D3-A51T TCGA-D9-A3Z1 TCGA-DA-A1HY TCGA-DA-A1I0 
       45.83        46.98        13.94         4.01        51.12        10.03 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A3F8 TCGA-EE-A181 TCGA-EE-A29V TCGA-EE-A2A2 
       44.52        36.69        14.83         1.12         2.43        23.90 
TCGA-EE-A2GC TCGA-EE-A2GI TCGA-EE-A2GN TCGA-EE-A2MR TCGA-EE-A3AA TCGA-EE-A3AF 
       34.29        30.08        33.83        29.65       124.31        13.81 
TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-ER-A193 TCGA-ER-A19S 
       22.92        21.60        16.14        22.22        31.40        36.07 
TCGA-ER-A2NC TCGA-ER-A3ET TCGA-FS-A1YW TCGA-FS-A1Z3 TCGA-FS-A1ZA TCGA-FS-A1ZC 
       11.80         6.58        64.47        14.24         7.30        20.38 
TCGA-FS-A1ZS TCGA-FS-A1ZW TCGA-FS-A1ZZ TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-GN-A26D 
       49.15        27.39         5.23         0.99         0.13        14.70 

$`MLL WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.47         8.52       111.09        32.42        70.16       110.79 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 
       28.08        22.55        81.24        10.29        85.32         8.38 
TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF 
       21.14        88.50        68.22        69.90        11.41        30.87 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO 
        7.50        36.16         6.31        92.42        56.19        64.44 
TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC 
       45.11       114.67        15.25        46.32        82.29        61.38 
TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU 
       13.32        24.00         6.31         9.34       103.59        26.37 
TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K 
        5.39        80.22        42.71        15.09        41.10        17.72 
TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS 
        8.84        20.48        52.01        47.87         1.55         6.97 
TCGA-D3-A5GU TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1HV 
       23.11         2.89         9.90        11.31        13.22        48.79 
TCGA-DA-A1HW TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I8 TCGA-DA-A1IA 
       35.80        39.19        13.68         9.99        25.15         4.93 
TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-EB-A44Q 
       22.36         6.64        19.36         7.00        17.56        13.15 
TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y 
        0.20         0.00         0.00        13.22        11.57        10.55 
TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 
        6.31         8.12         1.35        12.20         5.13         4.31 
TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A 
       36.07         4.34         5.13         9.21         1.18         7.99 
TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H 
        9.90        37.97        11.15        38.63         8.55         4.41 
TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R 
        1.08        27.12         9.50        12.03         8.09         8.84 
TCGA-EE-A29S TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A5 
        9.99         8.68         8.09        11.31        49.22         9.67 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ 
        8.94        39.39        17.98        34.92        47.21        19.43 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR 
       16.01        35.54        28.31        30.84         5.42         1.15 
TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 
       13.02        34.98        36.33         8.84        98.27         2.70 
TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH 
        6.18        47.51         9.53        29.46        44.25         7.96 
TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN 
       14.56        63.42       111.78       111.91        56.02        25.08 
TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AB 
       26.99        21.60        27.16        23.05         5.56       122.73 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 
       25.84         3.68        30.15        15.95        12.72         3.22 
TCGA-EE-A3J7 TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 
       21.60        27.35         0.46        13.94        33.60        18.61 
TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C 
       12.95        38.40         5.72        76.41        25.18         3.78 
TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J 
        3.52        11.90        11.11       114.15        34.88         4.21 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19W 
       13.45        28.60        42.84        34.68         9.57        17.72 
TCGA-ER-A1A1 TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH 
       78.44         1.87         1.51        13.08        12.62        11.74 
TCGA-ER-A3ES TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
        9.04        22.49         1.71        18.41        85.74         4.90 
TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZB 
        3.45        11.01        23.80        15.52         7.33         3.39 
TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ 
        8.22        19.53        11.08         7.17        30.87        12.92 
TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZT 
       12.89        47.38        52.08         8.65         8.81        40.64 
TCGA-FS-A1ZU TCGA-FS-A1ZY TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 
        8.68         0.82        53.85         7.36        28.73        14.20 
TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TV 
       10.78         5.98         6.41         2.27         0.20         0.16 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 
        0.43         9.90         7.23        12.85        24.85        31.33 
TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-QB-A6FS 
       84.72        10.13        16.24        15.42        12.16         5.79 

  MLL MUTATED MLL WILD-TYPE 
         0.13          0.00 
  MLL MUTATED MLL WILD-TYPE 
       124.31        122.73 
  MLL MUTATED MLL WILD-TYPE 
       21.910        13.565 
[1] "0.1 - 124.3 (21.9)" "0.0 - 122.7 (13.6)"
[1] "hr=" "1.3"
D91V2, survival
               sevent
clus2             0   1
  MLL MUTATED    20  16
  MLL WILD-TYPE 112 115
  MLL MUTATED MLL WILD-TYPE 
           36           227 
  MLL MUTATED MLL WILD-TYPE 
           16           115 
$`MLL MUTATED`
TCGA-D3-A1QA TCGA-D3-A3C7 TCGA-D3-A51T TCGA-D9-A3Z1 TCGA-DA-A1HY TCGA-DA-A1I0 
       90.90        46.98        15.06        11.34       117.21        20.38 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A3F8 TCGA-EE-A181 TCGA-EE-A29V TCGA-EE-A2A2 
      107.34        61.18        15.68        33.73        25.87        24.43 
TCGA-EE-A2GC TCGA-EE-A2GI TCGA-EE-A2GN TCGA-EE-A2MR TCGA-EE-A3AA TCGA-EE-A3AF 
       67.43        48.72        90.97       103.56       124.31        13.81 
TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-ER-A193 TCGA-ER-A19S 
      127.20        36.95        34.32        53.19        31.40        37.25 
TCGA-ER-A2NC TCGA-ER-A3ET TCGA-FS-A1YW TCGA-FS-A1Z3 TCGA-FS-A1ZA TCGA-FS-A1ZC 
       43.82        80.32       216.92        20.91        27.72       357.37 
TCGA-FS-A1ZS TCGA-FS-A1ZW TCGA-FS-A1ZZ TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-GN-A26D 
      148.80        49.48        27.02        22.92        47.54        39.58 

$`MLL WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.57        16.67       112.04       112.57        71.80       133.25 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 
       28.08        31.59        95.74        43.43       103.10        65.49 
TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF 
       23.77       115.53       168.00        69.90        11.87        48.76 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO 
      113.52        42.08        12.10       171.58        56.19        66.08 
TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC 
       45.11       130.72        58.06        46.32       166.52        86.93 
TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU 
       60.23        24.53        13.87         9.34       103.59        39.75 
TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K 
       21.47       161.85        43.69        40.14       131.90        18.38 
TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS 
       10.03        51.68       135.75       137.92       166.19         7.43 
TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z3 
      125.19       151.53        54.67         3.65         6.41         3.25 
TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1I1 
        9.90        25.18        66.25        48.89        36.03       194.83 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC 
      176.55        35.93        53.92        65.92        23.44        68.09 
TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG 
       28.60        10.49       215.44        13.87        10.16        45.11 
TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z 
       35.01         3.55        52.01        29.82        27.22         8.65 
TCGA-EE-A180 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B 
       94.98        14.70        26.89        68.15         4.96       109.64 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B 
      151.27        78.87       168.26        13.55        63.35        80.61 
TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L 
       47.84        13.97        39.62        72.07        32.19         2.60 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S 
       44.35        18.61        56.42        37.35        14.47        55.92 
TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A5 TCGA-EE-A2A6 
      171.55        17.92        46.82       102.90        39.29        58.75 
TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK 
       47.54       314.56       135.95       208.04        89.33        54.74 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS 
       79.66        75.48       101.95        13.91        14.30        55.59 
TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 
       44.88        94.82        21.67       129.27        28.83        19.76 
TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI 
       61.51        47.28       103.27       103.20        16.96       204.66 
TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP 
       96.23       144.76       203.05       167.90        47.54       248.65 
TCGA-EE-A2MQ TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AC 
       43.23       136.47        41.59        53.26       122.73        25.84 
TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J7 
        3.68        54.51        23.47       138.81       172.18        64.08 
TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 
       27.35        33.40       101.79       148.08        35.44        13.94 
TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D 
       50.76         9.17        77.75        98.40        48.89        12.59 
TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L 
       13.02        26.37       268.93       152.35         6.44       131.51 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19W TCGA-ER-A1A1 
       61.05        44.05       162.08        50.89       148.18        79.99 
TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES 
       23.34        20.15        16.37        31.27        32.05       247.04 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YX 
       46.98        33.21        92.98       174.21         4.90        48.59 
TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZB TCGA-FS-A1ZD 
      228.59       202.65        28.08         7.79        48.85        53.52 
TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK 
       40.27        15.45         9.70        32.75        47.38        23.93 
TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZT TCGA-FS-A1ZU 
      101.26        74.73       133.55        11.41        53.16        26.56 
TCGA-FS-A1ZY TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 
       27.09        77.82        66.67        28.73       174.84        12.43 
TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TV TCGA-FW-A5DY 
       26.73        49.45        77.88         0.20         0.16         2.40 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        9.90         7.23        14.04       120.46       117.93        84.72 
TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-QB-A6FS 
       10.13        64.44        62.79        32.48         6.67 

  MLL MUTATED MLL WILD-TYPE 
        11.34          0.16 
  MLL MUTATED MLL WILD-TYPE 
       357.37        314.56 
  MLL MUTATED MLL WILD-TYPE 
        45.40         48.85 
[1] "11.3 - 357.4 (45.4)" "0.2 - 314.6 (48.9)" 
[1] "hr=" "1.2"
D91V3, continuous
               vv
clus            DISTANT METASTASIS PRIMARY TUMOR
  MLL MUTATED                    8             0
  MLL WILD-TYPE                 27             4
               vv
clus            REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  MLL MUTATED                                           7                  22
  MLL WILD-TYPE                                        51                 148
D91V4, multiclass
                                           clus
vv                                          MLL MUTATED MLL WILD-TYPE
  DISTANT METASTASIS                                  8            27
  PRIMARY TUMOR                                       0             4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE           7            51
  REGIONAL LYMPH NODE                                22           148
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  MLL MUTATED             2       0       1        1        4        3
  MLL WILD-TYPE           8       6      21        9       20       14
               vv
clus            STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  MLL MUTATED           1         3         1         4          2          4
  MLL WILD-TYPE         9        11         8        27         11         18
               vv
clus            STAGE IIIC STAGE IV
  MLL MUTATED            6        3
  MLL WILD-TYPE         38        9
D91V5, multiclass
             clus
vv            MLL MUTATED MLL WILD-TYPE
  I OR II NOS           2             8
  STAGE 0               0             6
  STAGE I               1            21
  STAGE IA              1             9
  STAGE IB              4            20
  STAGE II              3            14
  STAGE IIA             1             9
  STAGE IIB             3            11
  STAGE IIC             1             8
  STAGE III             4            27
  STAGE IIIA            2            11
  STAGE IIIB            4            18
  STAGE IIIC            6            38
  STAGE IV              3             9
[1] 14  2
[1] 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
  MLL MUTATED       7 10  7  7
  MLL WILD-TYPE    44 48 46 48
D91V6, multiclass
       clus
vv      MLL MUTATED MLL WILD-TYPE
  T0+T1           7            44
  T2             10            48
  T3              7            46
  T4              7            48
[1] 4 2
[1] TRUE
[1] "dimension 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
  MLL MUTATED    18   9   4   4
  MLL WILD-TYPE 120  39  28  29
D91V7, multiclass
    clus
vv   MLL MUTATED MLL WILD-TYPE
  N0          18           120
  N1           9            39
  N2           4            28
  N3           4            29
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             M0  M1 M1A M1B M1C
  MLL MUTATED    31   1   1   0   1
  MLL WILD-TYPE 209   3   1   2   4
D91V8, multiclass
     clus
vv    MLL MUTATED MLL WILD-TYPE
  M0           31           209
  M1            1             3
  M1A           1             1
  M1B           0             2
  M1C           1             4
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D91V9, binary
               cls
clus             0  1
  MLL MUTATED   11 12
  MLL WILD-TYPE 91 55
[1] "tbl2"
               cls
clus            [,1] [,2]
  MLL MUTATED     11   12
  MLL WILD-TYPE   91   55
     clus
vv    MLL MUTATED MLL WILD-TYPE
  NO           11            91
  YES          12            55
[1] 2 2
[1] FALSE
D91V10, binary
               cls
clus              0   1
  MLL MUTATED     6  31
  MLL WILD-TYPE  27 204
[1] "tbl2"
               cls
clus            [,1] [,2]
  MLL MUTATED      6   31
  MLL WILD-TYPE   27  204
     clus
vv    MLL MUTATED MLL WILD-TYPE
  NO            6            27
  YES          31           204
[1] 2 2
[1] FALSE
D91V11, continuous
D91V12, binary
               cls
clus              0   1
  MLL MUTATED    13  24
  MLL WILD-TYPE  90 141
[1] "tbl2"
               cls
clus            [,1] [,2]
  MLL MUTATED     13   24
  MLL WILD-TYPE   90  141
        clus
vv       MLL MUTATED MLL WILD-TYPE
  FEMALE          13            90
  MALE            24           141
[1] 2 2
[1] FALSE
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MLL MUTATED       0                         0    37
  MLL WILD-TYPE     3                         1   227
D91V13, multiclass
                           clus
vv                          MLL MUTATED MLL WILD-TYPE
  ASIAN                               0             3
  BLACK OR AFRICAN AMERICAN           0             1
  WHITE                              37           227
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D91V14, binary
               cls
clus              0   1
  MLL MUTATED     1  36
  MLL WILD-TYPE   2 225
[1] "tbl2"
               cls
clus            [,1] [,2]
  MLL MUTATED      1   36
  MLL WILD-TYPE    2  225
                        clus
vv                       MLL MUTATED MLL WILD-TYPE
  HISPANIC OR LATINO               1             2
  NOT HISPANIC OR LATINO          36           225
[1] 2 2
[1] FALSE

Clustering(92) Variable = DIRC2 MUTATION ANALYSIS
D92V1, survival
                 sevent
clus2               0   1
  DIRC2 MUTATED     1   3
  DIRC2 WILD-TYPE 127 127
  DIRC2 MUTATED DIRC2 WILD-TYPE 
              4             254 
  DIRC2 MUTATED DIRC2 WILD-TYPE 
              3             127 
$`DIRC2 MUTATED`
TCGA-D3-A1Q3 TCGA-EE-A2GP TCGA-EE-A2M8 TCGA-FW-A3R5 
        8.52         5.42         6.18         0.99 

$`DIRC2 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       16.47       111.09        32.42        70.16       110.79        28.08 
TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 
       22.55        45.83        81.24        10.29        85.32         8.38 
TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF 
       21.14        88.50        68.22        69.90        11.41        30.87 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO 
        7.50        36.16         6.31        92.42        56.19        64.44 
TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB 
       45.11       114.67        15.25        46.98        46.32        82.29 
TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR 
       61.38        13.32        24.00         6.31         9.34       103.59 
TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J 
       26.37         5.39        80.22        42.71        15.09        41.10 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO 
       17.72         8.84        20.48        13.94        52.01        47.87 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 
        1.55         6.97        23.11         4.01         2.89         9.90 
TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 
       11.31        13.22        48.79        35.80        51.12        10.03 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 
       39.19        13.68         9.99        44.52        36.69        25.15 
TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 
        4.93        22.36         6.64        19.36         7.00        17.56 
TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN 
       14.83        13.15         0.20         0.00         0.00        13.22 
TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 
       11.57        10.55         6.31         8.12         1.12         1.35 
TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F 
       12.20         5.13         4.31        36.07         4.34         5.13 
TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D 
        9.21         1.18         7.99         9.90        37.97        11.15 
TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N 
       38.63         8.55         4.41         1.08        27.12         9.50 
TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W 
       12.03         8.09         8.84         9.99         2.43         8.68 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 
        8.09        11.31        49.22        23.90         9.67         8.94 
TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI 
       39.39        34.29        17.98        34.92        47.21        30.08 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO 
       19.43        16.01        35.54        28.31        33.83        30.84 
TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 
        1.15        13.02        34.98        36.33         8.84        98.27 
TCGA-EE-A2M7 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH 
        2.70        47.51         9.53        29.46        44.25         7.96 
TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN 
       14.56        63.42       111.78       111.91        56.02        25.08 
TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU 
       26.99        21.60        29.65        27.16        23.05         5.56 
TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF 
      124.31       122.73        25.84         3.68        30.15        13.81 
TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 
       15.95        12.72         3.22        22.92        21.60        21.60 
TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI 
       16.14        22.22        27.35         0.46        13.94        33.60 
TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A 
       31.40        18.61        12.95        38.40         5.72        76.41 
TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G 
       25.18         3.78         3.52        11.90        11.11       114.15 
TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P 
       34.88         4.21        13.45        28.60        42.84        34.68 
TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
        9.57        36.07        17.72        78.44        11.80         1.87 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET 
        1.51        13.08        12.62        11.74         9.04         6.58 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW 
       22.49         1.71        18.41        85.74         4.90        64.47 
TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 
        3.45        11.01        23.80        14.24        15.52         7.33 
TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF 
        7.30         3.39        20.38         8.22        19.53        11.08 
TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP 
        7.17        30.87        12.92        12.89        47.38        52.08 
TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW 
        8.65         8.81        49.15        40.64         8.68        27.39 
TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 
        0.82         5.23        53.85         7.36        28.73        14.20 
TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU 
       10.78         5.98         6.41         2.27         0.20         0.13 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 
        0.16         0.43         9.90         7.23        12.85        24.85 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
       31.33        84.72        10.13        16.24        15.42        12.16 
TCGA-GN-A26D TCGA-QB-A6FS 
       14.70         5.79 

  DIRC2 MUTATED DIRC2 WILD-TYPE 
           0.99            0.00 
  DIRC2 MUTATED DIRC2 WILD-TYPE 
           8.52          124.31 
  DIRC2 MUTATED DIRC2 WILD-TYPE 
           5.80           15.17 
[1] "1.0 - 8.5 (5.8)"    "0.0 - 124.3 (15.2)"
[1] "hr=" "7.4"
D92V2, survival
                 sevent
clus2               0   1
  DIRC2 MUTATED     1   3
  DIRC2 WILD-TYPE 131 128
  DIRC2 MUTATED DIRC2 WILD-TYPE 
              4             259 
  DIRC2 MUTATED DIRC2 WILD-TYPE 
              3             128 
$`DIRC2 MUTATED`
TCGA-D3-A1Q3 TCGA-EE-A2GP TCGA-EE-A2M8 TCGA-FW-A3R5 
       16.67        13.91        19.76        22.92 

$`DIRC2 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       16.57       112.04       112.57        71.80       133.25        28.08 
TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 
       31.59        90.90        95.74        43.43       103.10        65.49 
TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF 
       23.77       115.53       168.00        69.90        11.87        48.76 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO 
      113.52        42.08        12.10       171.58        56.19        66.08 
TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB 
       45.11       130.72        58.06        46.98        46.32       166.52 
TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR 
       86.93        60.23        24.53        13.87         9.34       103.59 
TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J 
       39.75        21.47       161.85        43.69        40.14       131.90 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO 
       18.38        10.03        51.68        15.06       135.75       137.92 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW 
      166.19         7.43       125.19       151.53        54.67         3.65 
TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC 
        6.41        11.34         3.25         9.90        25.18        66.25 
TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 
       48.89        36.03       117.21        20.38       194.83       176.55 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB 
       35.93       107.34        61.18        53.92        65.92        23.44 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q 
       68.09        28.60        10.49       215.44        15.68        13.87 
TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X 
       10.16        45.11        35.01         3.55        52.01        29.82 
TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 
       27.22         8.65        94.98        33.73        14.70        26.89 
TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H 
       68.15         4.96       109.64       151.27        78.87       168.26 
TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E 
       13.55        63.35        80.61        47.84        13.97        39.62 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P 
       72.07        32.19         2.60        44.35        18.61        56.42 
TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X 
       37.35        14.47        55.92        25.87       171.55        17.92 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB 
       46.82       102.90        24.43        39.29        58.75        47.54 
TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ 
       67.43       314.56       135.95       208.04        48.72        89.33 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GR 
       54.74        79.66        75.48        90.97       101.95        14.30 
TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 
       55.59        44.88        94.82        21.67       129.27        28.83 
TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI 
       61.51        47.28       103.27       103.20        16.96       204.66 
TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP 
       96.23       144.76       203.05       167.90        47.54       248.65 
TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA 
       43.23       103.56       136.47        41.59        53.26       124.31 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG 
      122.73        25.84         3.68        54.51        13.81        23.47 
TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 
      138.81       172.18       127.20        36.95        64.08        34.32 
TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 
       53.19        27.35        33.40       101.79       148.08        31.40 
TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B 
       35.44        13.94        50.76         9.17        77.75        98.40 
TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H 
       48.89        12.59        13.02        26.37       268.93       152.35 
TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q 
        6.44       131.51        61.05        44.05       162.08        50.89 
TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE 
       37.25       148.18        79.99        43.82        23.34        20.15 
TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV 
       16.37        31.27        32.05       247.04        80.32        46.98 
TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX 
       33.21        92.98       174.21         4.90       216.92        48.59 
TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA 
      228.59       202.65        20.91        28.08         7.79        27.72 
TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG 
       48.85       357.37        53.52        40.27        15.45         9.70 
TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ 
       32.75        47.38        23.93       101.26        74.73       133.55 
TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY 
       11.41       148.80        53.16        26.56        49.48        27.09 
TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 
       27.02        77.82        66.67        28.73       174.84        12.43 
TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV 
       26.73        49.45        77.88         0.20        47.54         0.16 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 
        2.40         9.90         7.23        14.04       120.46       117.93 
TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D 
       84.72        10.13        64.44        62.79        32.48        39.58 
TCGA-QB-A6FS 
        6.67 

  DIRC2 MUTATED DIRC2 WILD-TYPE 
          13.91            0.16 
  DIRC2 MUTATED DIRC2 WILD-TYPE 
          22.92          357.37 
  DIRC2 MUTATED DIRC2 WILD-TYPE 
         18.215          48.760 
[1] "13.9 - 22.9 (18.2)" "0.2 - 357.4 (48.8)"
[1] "hr=" "6.2"
D92V3, continuous
                 vv
clus              DISTANT METASTASIS PRIMARY TUMOR
  DIRC2 MUTATED                    0             0
  DIRC2 WILD-TYPE                 35             4
                 vv
clus              REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  DIRC2 MUTATED                                           1                   3
  DIRC2 WILD-TYPE                                        57                 167
D92V4, multiclass
                                           clus
vv                                          DIRC2 MUTATED DIRC2 WILD-TYPE
  DISTANT METASTASIS                                    0              35
  PRIMARY TUMOR                                         0               4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE             1              57
  REGIONAL LYMPH NODE                                   3             167
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  DIRC2 MUTATED             0       0       0        0        0        0
  DIRC2 WILD-TYPE          10       6      22       10       24       17
                 vv
clus              STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DIRC2 MUTATED           0         0         1         2          0          1
  DIRC2 WILD-TYPE        10        14         8        29         13         21
                 vv
clus              STAGE IIIC STAGE IV
  DIRC2 MUTATED            0        0
  DIRC2 WILD-TYPE         44       12
D92V5, multiclass
             clus
vv            DIRC2 MUTATED DIRC2 WILD-TYPE
  I OR II NOS             0              10
  STAGE 0                 0               6
  STAGE I                 0              22
  STAGE IA                0              10
  STAGE IB                0              24
  STAGE II                0              17
  STAGE IIA               0              10
  STAGE IIB               0              14
  STAGE IIC               1               8
  STAGE III               2              29
  STAGE IIIA              0              13
  STAGE IIIB              1              21
  STAGE IIIC              0              44
  STAGE IV                0              12
[1] 14  2
[1] 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
  DIRC2 MUTATED       0  0  1  2
  DIRC2 WILD-TYPE    51 58 52 53
D92V6, multiclass
       clus
vv      DIRC2 MUTATED DIRC2 WILD-TYPE
  T0+T1             0              51
  T2                0              58
  T3                1              52
  T4                2              53
[1] 4 2
[1] TRUE
[1] "dimension 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
  DIRC2 MUTATED     1   2   1   0
  DIRC2 WILD-TYPE 137  46  31  33
D92V7, multiclass
    clus
vv   DIRC2 MUTATED DIRC2 WILD-TYPE
  N0             1             137
  N1             2              46
  N2             1              31
  N3             0              33
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               M0  M1 M1A M1B M1C
  DIRC2 MUTATED     4   0   0   0   0
  DIRC2 WILD-TYPE 236   4   2   2   5
D92V8, multiclass
     clus
vv    DIRC2 MUTATED DIRC2 WILD-TYPE
  M0              4             236
  M1              0               4
  M1A             0               2
  M1B             0               2
  M1C             0               5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D92V9, binary
                 cls
clus                0   1
  DIRC2 MUTATED     1   2
  DIRC2 WILD-TYPE 101  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DIRC2 MUTATED      1    2
  DIRC2 WILD-TYPE  101   65
     clus
vv    DIRC2 MUTATED DIRC2 WILD-TYPE
  NO              1             101
  YES             2              65
[1] 2 2
[1] FALSE
D92V10, binary
                 cls
clus                0   1
  DIRC2 MUTATED     0   4
  DIRC2 WILD-TYPE  33 231
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DIRC2 MUTATED      0    4
  DIRC2 WILD-TYPE   33  231
     clus
vv    DIRC2 MUTATED DIRC2 WILD-TYPE
  NO              0              33
  YES             4             231
[1] 2 2
[1] FALSE
D92V11, continuous
D92V12, binary
                 cls
clus                0   1
  DIRC2 MUTATED     1   3
  DIRC2 WILD-TYPE 102 162
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DIRC2 MUTATED      1    3
  DIRC2 WILD-TYPE  102  162
        clus
vv       DIRC2 MUTATED DIRC2 WILD-TYPE
  FEMALE             1             102
  MALE               3             162
[1] 2 2
[1] FALSE
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DIRC2 MUTATED       0                         0     4
  DIRC2 WILD-TYPE     3                         1   260
D92V13, multiclass
                           clus
vv                          DIRC2 MUTATED DIRC2 WILD-TYPE
  ASIAN                                 0               3
  BLACK OR AFRICAN AMERICAN             0               1
  WHITE                                 4             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"
D92V14, binary
                 cls
clus                0   1
  DIRC2 MUTATED     0   4
  DIRC2 WILD-TYPE   3 257
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DIRC2 MUTATED      0    4
  DIRC2 WILD-TYPE    3  257
                        clus
vv                       DIRC2 MUTATED DIRC2 WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO             4             257
[1] 2 2
[1] FALSE

Clustering(93) Variable = ADAM22 MUTATION ANALYSIS
D93V1, survival
                  sevent
clus2                0   1
  ADAM22 MUTATED    11   8
  ADAM22 WILD-TYPE 117 122
  ADAM22 MUTATED ADAM22 WILD-TYPE 
              19              239 
  ADAM22 MUTATED ADAM22 WILD-TYPE 
               8              122 
$`ADAM22 MUTATED`
TCGA-D3-A3MR TCGA-D3-A51E TCGA-D9-A6EC TCGA-EE-A29C TCGA-EE-A29H TCGA-EE-A29M 
      103.59        80.22        13.22        37.97         4.41        27.12 
TCGA-EE-A29N TCGA-EE-A29V TCGA-EE-A2GI TCGA-EE-A2MU TCGA-EE-A3J5 TCGA-ER-A19E 
        9.50         2.43        30.08         5.56        21.60        11.90 
TCGA-FS-A1ZQ TCGA-FS-A1ZZ TCGA-FS-A4F4 TCGA-FW-A3R5 TCGA-GF-A6C8 TCGA-GN-A265 
        8.65         5.23         7.36         0.99        12.85        84.72 
TCGA-GN-A266 
       10.13 

$`ADAM22 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.47         8.52       111.09        32.42        70.16       110.79 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       28.08        22.55        45.83        81.24        10.29        85.32 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
        8.38        21.14        88.50        68.22        69.90        11.41 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       30.87         7.50        36.16         6.31        92.42        56.19 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 
       64.44        45.11       114.67        15.25        46.98        46.32 
TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO 
       82.29        61.38        13.32        24.00         6.31         9.34 
TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K 
       26.37         5.39        42.71        15.09        41.10        17.72 
TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR 
        8.84        20.48        13.94        52.01        47.87         1.55 
TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA 
        6.97        23.11         4.01         2.89         9.90        11.31 
TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 
       48.79        35.80        51.12        10.03        39.19        13.68 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB 
        9.99        44.52        36.69        25.15         4.93        22.36 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q 
        6.64        19.36         7.00        17.56        14.83        13.15 
TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y 
        0.20         0.00         0.00        13.22        11.57        10.55 
TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 
        6.31         8.12         1.12         1.35        12.20         5.13 
TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I 
        4.31        36.07         4.34         5.13         9.21         1.18 
TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29L 
        7.99         9.90        11.15        38.63         8.55         1.08 
TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29W TCGA-EE-A29X 
       12.03         8.09         8.84         9.99         8.68         8.09 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB 
       11.31        49.22        23.90         9.67         8.94        39.39 
TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK 
       34.29        17.98        34.92        47.21        19.43        16.01 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR 
       35.54        28.31        33.83        30.84         5.42         1.15 
TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 
       13.02        34.98        36.33         8.84        98.27         2.70 
TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH 
        6.18        47.51         9.53        29.46        44.25         7.96 
TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN 
       14.56        63.42       111.78       111.91        56.02        25.08 
TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AA 
       26.99        21.60        29.65        27.16        23.05       124.31 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG 
      122.73        25.84         3.68        30.15        13.81        15.95 
TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA 
       12.72         3.22        22.92        21.60        16.14        22.22 
TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 
       27.35         0.46        13.94        33.60        31.40        18.61 
TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C 
       12.95        38.40         5.72        76.41        25.18         3.78 
TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L 
        3.52        11.11       114.15        34.88         4.21        13.45 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W 
       28.60        42.84        34.68         9.57        36.07        17.72 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG 
       78.44        11.80         1.87         1.51        13.08        12.62 
TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN 
       11.74         9.04         6.58        22.49         1.71        18.41 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 
       85.74         4.90        64.47         3.45        11.01        23.80 
TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC 
       14.24        15.52         7.33         7.30         3.39        20.38 
TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ 
        8.22        19.53        11.08         7.17        30.87        12.92 
TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT 
       12.89        47.38        52.08         8.81        49.15        40.64 
TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A4F0 TCGA-FS-A4F5 TCGA-FS-A4F8 
        8.68        27.39         0.82        53.85        28.73        14.20 
TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU 
       10.78         5.98         6.41         2.27         0.20         0.13 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GN-A262 TCGA-GN-A264 
        0.16         0.43         9.90         7.23        24.85        31.33 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS 
       16.24        15.42        12.16        14.70         5.79 

  ADAM22 MUTATED ADAM22 WILD-TYPE 
            0.99             0.00 
  ADAM22 MUTATED ADAM22 WILD-TYPE 
          103.59           124.31 
  ADAM22 MUTATED ADAM22 WILD-TYPE 
           11.90            15.25 
[1] "1.0 - 103.6 (11.9)" "0.0 - 124.3 (15.2)"
[1] "hr=" "1.1"
D93V2, survival
                  sevent
clus2                0   1
  ADAM22 MUTATED    11   8
  ADAM22 WILD-TYPE 121 123
  ADAM22 MUTATED ADAM22 WILD-TYPE 
              19              244 
  ADAM22 MUTATED ADAM22 WILD-TYPE 
               8              123 
$`ADAM22 MUTATED`
TCGA-D3-A3MR TCGA-D3-A51E TCGA-D9-A6EC TCGA-EE-A29C TCGA-EE-A29H TCGA-EE-A29M 
      103.59       161.85        66.25        47.84        32.19        44.35 
TCGA-EE-A29N TCGA-EE-A29V TCGA-EE-A2GI TCGA-EE-A2MU TCGA-EE-A3J5 TCGA-ER-A19E 
       18.61        25.87        48.72        53.26        36.95        13.02 
TCGA-FS-A1ZQ TCGA-FS-A1ZZ TCGA-FS-A4F4 TCGA-FW-A3R5 TCGA-GF-A6C8 TCGA-GN-A265 
      133.55        27.02        66.67        22.92        14.04        84.72 
TCGA-GN-A266 
       10.13 

$`ADAM22 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.57        16.67       112.04       112.57        71.80       133.25 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       28.08        31.59        90.90        95.74        43.43       103.10 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
       65.49        23.77       115.53       168.00        69.90        11.87 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       48.76       113.52        42.08        12.10       171.58        56.19 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 
       66.08        45.11       130.72        58.06        46.98        46.32 
TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO 
      166.52        86.93        60.23        24.53        13.87         9.34 
TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K 
       39.75        21.47        43.69        40.14       131.90        18.38 
TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR 
       10.03        51.68        15.06       135.75       137.92       166.19 
TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX 
        7.43       125.19       151.53        54.67         3.65         6.41 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-DA-A1HV TCGA-DA-A1HW 
       11.34         3.25         9.90        25.18        48.89        36.03 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 
      117.21        20.38       194.83       176.55        35.93       107.34 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
       61.18        53.92        65.92        23.44        68.09        28.60 
TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG 
       10.49       215.44        15.68        13.87        10.16        45.11 
TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z 
       35.01         3.55        52.01        29.82        27.22         8.65 
TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 
       94.98        33.73        14.70        26.89        68.15         4.96 
TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A 
      109.64       151.27        78.87       168.26        13.55        63.35 
TCGA-EE-A29B TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29L TCGA-EE-A29P 
       80.61        13.97        39.62        72.07         2.60        56.42 
TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 
       37.35        14.47        55.92       171.55        17.92        46.82 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC 
      102.90        24.43        39.29        58.75        47.54        67.43 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
      314.56       135.95       208.04        89.33        54.74        79.66 
TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS 
       75.48        90.97       101.95        13.91        14.30        55.59 
TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 
       44.88        94.82        21.67       129.27        28.83        19.76 
TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI 
       61.51        47.28       103.27       103.20        16.96       204.66 
TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP 
       96.23       144.76       203.05       167.90        47.54       248.65 
TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AB 
       43.23       103.56       136.47        41.59       124.31       122.73 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH 
       25.84         3.68        54.51        13.81        23.47       138.81 
TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JD 
      172.18       127.20        64.08        34.32        53.19        27.35 
TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 
       33.40       101.79       148.08        31.40        35.44        13.94 
TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D 
       50.76         9.17        77.75        98.40        48.89        12.59 
TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M 
       26.37       268.93       152.35         6.44       131.51        61.05 
TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 
       44.05       162.08        50.89        37.25       148.18        79.99 
TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH 
       43.82        23.34        20.15        16.37        31.27        32.05 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A 
      247.04        80.32        46.98        33.21        92.98       174.21 
TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
        4.90       216.92        48.59       228.59       202.65        20.91 
TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD 
       28.08         7.79        27.72        48.85       357.37        53.52 
TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK 
       40.27        15.45         9.70        32.75        47.38        23.93 
TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU 
      101.26        74.73        11.41       148.80        53.16        26.56 
TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A4F0 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 
       49.48        27.09        77.82        28.73       174.84        12.43 
TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV 
       26.73        49.45        77.88         0.20        47.54         0.16 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A267 
        2.40         9.90         7.23       120.46       117.93        64.44 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS 
       62.79        32.48        39.58         6.67 

  ADAM22 MUTATED ADAM22 WILD-TYPE 
           10.13             0.16 
  ADAM22 MUTATED ADAM22 WILD-TYPE 
          161.85           357.37 
  ADAM22 MUTATED ADAM22 WILD-TYPE 
          44.350           48.805 
[1] "10.1 - 161.8 (44.4)" "0.2 - 357.4 (48.8)" 
[1] "hr=" "1.1"
D93V3, continuous
                  vv
clus               DISTANT METASTASIS PRIMARY TUMOR
  ADAM22 MUTATED                    3             1
  ADAM22 WILD-TYPE                 32             3
                  vv
clus               REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  ADAM22 MUTATED                                           6
  ADAM22 WILD-TYPE                                        52
                  vv
clus               REGIONAL LYMPH NODE
  ADAM22 MUTATED                     9
  ADAM22 WILD-TYPE                 161
D93V4, multiclass
                                           clus
vv                                          ADAM22 MUTATED ADAM22 WILD-TYPE
  DISTANT METASTASIS                                     3               32
  PRIMARY TUMOR                                          1                3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE              6               52
  REGIONAL LYMPH NODE                                    9              161
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  ADAM22 MUTATED             3       0       0        3        3        0
  ADAM22 WILD-TYPE           7       6      22        7       21       17
                  vv
clus               STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  ADAM22 MUTATED           1         2         0         3          1
  ADAM22 WILD-TYPE         9        12         9        28         12
                  vv
clus               STAGE IIIB STAGE IIIC STAGE IV
  ADAM22 MUTATED            0          1        0
  ADAM22 WILD-TYPE         22         43       12
D93V5, multiclass
             clus
vv            ADAM22 MUTATED ADAM22 WILD-TYPE
  I OR II NOS              3                7
  STAGE 0                  0                6
  STAGE I                  0               22
  STAGE IA                 3                7
  STAGE IB                 3               21
  STAGE II                 0               17
  STAGE IIA                1                9
  STAGE IIB                2               12
  STAGE IIC                0                9
  STAGE III                3               28
  STAGE IIIA               1               12
  STAGE IIIB               0               22
  STAGE IIIC               1               43
  STAGE IV                 0               12
[1] 14  2
[1] 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
  ADAM22 MUTATED       4  5  4  1
  ADAM22 WILD-TYPE    47 53 49 54
D93V6, multiclass
       clus
vv      ADAM22 MUTATED ADAM22 WILD-TYPE
  T0+T1              4               47
  T2                 5               53
  T3                 4               49
  T4                 1               54
[1] 4 2
[1] TRUE
[1] "dimension 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
  ADAM22 MUTATED    11   4   1   0
  ADAM22 WILD-TYPE 127  44  31  33
D93V7, multiclass
    clus
vv   ADAM22 MUTATED ADAM22 WILD-TYPE
  N0             11              127
  N1              4               44
  N2              1               31
  N3              0               33
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                M0  M1 M1A M1B M1C
  ADAM22 MUTATED    17   0   0   0   0
  ADAM22 WILD-TYPE 223   4   2   2   5
D93V8, multiclass
     clus
vv    ADAM22 MUTATED ADAM22 WILD-TYPE
  M0              17              223
  M1               0                4
  M1A              0                2
  M1B              0                2
  M1C              0                5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D93V9, binary
                  cls
clus                0  1
  ADAM22 MUTATED    8  4
  ADAM22 WILD-TYPE 94 63
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ADAM22 MUTATED      8    4
  ADAM22 WILD-TYPE   94   63
     clus
vv    ADAM22 MUTATED ADAM22 WILD-TYPE
  NO               8               94
  YES              4               63
[1] 2 2
[1] FALSE
D93V10, binary
                  cls
clus                 0   1
  ADAM22 MUTATED     3  16
  ADAM22 WILD-TYPE  30 219
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ADAM22 MUTATED      3   16
  ADAM22 WILD-TYPE   30  219
     clus
vv    ADAM22 MUTATED ADAM22 WILD-TYPE
  NO               3               30
  YES             16              219
[1] 2 2
[1] FALSE
D93V11, continuous
D93V12, binary
                  cls
clus                 0   1
  ADAM22 MUTATED     7  12
  ADAM22 WILD-TYPE  96 153
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ADAM22 MUTATED      7   12
  ADAM22 WILD-TYPE   96  153
        clus
vv       ADAM22 MUTATED ADAM22 WILD-TYPE
  FEMALE              7               96
  MALE               12              153
[1] 2 2
[1] FALSE
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ADAM22 MUTATED       0                         0    19
  ADAM22 WILD-TYPE     3                         1   245
D93V13, multiclass
                           clus
vv                          ADAM22 MUTATED ADAM22 WILD-TYPE
  ASIAN                                  0                3
  BLACK OR AFRICAN AMERICAN              0                1
  WHITE                                 19              245
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D93V14, binary
                  cls
clus                 0   1
  ADAM22 MUTATED     1  17
  ADAM22 WILD-TYPE   2 244
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ADAM22 MUTATED      1   17
  ADAM22 WILD-TYPE    2  244
                        clus
vv                       ADAM22 MUTATED ADAM22 WILD-TYPE
  HISPANIC OR LATINO                  1                2
  NOT HISPANIC OR LATINO             17              244
[1] 2 2
[1] FALSE

Clustering(94) Variable = PLCXD2 MUTATION ANALYSIS
D94V1, survival
                  sevent
clus2                0   1
  PLCXD2 MUTATED     5   3
  PLCXD2 WILD-TYPE 123 127
  PLCXD2 MUTATED PLCXD2 WILD-TYPE 
               8              250 
  PLCXD2 MUTATED PLCXD2 WILD-TYPE 
               3              127 
$`PLCXD2 MUTATED`
TCGA-D3-A2JF TCGA-D9-A6EA TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2MD TCGA-EE-A3AH 
       30.87        11.31         1.15        13.02         9.53        12.72 
TCGA-EE-A3J3 TCGA-FW-A3R5 
        3.22         0.99 

$`PLCXD2 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.47         8.52       111.09        32.42        70.16       110.79 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       28.08        22.55        45.83        81.24        10.29        85.32 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
        8.38        21.14        88.50        68.22        69.90        11.41 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO 
        7.50        36.16         6.31        92.42        56.19        64.44 
TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB 
       45.11       114.67        15.25        46.98        46.32        82.29 
TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR 
       61.38        13.32        24.00         6.31         9.34       103.59 
TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J 
       26.37         5.39        80.22        42.71        15.09        41.10 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO 
       17.72         8.84        20.48        13.94        52.01        47.87 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 
        1.55         6.97        23.11         4.01         2.89         9.90 
TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 
       13.22        48.79        35.80        51.12        10.03        39.19 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA 
       13.68         9.99        44.52        36.69        25.15         4.93 
TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 
       22.36         6.64        19.36         7.00        17.56        14.83 
TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EE-A17X 
       13.15         0.20         0.00         0.00        13.22        11.57 
TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 
       10.55         6.31         8.12         1.12         1.35        12.20 
TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H 
        5.13         4.31        36.07         4.34         5.13         9.21 
TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E 
        1.18         7.99         9.90        37.97        11.15        38.63 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P 
        8.55         4.41         1.08        27.12         9.50        12.03 
TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X 
        8.09         8.84         9.99         2.43         8.68         8.09 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB 
       11.31        49.22        23.90         9.67         8.94        39.39 
TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ 
       34.29        17.98        34.92        47.21        30.08        19.43 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP 
       16.01        35.54        28.31        33.83        30.84         5.42 
TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 
       34.98        36.33         8.84        98.27         2.70         6.18 
TCGA-EE-A2MC TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ 
       47.51        29.46        44.25         7.96        14.56        63.42 
TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ 
      111.78       111.91        56.02        25.08        26.99        21.60 
TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB 
       29.65        27.16        23.05         5.56       124.31       122.73 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3J4 
       25.84         3.68        30.15        13.81        15.95        22.92 
TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE 
       21.60        21.60        16.14        22.22        27.35         0.46 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 
       13.94        33.60        31.40        18.61        12.95        38.40 
TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E 
        5.72        76.41        25.18         3.78         3.52        11.90 
TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M 
       11.11       114.15        34.88         4.21        13.45        28.60 
TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 
       42.84        34.68         9.57        36.07        17.72        78.44 
TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH 
       11.80         1.87         1.51        13.08        12.62        11.74 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A 
        9.04         6.58        22.49         1.71        18.41        85.74 
TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
        4.90        64.47         3.45        11.01        23.80        14.24 
TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD 
       15.52         7.33         7.30         3.39        20.38         8.22 
TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK 
       19.53        11.08         7.17        30.87        12.92        12.89 
TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT 
       47.38        52.08         8.65         8.81        49.15        40.64 
TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 
        8.68        27.39         0.82         5.23        53.85         7.36 
TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD 
       28.73        14.20        10.78         5.98         6.41         2.27 
TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
        0.20         0.13         0.16         0.43         9.90         7.23 
TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 
       12.85        24.85        31.33        84.72        10.13        16.24 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS 
       15.42        12.16        14.70         5.79 

  PLCXD2 MUTATED PLCXD2 WILD-TYPE 
            0.99             0.00 
  PLCXD2 MUTATED PLCXD2 WILD-TYPE 
           30.87           124.31 
  PLCXD2 MUTATED PLCXD2 WILD-TYPE 
          10.420           15.335 
[1] "1.0 - 30.9 (10.4)"  "0.0 - 124.3 (15.3)"
[1] "hr=" "1.4"
D94V2, survival
                  sevent
clus2                0   1
  PLCXD2 MUTATED     5   3
  PLCXD2 WILD-TYPE 127 128
  PLCXD2 MUTATED PLCXD2 WILD-TYPE 
               8              255 
  PLCXD2 MUTATED PLCXD2 WILD-TYPE 
               3              128 
$`PLCXD2 MUTATED`
TCGA-D3-A2JF TCGA-D9-A6EA TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2MD TCGA-EE-A3AH 
       48.76        25.18        14.30        55.59        47.28       138.81 
TCGA-EE-A3J3 TCGA-FW-A3R5 
      172.18        22.92 

$`PLCXD2 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.57        16.67       112.04       112.57        71.80       133.25 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       28.08        31.59        90.90        95.74        43.43       103.10 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
       65.49        23.77       115.53       168.00        69.90        11.87 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO 
      113.52        42.08        12.10       171.58        56.19        66.08 
TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB 
       45.11       130.72        58.06        46.98        46.32       166.52 
TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR 
       86.93        60.23        24.53        13.87         9.34       103.59 
TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J 
       39.75        21.47       161.85        43.69        40.14       131.90 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO 
       18.38        10.03        51.68        15.06       135.75       137.92 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW 
      166.19         7.43       125.19       151.53        54.67         3.65 
TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EC TCGA-DA-A1HV 
        6.41        11.34         3.25         9.90        66.25        48.89 
TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 
       36.03       117.21        20.38       194.83       176.55        35.93 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC 
      107.34        61.18        53.92        65.92        23.44        68.09 
TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R 
       28.60        10.49       215.44        15.68        13.87        10.16 
TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y 
       45.11        35.01         3.55        52.01        29.82        27.22 
TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 
        8.65        94.98        33.73        14.70        26.89        68.15 
TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I 
        4.96       109.64       151.27        78.87       168.26        13.55 
TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G 
       63.35        80.61        47.84        13.97        39.62        72.07 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
       32.19         2.60        44.35        18.61        56.42        37.35 
TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 
       14.47        55.92        25.87       171.55        17.92        46.82 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC 
      102.90        24.43        39.29        58.75        47.54        67.43 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK 
      314.56       135.95       208.04        48.72        89.33        54.74 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GT 
       79.66        75.48        90.97       101.95        13.91        44.88 
TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC 
       94.82        21.67       129.27        28.83        19.76        61.51 
TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK 
      103.27       103.20        16.96       204.66        96.23       144.76 
TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR 
      203.05       167.90        47.54       248.65        43.23       103.56 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC 
      136.47        41.59        53.26       124.31       122.73        25.84 
TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3J4 TCGA-EE-A3J5 
        3.68        54.51        13.81        23.47       127.20        36.95 
TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH 
       64.08        34.32        53.19        27.35        33.40       101.79 
TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 
      148.08        31.40        35.44        13.94        50.76         9.17 
TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F 
       77.75        98.40        48.89        12.59        13.02        26.37 
TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N 
      268.93       152.35         6.44       131.51        61.05        44.05 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
      162.08        50.89        37.25       148.18        79.99        43.82 
TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES 
       23.34        20.15        16.37        31.27        32.05       247.04 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
       80.32        46.98        33.21        92.98       174.21         4.90 
TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 
      216.92        48.59       228.59       202.65        20.91        28.08 
TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE 
        7.79        27.72        48.85       357.37        53.52        40.27 
TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM 
       15.45         9.70        32.75        47.38        23.93       101.26 
TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU 
       74.73       133.55        11.41       148.80        53.16        26.56 
TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 
       49.48        27.09        27.02        77.82        66.67        28.73 
TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 
      174.84        12.43        26.73        49.45        77.88         0.20 
TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 
       47.54         0.16         2.40         9.90         7.23        14.04 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 
      120.46       117.93        84.72        10.13        64.44        62.79 
TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS 
       32.48        39.58         6.67 

  PLCXD2 MUTATED PLCXD2 WILD-TYPE 
           14.30             0.16 
  PLCXD2 MUTATED PLCXD2 WILD-TYPE 
          172.18           357.37 
  PLCXD2 MUTATED PLCXD2 WILD-TYPE 
           48.02            48.59 
[1] "14.3 - 172.2 (48.0)" "0.2 - 357.4 (48.6)" 
[1] "hr=" "1.3"
D94V3, continuous
                  vv
clus               DISTANT METASTASIS PRIMARY TUMOR
  PLCXD2 MUTATED                    2             1
  PLCXD2 WILD-TYPE                 33             3
                  vv
clus               REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  PLCXD2 MUTATED                                           2
  PLCXD2 WILD-TYPE                                        56
                  vv
clus               REGIONAL LYMPH NODE
  PLCXD2 MUTATED                     4
  PLCXD2 WILD-TYPE                 166
D94V4, multiclass
                                           clus
vv                                          PLCXD2 MUTATED PLCXD2 WILD-TYPE
  DISTANT METASTASIS                                     2               33
  PRIMARY TUMOR                                          1                3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE              2               56
  REGIONAL LYMPH NODE                                    4              166
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  PLCXD2 MUTATED             1       0       0        1        2        3
  PLCXD2 WILD-TYPE           9       6      22        9       22       14
                  vv
clus               STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  PLCXD2 MUTATED           0         0         0         1          0
  PLCXD2 WILD-TYPE        10        14         9        30         13
                  vv
clus               STAGE IIIB STAGE IIIC STAGE IV
  PLCXD2 MUTATED            0          1        0
  PLCXD2 WILD-TYPE         22         43       12
D94V5, multiclass
             clus
vv            PLCXD2 MUTATED PLCXD2 WILD-TYPE
  I OR II NOS              1                9
  STAGE 0                  0                6
  STAGE I                  0               22
  STAGE IA                 1                9
  STAGE IB                 2               22
  STAGE II                 3               14
  STAGE IIA                0               10
  STAGE IIB                0               14
  STAGE IIC                0                9
  STAGE III                1               30
  STAGE IIIA               0               13
  STAGE IIIB               0               22
  STAGE IIIC               1               43
  STAGE IV                 0               12
[1] 14  2
[1] 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
  PLCXD2 MUTATED       1  3  2  2
  PLCXD2 WILD-TYPE    50 55 51 53
D94V6, multiclass
       clus
vv      PLCXD2 MUTATED PLCXD2 WILD-TYPE
  T0+T1              1               50
  T2                 3               55
  T3                 2               51
  T4                 2               53
[1] 4 2
[1] TRUE
[1] "dimension 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
  PLCXD2 MUTATED     7   0   1   1
  PLCXD2 WILD-TYPE 131  48  31  32
D94V7, multiclass
    clus
vv   PLCXD2 MUTATED PLCXD2 WILD-TYPE
  N0              7              131
  N1              0               48
  N2              1               31
  N3              1               32
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                M0  M1 M1A M1B M1C
  PLCXD2 MUTATED     9   0   0   0   0
  PLCXD2 WILD-TYPE 231   4   2   2   5
D94V8, multiclass
     clus
vv    PLCXD2 MUTATED PLCXD2 WILD-TYPE
  M0               9              231
  M1               0                4
  M1A              0                2
  M1B              0                2
  M1C              0                5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D94V9, binary
                  cls
clus                0  1
  PLCXD2 MUTATED    4  1
  PLCXD2 WILD-TYPE 98 66
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PLCXD2 MUTATED      4    1
  PLCXD2 WILD-TYPE   98   66
     clus
vv    PLCXD2 MUTATED PLCXD2 WILD-TYPE
  NO               4               98
  YES              1               66
[1] 2 2
[1] FALSE
D94V10, binary
                  cls
clus                 0   1
  PLCXD2 MUTATED     0   9
  PLCXD2 WILD-TYPE  33 226
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PLCXD2 MUTATED      0    9
  PLCXD2 WILD-TYPE   33  226
     clus
vv    PLCXD2 MUTATED PLCXD2 WILD-TYPE
  NO               0               33
  YES              9              226
[1] 2 2
[1] FALSE
D94V11, continuous
D94V12, binary
                  cls
clus                 0   1
  PLCXD2 MUTATED     2   7
  PLCXD2 WILD-TYPE 101 158
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PLCXD2 MUTATED      2    7
  PLCXD2 WILD-TYPE  101  158
        clus
vv       PLCXD2 MUTATED PLCXD2 WILD-TYPE
  FEMALE              2              101
  MALE                7              158
[1] 2 2
[1] FALSE
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PLCXD2 MUTATED       0                         0     9
  PLCXD2 WILD-TYPE     3                         1   255
D94V13, multiclass
                           clus
vv                          PLCXD2 MUTATED PLCXD2 WILD-TYPE
  ASIAN                                  0                3
  BLACK OR AFRICAN AMERICAN              0                1
  WHITE                                  9              255
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D94V14, binary
                  cls
clus                 0   1
  PLCXD2 MUTATED     0   9
  PLCXD2 WILD-TYPE   3 252
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PLCXD2 MUTATED      0    9
  PLCXD2 WILD-TYPE    3  252
                        clus
vv                       PLCXD2 MUTATED PLCXD2 WILD-TYPE
  HISPANIC OR LATINO                  0                3
  NOT HISPANIC OR LATINO              9              252
[1] 2 2
[1] FALSE

Clustering(95) Variable = EDN1 MUTATION ANALYSIS
D95V1, survival
                sevent
clus2              0   1
  EDN1 MUTATED     4   5
  EDN1 WILD-TYPE 124 125
  EDN1 MUTATED EDN1 WILD-TYPE 
             9            249 
  EDN1 MUTATED EDN1 WILD-TYPE 
             5            125 
$`EDN1 MUTATED`
TCGA-D3-A1Q5 TCGA-D3-A2J9 TCGA-D3-A51T TCGA-EE-A180 TCGA-EE-A29D TCGA-EE-A2A6 
       32.42        21.14        13.94         8.12        11.15         8.94 
TCGA-EE-A2MR TCGA-FW-A3R5 TCGA-GN-A266 
       29.65         0.99        10.13 

$`EDN1 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       16.47         8.52       111.09        70.16       110.79        28.08 
TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 
       22.55        45.83        81.24        10.29        85.32         8.38 
TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JG 
       88.50        68.22        69.90        11.41        30.87         7.50 
TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP 
       36.16         6.31        92.42        56.19        64.44        45.11 
TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC 
      114.67        15.25        46.98        46.32        82.29        61.38 
TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU 
       13.32        24.00         6.31         9.34       103.59        26.37 
TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K 
        5.39        80.22        42.71        15.09        41.10        17.72 
TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS 
        8.84        20.48        52.01        47.87         1.55         6.97 
TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC 
       23.11         4.01         2.89         9.90        11.31        13.22 
TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 
       48.79        35.80        51.12        10.03        39.19        13.68 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB 
        9.99        44.52        36.69        25.15         4.93        22.36 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q 
        6.64        19.36         7.00        17.56        14.83        13.15 
TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y 
        0.20         0.00         0.00        13.22        11.57        10.55 
TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 
        6.31         1.12         1.35        12.20         5.13         4.31 
TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A 
       36.07         4.34         5.13         9.21         1.18         7.99 
TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L 
        9.90        37.97        38.63         8.55         4.41         1.08 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S 
       27.12         9.50        12.03         8.09         8.84         9.99 
TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 
        2.43         8.68         8.09        11.31        49.22        23.90 
TCGA-EE-A2A5 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH 
        9.67        39.39        34.29        17.98        34.92        47.21 
TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN 
       30.08        19.43        16.01        35.54        28.31        33.83 
TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU 
       30.84         5.42         1.15        13.02        34.98        36.33 
TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD 
        8.84        98.27         2.70         6.18        47.51         9.53 
TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK 
       29.46        44.25         7.96        14.56        63.42       111.78 
TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MS 
      111.91        56.02        25.08        26.99        21.60        27.16 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD 
       23.05         5.56       124.31       122.73        25.84         3.68 
TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 
       30.15        13.81        15.95        12.72         3.22        22.92 
TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE 
       21.60        21.60        16.14        22.22        27.35         0.46 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 
       13.94        33.60        31.40        18.61        12.95        38.40 
TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E 
        5.72        76.41        25.18         3.78         3.52        11.90 
TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M 
       11.11       114.15        34.88         4.21        13.45        28.60 
TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 
       42.84        34.68         9.57        36.07        17.72        78.44 
TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH 
       11.80         1.87         1.51        13.08        12.62        11.74 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A 
        9.04         6.58        22.49         1.71        18.41        85.74 
TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
        4.90        64.47         3.45        11.01        23.80        14.24 
TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD 
       15.52         7.33         7.30         3.39        20.38         8.22 
TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK 
       19.53        11.08         7.17        30.87        12.92        12.89 
TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT 
       47.38        52.08         8.65         8.81        49.15        40.64 
TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 
        8.68        27.39         0.82         5.23        53.85         7.36 
TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD 
       28.73        14.20        10.78         5.98         6.41         2.27 
TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
        0.20         0.13         0.16         0.43         9.90         7.23 
TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 
       12.85        24.85        31.33        84.72        16.24        15.42 
TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS 
       12.16        14.70         5.79 

  EDN1 MUTATED EDN1 WILD-TYPE 
          0.99           0.00 
  EDN1 MUTATED EDN1 WILD-TYPE 
         32.42         124.31 
  EDN1 MUTATED EDN1 WILD-TYPE 
         11.15          15.09 
[1] "1.0 - 32.4 (11.2)"  "0.0 - 124.3 (15.1)"
[1] "hr=" "1.4"
D95V2, survival
                sevent
clus2              0   1
  EDN1 MUTATED     4   5
  EDN1 WILD-TYPE 128 126
  EDN1 MUTATED EDN1 WILD-TYPE 
             9            254 
  EDN1 MUTATED EDN1 WILD-TYPE 
             5            126 
$`EDN1 MUTATED`
TCGA-D3-A1Q5 TCGA-D3-A2J9 TCGA-D3-A51T TCGA-EE-A180 TCGA-EE-A29D TCGA-EE-A2A6 
      112.57        23.77        15.06        94.98        13.97        58.75 
TCGA-EE-A2MR TCGA-FW-A3R5 TCGA-GN-A266 
      103.56        22.92        10.13 

$`EDN1 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       16.57        16.67       112.04        71.80       133.25        28.08 
TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 
       31.59        90.90        95.74        43.43       103.10        65.49 
TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JG 
      115.53       168.00        69.90        11.87        48.76       113.52 
TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP 
       42.08        12.10       171.58        56.19        66.08        45.11 
TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC 
      130.72        58.06        46.98        46.32       166.52        86.93 
TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU 
       60.23        24.53        13.87         9.34       103.59        39.75 
TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K 
       21.47       161.85        43.69        40.14       131.90        18.38 
TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS 
       10.03        51.68       135.75       137.92       166.19         7.43 
TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 
      125.19       151.53        54.67         3.65         6.41        11.34 
TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1HW 
        3.25         9.90        25.18        66.25        48.89        36.03 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 
      117.21        20.38       194.83       176.55        35.93       107.34 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
       61.18        53.92        65.92        23.44        68.09        28.60 
TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG 
       10.49       215.44        15.68        13.87        10.16        45.11 
TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z 
       35.01         3.55        52.01        29.82        27.22         8.65 
TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B 
       33.73        14.70        26.89        68.15         4.96       109.64 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B 
      151.27        78.87       168.26        13.55        63.35        80.61 
TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M 
       47.84        39.62        72.07        32.19         2.60        44.35 
TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V 
       18.61        56.42        37.35        14.47        55.92        25.87 
TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 
      171.55        17.92        46.82       102.90        24.43        39.29 
TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI 
       47.54        67.43       314.56       135.95       208.04        48.72 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO 
       89.33        54.74        79.66        75.48        90.97       101.95 
TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 
       13.91        14.30        55.59        44.88        94.82        21.67 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME 
      129.27        28.83        19.76        61.51        47.28       103.27 
TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML 
      103.20        16.96       204.66        96.23       144.76       203.05 
TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MS TCGA-EE-A2MT 
      167.90        47.54       248.65        43.23       136.47        41.59 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE 
       53.26       124.31       122.73        25.84         3.68        54.51 
TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 
       13.81        23.47       138.81       172.18       127.20        36.95 
TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH 
       64.08        34.32        53.19        27.35        33.40       101.79 
TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 
      148.08        31.40        35.44        13.94        50.76         9.17 
TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F 
       77.75        98.40        48.89        12.59        13.02        26.37 
TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N 
      268.93       152.35         6.44       131.51        61.05        44.05 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
      162.08        50.89        37.25       148.18        79.99        43.82 
TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES 
       23.34        20.15        16.37        31.27        32.05       247.04 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
       80.32        46.98        33.21        92.98       174.21         4.90 
TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 
      216.92        48.59       228.59       202.65        20.91        28.08 
TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE 
        7.79        27.72        48.85       357.37        53.52        40.27 
TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM 
       15.45         9.70        32.75        47.38        23.93       101.26 
TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU 
       74.73       133.55        11.41       148.80        53.16        26.56 
TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 
       49.48        27.09        27.02        77.82        66.67        28.73 
TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 
      174.84        12.43        26.73        49.45        77.88         0.20 
TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 
       47.54         0.16         2.40         9.90         7.23        14.04 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
      120.46       117.93        84.72        64.44        62.79        32.48 
TCGA-GN-A26D TCGA-QB-A6FS 
       39.58         6.67 

  EDN1 MUTATED EDN1 WILD-TYPE 
         10.13           0.16 
  EDN1 MUTATED EDN1 WILD-TYPE 
        112.57         357.37 
  EDN1 MUTATED EDN1 WILD-TYPE 
        23.770         48.655 
[1] "10.1 - 112.6 (23.8)" "0.2 - 357.4 (48.7)" 
[1] "hr=" "1.6"
D95V3, continuous
                vv
clus             DISTANT METASTASIS PRIMARY TUMOR
  EDN1 MUTATED                    1             0
  EDN1 WILD-TYPE                 34             4
                vv
clus             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  EDN1 MUTATED                                           1                   7
  EDN1 WILD-TYPE                                        57                 163
D95V4, multiclass
                                           clus
vv                                          EDN1 MUTATED EDN1 WILD-TYPE
  DISTANT METASTASIS                                   1             34
  PRIMARY TUMOR                                        0              4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE            1             57
  REGIONAL LYMPH NODE                                  7            163
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  EDN1 MUTATED             1       0       1        1        0        0
  EDN1 WILD-TYPE           9       6      21        9       24       17
                vv
clus             STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  EDN1 MUTATED           0         0         0         2          0          0
  EDN1 WILD-TYPE        10        14         9        29         13         22
                vv
clus             STAGE IIIC STAGE IV
  EDN1 MUTATED            3        0
  EDN1 WILD-TYPE         41       12
D95V5, multiclass
             clus
vv            EDN1 MUTATED EDN1 WILD-TYPE
  I OR II NOS            1              9
  STAGE 0                0              6
  STAGE I                1             21
  STAGE IA               1              9
  STAGE IB               0             24
  STAGE II               0             17
  STAGE IIA              0             10
  STAGE IIB              0             14
  STAGE IIC              0              9
  STAGE III              2             29
  STAGE IIIA             0             13
  STAGE IIIB             0             22
  STAGE IIIC             3             41
  STAGE IV               0             12
[1] 14  2
[1] 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
  EDN1 MUTATED       1  1  1  3
  EDN1 WILD-TYPE    50 57 52 52
D95V6, multiclass
       clus
vv      EDN1 MUTATED EDN1 WILD-TYPE
  T0+T1            1             50
  T2               1             57
  T3               1             52
  T4               3             52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  EDN1 MUTATED     4   2   1   1
  EDN1 WILD-TYPE 134  46  31  32
D95V7, multiclass
    clus
vv   EDN1 MUTATED EDN1 WILD-TYPE
  N0            4            134
  N1            2             46
  N2            1             31
  N3            1             32
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              M0  M1 M1A M1B M1C
  EDN1 MUTATED     8   0   0   0   0
  EDN1 WILD-TYPE 232   4   2   2   5
D95V8, multiclass
     clus
vv    EDN1 MUTATED EDN1 WILD-TYPE
  M0             8            232
  M1             0              4
  M1A            0              2
  M1B            0              2
  M1C            0              5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D95V9, binary
                cls
clus              0  1
  EDN1 MUTATED    3  3
  EDN1 WILD-TYPE 99 64
[1] "tbl2"
                cls
clus             [,1] [,2]
  EDN1 MUTATED      3    3
  EDN1 WILD-TYPE   99   64
     clus
vv    EDN1 MUTATED EDN1 WILD-TYPE
  NO             3             99
  YES            3             64
[1] 2 2
[1] FALSE
D95V10, binary
                cls
clus               0   1
  EDN1 MUTATED     1   8
  EDN1 WILD-TYPE  32 227
[1] "tbl2"
                cls
clus             [,1] [,2]
  EDN1 MUTATED      1    8
  EDN1 WILD-TYPE   32  227
     clus
vv    EDN1 MUTATED EDN1 WILD-TYPE
  NO             1             32
  YES            8            227
[1] 2 2
[1] FALSE
D95V11, continuous
D95V12, binary
                cls
clus               0   1
  EDN1 MUTATED     1   8
  EDN1 WILD-TYPE 102 157
[1] "tbl2"
                cls
clus             [,1] [,2]
  EDN1 MUTATED      1    8
  EDN1 WILD-TYPE  102  157
        clus
vv       EDN1 MUTATED EDN1 WILD-TYPE
  FEMALE            1            102
  MALE              8            157
[1] 2 2
[1] FALSE
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  EDN1 MUTATED       0                         0     9
  EDN1 WILD-TYPE     3                         1   255
D95V13, multiclass
                           clus
vv                          EDN1 MUTATED EDN1 WILD-TYPE
  ASIAN                                0              3
  BLACK OR AFRICAN AMERICAN            0              1
  WHITE                                9            255
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D95V14, binary
                cls
clus               0   1
  EDN1 MUTATED     0   9
  EDN1 WILD-TYPE   3 252
[1] "tbl2"
                cls
clus             [,1] [,2]
  EDN1 MUTATED      0    9
  EDN1 WILD-TYPE    3  252
                        clus
vv                       EDN1 MUTATED EDN1 WILD-TYPE
  HISPANIC OR LATINO                0              3
  NOT HISPANIC OR LATINO            9            252
[1] 2 2
[1] FALSE

Clustering(96) Variable = HTR7 MUTATION ANALYSIS
D96V1, survival
                sevent
clus2              0   1
  HTR7 MUTATED     4   5
  HTR7 WILD-TYPE 124 125
  HTR7 MUTATED HTR7 WILD-TYPE 
             9            249 
  HTR7 MUTATED HTR7 WILD-TYPE 
             5            125 
$`HTR7 MUTATED`
TCGA-D3-A2J9 TCGA-DA-A1HV TCGA-EE-A29E TCGA-EE-A29Q TCGA-EE-A2GS TCGA-EE-A3AH 
       21.14        48.79        38.63         8.09        13.02        12.72 
TCGA-FS-A1ZA TCGA-FS-A4FC TCGA-GN-A266 
        7.30         6.41        10.13 

$`HTR7 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.47         8.52       111.09        32.42        70.16       110.79 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       28.08        22.55        45.83        81.24        10.29        85.32 
TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF 
        8.38        88.50        68.22        69.90        11.41        30.87 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO 
        7.50        36.16         6.31        92.42        56.19        64.44 
TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB 
       45.11       114.67        15.25        46.98        46.32        82.29 
TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR 
       61.38        13.32        24.00         6.31         9.34       103.59 
TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J 
       26.37         5.39        80.22        42.71        15.09        41.10 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO 
       17.72         8.84        20.48        13.94        52.01        47.87 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 
        1.55         6.97        23.11         4.01         2.89         9.90 
TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 
       11.31        13.22        35.80        51.12        10.03        39.19 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA 
       13.68         9.99        44.52        36.69        25.15         4.93 
TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 
       22.36         6.64        19.36         7.00        17.56        14.83 
TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EE-A17X 
       13.15         0.20         0.00         0.00        13.22        11.57 
TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 
       10.55         6.31         8.12         1.12         1.35        12.20 
TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H 
        5.13         4.31        36.07         4.34         5.13         9.21 
TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29G 
        1.18         7.99         9.90        37.97        11.15         8.55 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29R 
        4.41         1.08        27.12         9.50        12.03         8.84 
TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 
        9.99         2.43         8.68         8.09        11.31        49.22 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD 
       23.90         9.67         8.94        39.39        34.29        17.98 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
       34.92        47.21        30.08        19.43        16.01        35.54 
TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GT 
       28.31        33.83        30.84         5.42         1.15        34.98 
TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC 
       36.33         8.84        98.27         2.70         6.18        47.51 
TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ 
        9.53        29.46        44.25         7.96        14.56        63.42 
TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ 
      111.78       111.91        56.02        25.08        26.99        21.60 
TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB 
       29.65        27.16        23.05         5.56       124.31       122.73 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3J3 
       25.84         3.68        30.15        13.81        15.95         3.22 
TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JD 
       22.92        21.60        21.60        16.14        22.22        27.35 
TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 
        0.46        13.94        33.60        31.40        18.61        12.95 
TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D 
       38.40         5.72        76.41        25.18         3.78         3.52 
TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L 
       11.90        11.11       114.15        34.88         4.21        13.45 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W 
       28.60        42.84        34.68         9.57        36.07        17.72 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG 
       78.44        11.80         1.87         1.51        13.08        12.62 
TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN 
       11.74         9.04         6.58        22.49         1.71        18.41 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 
       85.74         4.90        64.47         3.45        11.01        23.80 
TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD 
       14.24        15.52         7.33         3.39        20.38         8.22 
TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK 
       19.53        11.08         7.17        30.87        12.92        12.89 
TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT 
       47.38        52.08         8.65         8.81        49.15        40.64 
TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 
        8.68        27.39         0.82         5.23        53.85         7.36 
TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FD TCGA-FW-A3I3 
       28.73        14.20        10.78         5.98         2.27         0.20 
TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
        0.99         0.13         0.16         0.43         9.90         7.23 
TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 
       12.85        24.85        31.33        84.72        16.24        15.42 
TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS 
       12.16        14.70         5.79 

  HTR7 MUTATED HTR7 WILD-TYPE 
          6.41           0.00 
  HTR7 MUTATED HTR7 WILD-TYPE 
         48.79         124.31 
  HTR7 MUTATED HTR7 WILD-TYPE 
         12.72          15.09 
[1] "6.4 - 48.8 (12.7)"  "0.0 - 124.3 (15.1)"
[1] "hr=" "1.3"
D96V2, survival
                sevent
clus2              0   1
  HTR7 MUTATED     4   5
  HTR7 WILD-TYPE 128 126
  HTR7 MUTATED HTR7 WILD-TYPE 
             9            254 
  HTR7 MUTATED HTR7 WILD-TYPE 
             5            126 
$`HTR7 MUTATED`
TCGA-D3-A2J9 TCGA-DA-A1HV TCGA-EE-A29E TCGA-EE-A29Q TCGA-EE-A2GS TCGA-EE-A3AH 
       23.77        48.89        39.62        37.35        55.59       138.81 
TCGA-FS-A1ZA TCGA-FS-A4FC TCGA-GN-A266 
       27.72        49.45        10.13 

$`HTR7 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.57        16.67       112.04       112.57        71.80       133.25 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       28.08        31.59        90.90        95.74        43.43       103.10 
TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF 
       65.49       115.53       168.00        69.90        11.87        48.76 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO 
      113.52        42.08        12.10       171.58        56.19        66.08 
TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB 
       45.11       130.72        58.06        46.98        46.32       166.52 
TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR 
       86.93        60.23        24.53        13.87         9.34       103.59 
TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J 
       39.75        21.47       161.85        43.69        40.14       131.90 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO 
       18.38        10.03        51.68        15.06       135.75       137.92 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW 
      166.19         7.43       125.19       151.53        54.67         3.65 
TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC 
        6.41        11.34         3.25         9.90        25.18        66.25 
TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 
       36.03       117.21        20.38       194.83       176.55        35.93 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC 
      107.34        61.18        53.92        65.92        23.44        68.09 
TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R 
       28.60        10.49       215.44        15.68        13.87        10.16 
TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y 
       45.11        35.01         3.55        52.01        29.82        27.22 
TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 
        8.65        94.98        33.73        14.70        26.89        68.15 
TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I 
        4.96       109.64       151.27        78.87       168.26        13.55 
TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29H 
       63.35        80.61        47.84        13.97        72.07        32.19 
TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29R TCGA-EE-A29S 
        2.60        44.35        18.61        56.42        14.47        55.92 
TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 
       25.87       171.55        17.92        46.82       102.90        24.43 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE 
       39.29        58.75        47.54        67.43       314.56       135.95 
TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM 
      208.04        48.72        89.33        54.74        79.66        75.48 
TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GT TCGA-EE-A2GU 
       90.97       101.95        13.91        14.30        44.88        94.82 
TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD 
       21.67       129.27        28.83        19.76        61.51        47.28 
TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK 
      103.27       103.20        16.96       204.66        96.23       144.76 
TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR 
      203.05       167.90        47.54       248.65        43.23       103.56 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC 
      136.47        41.59        53.26       124.31       122.73        25.84 
TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3J3 TCGA-EE-A3J4 
        3.68        54.51        13.81        23.47       172.18       127.20 
TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE 
       36.95        64.08        34.32        53.19        27.35        33.40 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 
      101.79       148.08        31.40        35.44        13.94        50.76 
TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E 
        9.17        77.75        98.40        48.89        12.59        13.02 
TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M 
       26.37       268.93       152.35         6.44       131.51        61.05 
TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 
       44.05       162.08        50.89        37.25       148.18        79.99 
TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH 
       43.82        23.34        20.15        16.37        31.27        32.05 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A 
      247.04        80.32        46.98        33.21        92.98       174.21 
TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
        4.90       216.92        48.59       228.59       202.65        20.91 
TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE 
       28.08         7.79        48.85       357.37        53.52        40.27 
TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM 
       15.45         9.70        32.75        47.38        23.93       101.26 
TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU 
       74.73       133.55        11.41       148.80        53.16        26.56 
TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 
       49.48        27.09        27.02        77.82        66.67        28.73 
TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 
      174.84        12.43        26.73        77.88         0.20        22.92 
TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 
       47.54         0.16         2.40         9.90         7.23        14.04 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
      120.46       117.93        84.72        64.44        62.79        32.48 
TCGA-GN-A26D TCGA-QB-A6FS 
       39.58         6.67 

  HTR7 MUTATED HTR7 WILD-TYPE 
         10.13           0.16 
  HTR7 MUTATED HTR7 WILD-TYPE 
        138.81         357.37 
  HTR7 MUTATED HTR7 WILD-TYPE 
        39.620         48.655 
[1] "10.1 - 138.8 (39.6)" "0.2 - 357.4 (48.7)" 
[1] "hr=" "1.5"
D96V3, continuous
                vv
clus             DISTANT METASTASIS PRIMARY TUMOR
  HTR7 MUTATED                    1             0
  HTR7 WILD-TYPE                 34             4
                vv
clus             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  HTR7 MUTATED                                           3                   5
  HTR7 WILD-TYPE                                        55                 165
D96V4, multiclass
                                           clus
vv                                          HTR7 MUTATED HTR7 WILD-TYPE
  DISTANT METASTASIS                                   1             34
  PRIMARY TUMOR                                        0              4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE            3             55
  REGIONAL LYMPH NODE                                  5            165
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  HTR7 MUTATED             0       0       0        0        1        1
  HTR7 WILD-TYPE          10       6      22       10       23       16
                vv
clus             STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  HTR7 MUTATED           1         1         0         0          0          3
  HTR7 WILD-TYPE         9        13         9        31         13         19
                vv
clus             STAGE IIIC STAGE IV
  HTR7 MUTATED            1        0
  HTR7 WILD-TYPE         43       12
D96V5, multiclass
             clus
vv            HTR7 MUTATED HTR7 WILD-TYPE
  I OR II NOS            0             10
  STAGE 0                0              6
  STAGE I                0             22
  STAGE IA               0             10
  STAGE IB               1             23
  STAGE II               1             16
  STAGE IIA              1              9
  STAGE IIB              1             13
  STAGE IIC              0              9
  STAGE III              0             31
  STAGE IIIA             0             13
  STAGE IIIB             3             19
  STAGE IIIC             1             43
  STAGE IV               0             12
[1] 14  2
[1] 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
  HTR7 MUTATED       1  1  4  2
  HTR7 WILD-TYPE    50 57 49 53
D96V6, multiclass
       clus
vv      HTR7 MUTATED HTR7 WILD-TYPE
  T0+T1            1             50
  T2               1             57
  T3               4             49
  T4               2             53
[1] 4 2
[1] TRUE
[1] "dimension 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
  HTR7 MUTATED     4   1   2   1
  HTR7 WILD-TYPE 134  47  30  32
D96V7, multiclass
    clus
vv   HTR7 MUTATED HTR7 WILD-TYPE
  N0            4            134
  N1            1             47
  N2            2             30
  N3            1             32
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              M0  M1 M1A M1B M1C
  HTR7 MUTATED     8   0   0   0   0
  HTR7 WILD-TYPE 232   4   2   2   5
D96V8, multiclass
     clus
vv    HTR7 MUTATED HTR7 WILD-TYPE
  M0             8            232
  M1             0              4
  M1A            0              2
  M1B            0              2
  M1C            0              5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D96V9, binary
                cls
clus              0  1
  HTR7 MUTATED    4  3
  HTR7 WILD-TYPE 98 64
[1] "tbl2"
                cls
clus             [,1] [,2]
  HTR7 MUTATED      4    3
  HTR7 WILD-TYPE   98   64
     clus
vv    HTR7 MUTATED HTR7 WILD-TYPE
  NO             4             98
  YES            3             64
[1] 2 2
[1] FALSE
D96V10, binary
                cls
clus               0   1
  HTR7 MUTATED     2   7
  HTR7 WILD-TYPE  31 228
[1] "tbl2"
                cls
clus             [,1] [,2]
  HTR7 MUTATED      2    7
  HTR7 WILD-TYPE   31  228
     clus
vv    HTR7 MUTATED HTR7 WILD-TYPE
  NO             2             31
  YES            7            228
[1] 2 2
[1] FALSE
D96V11, continuous
D96V12, binary
                cls
clus               0   1
  HTR7 MUTATED     5   4
  HTR7 WILD-TYPE  98 161
[1] "tbl2"
                cls
clus             [,1] [,2]
  HTR7 MUTATED      5    4
  HTR7 WILD-TYPE   98  161
        clus
vv       HTR7 MUTATED HTR7 WILD-TYPE
  FEMALE            5             98
  MALE              4            161
[1] 2 2
[1] FALSE
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  HTR7 MUTATED       0                         0     9
  HTR7 WILD-TYPE     3                         1   255
D96V13, multiclass
                           clus
vv                          HTR7 MUTATED HTR7 WILD-TYPE
  ASIAN                                0              3
  BLACK OR AFRICAN AMERICAN            0              1
  WHITE                                9            255
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D96V14, binary
                cls
clus               0   1
  HTR7 MUTATED     0   9
  HTR7 WILD-TYPE   3 252
[1] "tbl2"
                cls
clus             [,1] [,2]
  HTR7 MUTATED      0    9
  HTR7 WILD-TYPE    3  252
                        clus
vv                       HTR7 MUTATED HTR7 WILD-TYPE
  HISPANIC OR LATINO                0              3
  NOT HISPANIC OR LATINO            9            252
[1] 2 2
[1] FALSE

Clustering(97) Variable = TLR9 MUTATION ANALYSIS
D97V1, survival
                sevent
clus2              0   1
  TLR9 MUTATED    11   7
  TLR9 WILD-TYPE 117 123
  TLR9 MUTATED TLR9 WILD-TYPE 
            18            240 
  TLR9 MUTATED TLR9 WILD-TYPE 
             7            123 
$`TLR9 MUTATED`
TCGA-D3-A2JF TCGA-D3-A2JL TCGA-D3-A3C7 TCGA-D3-A3ML TCGA-D3-A51J TCGA-D9-A3Z1 
       30.87        92.42        46.98         6.31        41.10         4.01 
TCGA-D9-A6EC TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-EE-A29R TCGA-EE-A2GC TCGA-EE-A2MC 
       13.22        10.03        39.19         8.84        34.29        47.51 
TCGA-EE-A2MJ TCGA-EE-A2MR TCGA-EE-A3AB TCGA-ER-A195 TCGA-FS-A1YY TCGA-FW-A3R5 
       63.42        29.65       122.73        18.61        11.01         0.99 

$`TLR9 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.47         8.52       111.09        32.42        70.16       110.79 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       28.08        22.55        45.83        81.24        10.29        85.32 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
        8.38        21.14        88.50        68.22        69.90        11.41 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP 
        7.50        36.16         6.31        56.19        64.44        45.11 
TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE 
      114.67        15.25        46.32        82.29        61.38        13.32 
TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E 
       24.00         9.34       103.59        26.37         5.39        80.22 
TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T 
       42.71        15.09        17.72         8.84        20.48        13.94 
TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z3 
       52.01        47.87         1.55         6.97        23.11         2.89 
TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I2 
        9.90        11.31        48.79        35.80        51.12        13.68 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB 
        9.99        44.52        36.69        25.15         4.93        22.36 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q 
        6.64        19.36         7.00        17.56        14.83        13.15 
TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y 
        0.20         0.00         0.00        13.22        11.57        10.55 
TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 
        6.31         8.12         1.12         1.35        12.20         5.13 
TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I 
        4.31        36.07         4.34         5.13         9.21         1.18 
TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G 
        7.99         9.90        37.97        11.15        38.63         8.55 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
        4.41         1.08        27.12         9.50        12.03         8.09 
TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 
        9.99         2.43         8.68         8.09        11.31        49.22 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE 
       23.90         9.67         8.94        39.39        17.98        34.92 
TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM 
       47.21        30.08        19.43        16.01        35.54        28.31 
TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT 
       33.83        30.84         5.42         1.15        13.02        34.98 
TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MD 
       36.33         8.84        98.27         2.70         6.18         9.53 
TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2ML 
       29.46        44.25         7.96        14.56       111.78       111.91 
TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MS TCGA-EE-A2MT 
       56.02        25.08        26.99        21.60        27.16        23.05 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF 
        5.56       124.31        25.84         3.68        30.15        13.81 
TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 
       15.95        12.72         3.22        22.92        21.60        21.60 
TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI 
       16.14        22.22        27.35         0.46        13.94        33.60 
TCGA-ER-A193 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B 
       31.40        12.95        38.40         5.72        76.41        25.18 
TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H 
        3.78         3.52        11.90        11.11       114.15        34.88 
TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q 
        4.21        13.45        28.60        42.84        34.68         9.57 
TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE 
       36.07        17.72        78.44        11.80         1.87         1.51 
TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV 
       13.08        12.62        11.74         9.04         6.58        22.49 
TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX 
        1.71        18.41        85.74         4.90        64.47         3.45 
TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB 
       23.80        14.24        15.52         7.33         7.30         3.39 
TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH 
       20.38         8.22        19.53        11.08         7.17        30.87 
TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR 
       12.92        12.89        47.38        52.08         8.65         8.81 
TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ 
       49.15        40.64         8.68        27.39         0.82         5.23 
TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB 
       53.85         7.36        28.73        14.20        10.78         5.98 
TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY 
        6.41         2.27         0.20         0.13         0.16         0.43 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        9.90         7.23        12.85        24.85        31.33        84.72 
TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS 
       10.13        16.24        15.42        12.16        14.70         5.79 

  TLR9 MUTATED TLR9 WILD-TYPE 
          0.99           0.00 
  TLR9 MUTATED TLR9 WILD-TYPE 
        122.73         124.31 
  TLR9 MUTATED TLR9 WILD-TYPE 
         30.26          14.40 
[1] "1.0 - 122.7 (30.3)" "0.0 - 124.3 (14.4)"
[1] "hr=" "1.7"
D97V2, survival
                sevent
clus2              0   1
  TLR9 MUTATED    11   7
  TLR9 WILD-TYPE 121 124
  TLR9 MUTATED TLR9 WILD-TYPE 
            18            245 
  TLR9 MUTATED TLR9 WILD-TYPE 
             7            124 
$`TLR9 MUTATED`
TCGA-D3-A2JF TCGA-D3-A2JL TCGA-D3-A3C7 TCGA-D3-A3ML TCGA-D3-A51J TCGA-D9-A3Z1 
       48.76       171.58        46.98        13.87       131.90        11.34 
TCGA-D9-A6EC TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-EE-A29R TCGA-EE-A2GC TCGA-EE-A2MC 
       66.25        20.38       194.83        14.47        67.43        61.51 
TCGA-EE-A2MJ TCGA-EE-A2MR TCGA-EE-A3AB TCGA-ER-A195 TCGA-FS-A1YY TCGA-FW-A3R5 
       96.23       103.56       122.73        35.44       228.59        22.92 

$`TLR9 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.57        16.67       112.04       112.57        71.80       133.25 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       28.08        31.59        90.90        95.74        43.43       103.10 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
       65.49        23.77       115.53       168.00        69.90        11.87 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP 
      113.52        42.08        12.10        56.19        66.08        45.11 
TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE 
      130.72        58.06        46.32       166.52        86.93        60.23 
TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E 
       24.53         9.34       103.59        39.75        21.47       161.85 
TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T 
       43.69        40.14        18.38        10.03        51.68        15.06 
TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 
      135.75       137.92       166.19         7.43       125.19       151.53 
TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA 
       54.67         3.65         6.41         3.25         9.90        25.18 
TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 
       48.89        36.03       117.21       176.55        35.93       107.34 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
       61.18        53.92        65.92        23.44        68.09        28.60 
TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG 
       10.49       215.44        15.68        13.87        10.16        45.11 
TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z 
       35.01         3.55        52.01        29.82        27.22         8.65 
TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 
       94.98        33.73        14.70        26.89        68.15         4.96 
TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A 
      109.64       151.27        78.87       168.26        13.55        63.35 
TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H 
       80.61        47.84        13.97        39.62        72.07        32.19 
TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29S 
        2.60        44.35        18.61        56.42        37.35        55.92 
TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 
       25.87       171.55        17.92        46.82       102.90        24.43 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH 
       39.29        58.75        47.54       314.56       135.95       208.04 
TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN 
       48.72        89.33        54.74        79.66        75.48        90.97 
TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU 
      101.95        13.91        14.30        55.59        44.88        94.82 
TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MD TCGA-EE-A2ME 
       21.67       129.27        28.83        19.76        47.28       103.27 
TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM 
      103.20        16.96       204.66       144.76       203.05       167.90 
TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU 
       47.54       248.65        43.23       136.47        41.59        53.26 
TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG 
      124.31        25.84         3.68        54.51        13.81        23.47 
TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 
      138.81       172.18       127.20        36.95        64.08        34.32 
TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 
       53.19        27.35        33.40       101.79       148.08        31.40 
TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C 
       13.94        50.76         9.17        77.75        98.40        48.89 
TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J 
       12.59        13.02        26.37       268.93       152.35         6.44 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S 
      131.51        61.05        44.05       162.08        50.89        37.25 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF 
      148.18        79.99        43.82        23.34        20.15        16.37 
TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL 
       31.27        32.05       247.04        80.32        46.98        33.21 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1Z0 
       92.98       174.21         4.90       216.92        48.59       202.65 
TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC 
       20.91        28.08         7.79        27.72        48.85       357.37 
TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ 
       53.52        40.27        15.45         9.70        32.75        47.38 
TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS 
       23.93       101.26        74.73       133.55        11.41       148.80 
TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 
       53.16        26.56        49.48        27.09        27.02        77.82 
TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC 
       66.67        28.73       174.84        12.43        26.73        49.45 
TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
       77.88         0.20        47.54         0.16         2.40         9.90 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 
        7.23        14.04       120.46       117.93        84.72        10.13 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS 
       64.44        62.79        32.48        39.58         6.67 

  TLR9 MUTATED TLR9 WILD-TYPE 
         11.34           0.16 
  TLR9 MUTATED TLR9 WILD-TYPE 
        228.59         357.37 
  TLR9 MUTATED TLR9 WILD-TYPE 
         63.88          47.54 
[1] "11.3 - 228.6 (63.9)" "0.2 - 357.4 (47.5)" 
[1] "hr=" "1.6"
D97V3, continuous
                vv
clus             DISTANT METASTASIS PRIMARY TUMOR
  TLR9 MUTATED                    2             1
  TLR9 WILD-TYPE                 33             3
                vv
clus             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  TLR9 MUTATED                                           3                  12
  TLR9 WILD-TYPE                                        55                 158
D97V4, multiclass
                                           clus
vv                                          TLR9 MUTATED TLR9 WILD-TYPE
  DISTANT METASTASIS                                   2             33
  PRIMARY TUMOR                                        1              3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE            3             55
  REGIONAL LYMPH NODE                                 12            158
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  TLR9 MUTATED             1       0       2        1        0        0
  TLR9 WILD-TYPE           9       6      20        9       24       17
                vv
clus             STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  TLR9 MUTATED           1         1         0         5          2          0
  TLR9 WILD-TYPE         9        13         9        26         11         22
                vv
clus             STAGE IIIC STAGE IV
  TLR9 MUTATED            3        1
  TLR9 WILD-TYPE         41       11
D97V5, multiclass
             clus
vv            TLR9 MUTATED TLR9 WILD-TYPE
  I OR II NOS            1              9
  STAGE 0                0              6
  STAGE I                2             20
  STAGE IA               1              9
  STAGE IB               0             24
  STAGE II               0             17
  STAGE IIA              1              9
  STAGE IIB              1             13
  STAGE IIC              0              9
  STAGE III              5             26
  STAGE IIIA             2             11
  STAGE IIIB             0             22
  STAGE IIIC             3             41
  STAGE IV               1             11
[1] 14  2
[1] 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
  TLR9 MUTATED       5  3  5  2
  TLR9 WILD-TYPE    46 55 48 53
D97V6, multiclass
       clus
vv      TLR9 MUTATED TLR9 WILD-TYPE
  T0+T1            5             46
  T2               3             55
  T3               5             48
  T4               2             53
[1] 4 2
[1] TRUE
[1] "dimension 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
  TLR9 MUTATED     8   4   3   3
  TLR9 WILD-TYPE 130  44  29  30
D97V7, multiclass
    clus
vv   TLR9 MUTATED TLR9 WILD-TYPE
  N0            8            130
  N1            4             44
  N2            3             29
  N3            3             30
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              M0  M1 M1A M1B M1C
  TLR9 MUTATED    17   0   1   0   0
  TLR9 WILD-TYPE 223   4   1   2   5
D97V8, multiclass
     clus
vv    TLR9 MUTATED TLR9 WILD-TYPE
  M0            17            223
  M1             0              4
  M1A            1              1
  M1B            0              2
  M1C            0              5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D97V9, binary
                cls
clus              0  1
  TLR9 MUTATED    7  3
  TLR9 WILD-TYPE 95 64
[1] "tbl2"
                cls
clus             [,1] [,2]
  TLR9 MUTATED      7    3
  TLR9 WILD-TYPE   95   64
     clus
vv    TLR9 MUTATED TLR9 WILD-TYPE
  NO             7             95
  YES            3             64
[1] 2 2
[1] FALSE
D97V10, binary
                cls
clus               0   1
  TLR9 MUTATED     4  14
  TLR9 WILD-TYPE  29 221
[1] "tbl2"
                cls
clus             [,1] [,2]
  TLR9 MUTATED      4   14
  TLR9 WILD-TYPE   29  221
     clus
vv    TLR9 MUTATED TLR9 WILD-TYPE
  NO             4             29
  YES           14            221
[1] 2 2
[1] FALSE
D97V11, continuous
D97V12, binary
                cls
clus               0   1
  TLR9 MUTATED     5  13
  TLR9 WILD-TYPE  98 152
[1] "tbl2"
                cls
clus             [,1] [,2]
  TLR9 MUTATED      5   13
  TLR9 WILD-TYPE   98  152
        clus
vv       TLR9 MUTATED TLR9 WILD-TYPE
  FEMALE            5             98
  MALE             13            152
[1] 2 2
[1] FALSE
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TLR9 MUTATED       0                         0    18
  TLR9 WILD-TYPE     3                         1   246
D97V13, multiclass
                           clus
vv                          TLR9 MUTATED TLR9 WILD-TYPE
  ASIAN                                0              3
  BLACK OR AFRICAN AMERICAN            0              1
  WHITE                               18            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"
D97V14, binary
                cls
clus               0   1
  TLR9 MUTATED     0  18
  TLR9 WILD-TYPE   3 243
[1] "tbl2"
                cls
clus             [,1] [,2]
  TLR9 MUTATED      0   18
  TLR9 WILD-TYPE    3  243
                        clus
vv                       TLR9 MUTATED TLR9 WILD-TYPE
  HISPANIC OR LATINO                0              3
  NOT HISPANIC OR LATINO           18            243
[1] 2 2
[1] FALSE

Clustering(98) Variable = MYH1 MUTATION ANALYSIS
D98V1, survival
                sevent
clus2              0   1
  MYH1 MUTATED    35  26
  MYH1 WILD-TYPE  93 104
  MYH1 MUTATED MYH1 WILD-TYPE 
            61            197 
  MYH1 MUTATED MYH1 WILD-TYPE 
            26            104 
$`MYH1 MUTATED`
TCGA-D3-A1Q6 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A2JF TCGA-D3-A2JO TCGA-D3-A3CB 
       70.16        28.08        45.83        30.87        64.44        82.29 
TCGA-D3-A51J TCGA-D3-A51R TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D9-A6EA TCGA-D9-A6EC 
       41.10        20.48         1.55         6.97        11.31        13.22 
TCGA-DA-A1HW TCGA-DA-A1I7 TCGA-EE-A17X TCGA-EE-A183 TCGA-EE-A20C TCGA-EE-A20H 
       35.80        36.69        11.57        12.20         4.34         9.21 
TCGA-EE-A29A TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M 
        7.99        11.15        38.63         4.41         1.08        27.12 
TCGA-EE-A2A2 TCGA-EE-A2GC TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GR TCGA-EE-A2GT 
       23.90        34.29        47.21        19.43         1.15        34.98 
TCGA-EE-A2MD TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MR TCGA-EE-A2MS 
        9.53        63.42       111.91        56.02        29.65        27.16 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AD TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J5 
       23.05         5.56         3.68        15.95        12.72        21.60 
TCGA-EE-A3J7 TCGA-EE-A3JD TCGA-EE-A3JE TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A19P 
       21.60        27.35         0.46        31.40        18.61        34.68 
TCGA-ER-A1A1 TCGA-ER-A2NH TCGA-FR-A44A TCGA-FS-A1ZA TCGA-FS-A1ZM TCGA-FS-A1ZP 
       78.44        11.74        85.74         7.30        47.38        52.08 
TCGA-FS-A1ZZ TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-GF-A6C8 TCGA-GN-A265 TCGA-GN-A266 
        5.23         0.99         0.13        12.85        84.72        10.13 
TCGA-QB-A6FS 
        5.79 

$`MYH1 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q9 
       16.47         8.52       111.09        32.42       110.79        22.55 
TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA 
       81.24        10.29        85.32         8.38        21.14        88.50 
TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK 
       68.22        69.90        11.41         7.50        36.16         6.31 
TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 
       92.42        56.19        45.11       114.67        15.25        46.98 
TCGA-D3-A3C8 TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO 
       46.32        61.38        13.32        24.00         6.31         9.34 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H 
      103.59        26.37         5.39        80.22        42.71        15.09 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GU 
       17.72         8.84        13.94        52.01        47.87        23.11 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I0 
        4.01         2.89         9.90        48.79        51.12        10.03 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I8 TCGA-DA-A1IA 
       39.19        13.68         9.99        44.52        25.15         4.93 
TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 
       22.36         6.64        19.36         7.00        17.56        14.83 
TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EE-A17Y 
       13.15         0.20         0.00         0.00        13.22        10.55 
TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A184 TCGA-EE-A185 
        6.31         8.12         1.12         1.35         5.13         4.31 
TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29G 
       36.07         5.13         1.18         9.90        37.97         8.55 
TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V 
        9.50        12.03         8.09         8.84         9.99         2.43 
TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A5 TCGA-EE-A2A6 
        8.68         8.09        11.31        49.22         9.67         8.94 
TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GI TCGA-EE-A2GK TCGA-EE-A2GL 
       39.39        17.98        34.92        30.08        16.01        35.54 
TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GS TCGA-EE-A2GU 
       28.31        33.83        30.84         5.42        13.02        36.33 
TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2ME 
        8.84        98.27         2.70         6.18        47.51        29.46 
TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2MN TCGA-EE-A2MP 
       44.25         7.96        14.56       111.78        25.08        26.99 
TCGA-EE-A2MQ TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AE TCGA-EE-A3AF 
       21.60       124.31       122.73        25.84        30.15        13.81 
TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JH TCGA-EE-A3JI 
        3.22        22.92        16.14        22.22        13.94        33.60 
TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C 
       12.95        38.40         5.72        76.41        25.18         3.78 
TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J 
        3.52        11.90        11.11       114.15        34.88         4.21 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W 
       13.45        28.60        42.84         9.57        36.07        17.72 
TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES 
       11.80         1.87         1.51        13.08        12.62         9.04 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A69P TCGA-FS-A1YW 
        6.58        22.49         1.71        18.41         4.90        64.47 
TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 
        3.45        11.01        23.80        14.24        15.52         7.33 
TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG 
        3.39        20.38         8.22        19.53        11.08         7.17 
TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS 
       30.87        12.92        12.89         8.65         8.81        49.15 
TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A4F0 TCGA-FS-A4F4 
       40.64         8.68        27.39         0.82        53.85         7.36 
TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD 
       28.73        14.20        10.78         5.98         6.41         2.27 
TCGA-FW-A3I3 TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GN-A262 
        0.20         0.16         0.43         9.90         7.23        24.85 
TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D 
       31.33        16.24        15.42        12.16        14.70 

  MYH1 MUTATED MYH1 WILD-TYPE 
          0.13           0.00 
  MYH1 MUTATED MYH1 WILD-TYPE 
        111.91         124.31 
  MYH1 MUTATED MYH1 WILD-TYPE 
         21.60          13.94 
[1] "0.1 - 111.9 (21.6)" "0.0 - 124.3 (13.9)"
[1] "hr=" "1.4"
D98V2, survival
                sevent
clus2              0   1
  MYH1 MUTATED    36  27
  MYH1 WILD-TYPE  96 104
  MYH1 MUTATED MYH1 WILD-TYPE 
            63            200 
  MYH1 MUTATED MYH1 WILD-TYPE 
            27            104 
$`MYH1 MUTATED`
TCGA-D3-A1Q6 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A2JF TCGA-D3-A2JO TCGA-D3-A3CB 
       71.80        28.08        90.90        48.76        66.08       166.52 
TCGA-D3-A51J TCGA-D3-A51R TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D9-A1JX TCGA-D9-A6EA 
      131.90        51.68       166.19         7.43         6.41        25.18 
TCGA-D9-A6EC TCGA-DA-A1HW TCGA-DA-A1I7 TCGA-EB-A5UL TCGA-EE-A17X TCGA-EE-A183 
       66.25        36.03        61.18         3.55        29.82        26.89 
TCGA-EE-A20C TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H 
      151.27       168.26        63.35        13.97        39.62        32.19 
TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A2A2 TCGA-EE-A2GC TCGA-EE-A2GH TCGA-EE-A2GJ 
        2.60        44.35        24.43        67.43       208.04        89.33 
TCGA-EE-A2GR TCGA-EE-A2GT TCGA-EE-A2MD TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MM 
       14.30        44.88        47.28        96.23       203.05       167.90 
TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AD TCGA-EE-A3AG 
      103.56       136.47        41.59        53.26         3.68        23.47 
TCGA-EE-A3AH TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3JD TCGA-EE-A3JE TCGA-ER-A193 
      138.81        36.95        64.08        27.35        33.40        31.40 
TCGA-ER-A195 TCGA-ER-A19P TCGA-ER-A1A1 TCGA-ER-A2NH TCGA-FR-A44A TCGA-FS-A1ZA 
       35.44       162.08        79.99        32.05       174.21        27.72 
TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZZ TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-GF-A6C8 
      101.26        74.73        27.02        22.92        47.54        14.04 
TCGA-GN-A265 TCGA-GN-A266 TCGA-QB-A6FS 
       84.72        10.13         6.67 

$`MYH1 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q9 
       16.57        16.67       112.04       112.57       133.25        31.59 
TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA 
       95.74        43.43       103.10        65.49        23.77       115.53 
TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK 
      168.00        69.90        11.87       113.52        42.08        12.10 
TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 
      171.58        56.19        45.11       130.72        58.06        46.98 
TCGA-D3-A3C8 TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO 
       46.32        86.93        60.23        24.53        13.87         9.34 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H 
      103.59        39.75        21.47       161.85        43.69        40.14 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GU 
       18.38        10.03        15.06       135.75       137.92       125.19 
TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 
      151.53        54.67         3.65        11.34         3.25         9.90 
TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 
       48.89       117.21        20.38       194.83       176.55        35.93 
TCGA-DA-A1I5 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
      107.34        53.92        65.92        23.44        68.09        28.60 
TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG 
       10.49       215.44        15.68        13.87        10.16        45.11 
TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 
       35.01        52.01        27.22         8.65        94.98        33.73 
TCGA-EE-A182 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20I 
       14.70        68.15         4.96       109.64        78.87        13.55 
TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29G TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
       80.61        47.84        72.07        18.61        56.42        37.35 
TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 
       14.47        55.92        25.87       171.55        17.92        46.82 
TCGA-EE-A2A1 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE 
      102.90        39.29        58.75        47.54       314.56       135.95 
TCGA-EE-A2GI TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO 
       48.72        54.74        79.66        75.48        90.97       101.95 
TCGA-EE-A2GP TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 
       13.91        55.59        94.82        21.67       129.27        28.83 
TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI 
       19.76        61.51       103.27       103.20        16.96       204.66 
TCGA-EE-A2MK TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A3AA TCGA-EE-A3AB 
      144.76        47.54       248.65        43.23       124.31       122.73 
TCGA-EE-A3AC TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J8 
       25.84        54.51        13.81       172.18       127.20        34.32 
TCGA-EE-A3JA TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 
       53.19       101.79       148.08        13.94        50.76         9.17 
TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F 
       77.75        98.40        48.89        12.59        13.02        26.37 
TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N 
      268.93       152.35         6.44       131.51        61.05        44.05 
TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE 
       50.89        37.25       148.18        43.82        23.34        20.15 
TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL 
       16.37        31.27       247.04        80.32        46.98        33.21 
TCGA-FR-A3YN TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 
       92.98         4.90       216.92        48.59       228.59       202.65 
TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD 
       20.91        28.08         7.79        48.85       357.37        53.52 
TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK 
       40.27        15.45         9.70        32.75        47.38        23.93 
TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW 
      133.55        11.41       148.80        53.16        26.56        49.48 
TCGA-FS-A1ZY TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 
       27.09        77.82        66.67        28.73       174.84        12.43 
TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TV TCGA-FW-A5DY 
       26.73        49.45        77.88         0.20         0.16         2.40 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A268 
        9.90         7.23       120.46       117.93        64.44        62.79 
TCGA-GN-A26A TCGA-GN-A26D 
       32.48        39.58 

  MYH1 MUTATED MYH1 WILD-TYPE 
          2.60           0.16 
  MYH1 MUTATED MYH1 WILD-TYPE 
        208.04         357.37 
  MYH1 MUTATED MYH1 WILD-TYPE 
        47.280         48.785 
[1] "2.6 - 208.0 (47.3)" "0.2 - 357.4 (48.8)"
[1] "hr=" "1.2"
D98V3, continuous
                vv
clus             DISTANT METASTASIS PRIMARY TUMOR
  MYH1 MUTATED                    7             2
  MYH1 WILD-TYPE                 28             2
                vv
clus             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  MYH1 MUTATED                                          12                  42
  MYH1 WILD-TYPE                                        46                 128
D98V4, multiclass
                                           clus
vv                                          MYH1 MUTATED MYH1 WILD-TYPE
  DISTANT METASTASIS                                   7             28
  PRIMARY TUMOR                                        2              2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE           12             46
  REGIONAL LYMPH NODE                                 42            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             I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  MYH1 MUTATED             1       2       5        5        3        7
  MYH1 WILD-TYPE           9       4      17        5       21       10
                vv
clus             STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  MYH1 MUTATED           2         4         0        11          2          5
  MYH1 WILD-TYPE         8        10         9        20         11         17
                vv
clus             STAGE IIIC STAGE IV
  MYH1 MUTATED            8        2
  MYH1 WILD-TYPE         36       10
D98V5, multiclass
             clus
vv            MYH1 MUTATED MYH1 WILD-TYPE
  I OR II NOS            1              9
  STAGE 0                2              4
  STAGE I                5             17
  STAGE IA               5              5
  STAGE IB               3             21
  STAGE II               7             10
  STAGE IIA              2              8
  STAGE IIB              4             10
  STAGE IIC              0              9
  STAGE III             11             20
  STAGE IIIA             2             11
  STAGE IIIB             5             17
  STAGE IIIC             8             36
  STAGE IV               2             10
[1] 14  2
[1] 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
  MYH1 MUTATED      14 10 17  9
  MYH1 WILD-TYPE    37 48 36 46
D98V6, multiclass
       clus
vv      MYH1 MUTATED MYH1 WILD-TYPE
  T0+T1           14             37
  T2              10             48
  T3              17             36
  T4               9             46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  MYH1 MUTATED    31  14   6   7
  MYH1 WILD-TYPE 107  34  26  26
D98V7, multiclass
    clus
vv   MYH1 MUTATED MYH1 WILD-TYPE
  N0           31            107
  N1           14             34
  N2            6             26
  N3            7             26
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              M0  M1 M1A M1B M1C
  MYH1 MUTATED    58   0   0   1   1
  MYH1 WILD-TYPE 182   4   2   1   4
D98V8, multiclass
     clus
vv    MYH1 MUTATED MYH1 WILD-TYPE
  M0            58            182
  M1             0              4
  M1A            0              2
  M1B            1              1
  M1C            1              4
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D98V9, binary
                cls
clus              0  1
  MYH1 MUTATED   26 11
  MYH1 WILD-TYPE 76 56
[1] "tbl2"
                cls
clus             [,1] [,2]
  MYH1 MUTATED     26   11
  MYH1 WILD-TYPE   76   56
     clus
vv    MYH1 MUTATED MYH1 WILD-TYPE
  NO            26             76
  YES           11             56
[1] 2 2
[1] FALSE
D98V10, binary
                cls
clus               0   1
  MYH1 MUTATED    10  53
  MYH1 WILD-TYPE  23 182
[1] "tbl2"
                cls
clus             [,1] [,2]
  MYH1 MUTATED     10   53
  MYH1 WILD-TYPE   23  182
     clus
vv    MYH1 MUTATED MYH1 WILD-TYPE
  NO            10             23
  YES           53            182
[1] 2 2
[1] FALSE
D98V11, continuous
D98V12, binary
                cls
clus               0   1
  MYH1 MUTATED    14  49
  MYH1 WILD-TYPE  89 116
[1] "tbl2"
                cls
clus             [,1] [,2]
  MYH1 MUTATED     14   49
  MYH1 WILD-TYPE   89  116
        clus
vv       MYH1 MUTATED MYH1 WILD-TYPE
  FEMALE           14             89
  MALE             49            116
[1] 2 2
[1] FALSE
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MYH1 MUTATED       0                         0    63
  MYH1 WILD-TYPE     3                         1   201
D98V13, multiclass
                           clus
vv                          MYH1 MUTATED MYH1 WILD-TYPE
  ASIAN                                0              3
  BLACK OR AFRICAN AMERICAN            0              1
  WHITE                               63            201
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D98V14, binary
                cls
clus               0   1
  MYH1 MUTATED     1  60
  MYH1 WILD-TYPE   2 201
[1] "tbl2"
                cls
clus             [,1] [,2]
  MYH1 MUTATED      1   60
  MYH1 WILD-TYPE    2  201
                        clus
vv                       MYH1 MUTATED MYH1 WILD-TYPE
  HISPANIC OR LATINO                1              2
  NOT HISPANIC OR LATINO           60            201
[1] 2 2
[1] FALSE

Clustering(99) Variable = EPHA3 MUTATION ANALYSIS
D99V1, survival
                 sevent
clus2               0   1
  EPHA3 MUTATED    15  13
  EPHA3 WILD-TYPE 113 117
  EPHA3 MUTATED EPHA3 WILD-TYPE 
             28             230 
  EPHA3 MUTATED EPHA3 WILD-TYPE 
             13             117 
$`EPHA3 MUTATED`
TCGA-D3-A1Q6 TCGA-D3-A2JA TCGA-D3-A2JD TCGA-D3-A3C7 TCGA-D3-A51T TCGA-D3-A5GS 
       70.16        88.50        11.41        46.98        13.94         6.97 
TCGA-D9-A6EC TCGA-DA-A1I7 TCGA-EE-A17X TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A20F 
       13.22        36.69        11.57         1.35        12.20         5.13 
TCGA-EE-A29M TCGA-EE-A2A5 TCGA-EE-A2GI TCGA-EE-A2GM TCGA-EE-A2GO TCGA-EE-A2M6 
       27.12         9.67        30.08        28.31        30.84        98.27 
TCGA-EE-A2MC TCGA-EE-A2MJ TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A199 TCGA-FS-A1Z3 
       47.51        63.42        29.65        27.35         5.72        14.24 
TCGA-FS-A1ZK TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-GN-A266 
       12.89         0.99         0.13        10.13 

$`EPHA3 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       16.47         8.52       111.09        32.42       110.79        28.08 
TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 
       22.55        45.83        81.24        10.29        85.32         8.38 
TCGA-D3-A2J9 TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH 
       21.14        68.22        69.90        30.87         7.50        36.16 
TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ 
        6.31        92.42        56.19        64.44        45.11       114.67 
TCGA-D3-A3C6 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF 
       15.25        46.32        82.29        61.38        13.32        24.00 
TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E 
        6.31         9.34       103.59        26.37         5.39        80.22 
TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R 
       42.71        15.09        41.10        17.72         8.84        20.48 
TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 
       52.01        47.87         1.55        23.11         4.01         2.89 
TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 
        9.90        11.31        48.79        35.80        51.12        10.03 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I8 TCGA-DA-A1IA 
       39.19        13.68         9.99        44.52        25.15         4.93 
TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 
       22.36         6.64        19.36         7.00        17.56        14.83 
TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EE-A17Y 
       13.15         0.20         0.00         0.00        13.22        10.55 
TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B 
        6.31         8.12         1.12         5.13         4.31        36.07 
TCGA-EE-A20C TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C 
        4.34         9.21         1.18         7.99         9.90        37.97 
TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29N 
       11.15        38.63         8.55         4.41         1.08         9.50 
TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W 
       12.03         8.09         8.84         9.99         2.43         8.68 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB 
        8.09        11.31        49.22        23.90         8.94        39.39 
TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK 
       34.29        17.98        34.92        47.21        19.43        16.01 
TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT 
       35.54        33.83         5.42         1.15        13.02        34.98 
TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MD TCGA-EE-A2ME 
       36.33         8.84         2.70         6.18         9.53        29.46 
TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM 
       44.25         7.96        14.56       111.78       111.91        56.02 
TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU 
       25.08        26.99        21.60        27.16        23.05         5.56 
TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF 
      124.31       122.73        25.84         3.68        30.15        13.81 
TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 
       15.95        12.72         3.22        22.92        21.60        21.60 
TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 
       16.14        22.22         0.46        13.94        33.60        31.40 
TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C 
       18.61        12.95        38.40        76.41        25.18         3.78 
TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J 
        3.52        11.90        11.11       114.15        34.88         4.21 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S 
       13.45        28.60        42.84        34.68         9.57        36.07 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF 
       17.72        78.44        11.80         1.87         1.51        13.08 
TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL 
       12.62        11.74         9.04         6.58        22.49         1.71 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY 
       18.41        85.74         4.90        64.47         3.45        11.01 
TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC 
       23.80        15.52         7.33         7.30         3.39        20.38 
TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ 
        8.22        19.53        11.08         7.17        30.87        12.92 
TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT 
       47.38        52.08         8.65         8.81        49.15        40.64 
TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 
        8.68        27.39         0.82         5.23        53.85         7.36 
TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD 
       28.73        14.20        10.78         5.98         6.41         2.27 
TCGA-FW-A3I3 TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 
        0.20         0.16         0.43         9.90         7.23        12.85 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
       24.85        31.33        84.72        16.24        15.42        12.16 
TCGA-GN-A26D TCGA-QB-A6FS 
       14.70         5.79 

  EPHA3 MUTATED EPHA3 WILD-TYPE 
           0.13            0.00 
  EPHA3 MUTATED EPHA3 WILD-TYPE 
          98.27          124.31 
  EPHA3 MUTATED EPHA3 WILD-TYPE 
          14.09           14.96 
[1] "0.1 - 98.3 (14.1)"  "0.0 - 124.3 (15.0)"
[1] "hr=" "1.2"
D99V2, survival
                 sevent
clus2               0   1
  EPHA3 MUTATED    15  13
  EPHA3 WILD-TYPE 117 118
  EPHA3 MUTATED EPHA3 WILD-TYPE 
             28             235 
  EPHA3 MUTATED EPHA3 WILD-TYPE 
             13             118 
$`EPHA3 MUTATED`
TCGA-D3-A1Q6 TCGA-D3-A2JA TCGA-D3-A2JD TCGA-D3-A3C7 TCGA-D3-A51T TCGA-D3-A5GS 
       71.80       115.53        11.87        46.98        15.06         7.43 
TCGA-D9-A6EC TCGA-DA-A1I7 TCGA-EE-A17X TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A20F 
       66.25        61.18        29.82        14.70        26.89        78.87 
TCGA-EE-A29M TCGA-EE-A2A5 TCGA-EE-A2GI TCGA-EE-A2GM TCGA-EE-A2GO TCGA-EE-A2M6 
       44.35        39.29        48.72        75.48       101.95       129.27 
TCGA-EE-A2MC TCGA-EE-A2MJ TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A199 TCGA-FS-A1Z3 
       61.51        96.23       103.56        27.35         9.17        20.91 
TCGA-FS-A1ZK TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-GN-A266 
       23.93        22.92        47.54        10.13 

$`EPHA3 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       16.57        16.67       112.04       112.57       133.25        28.08 
TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 
       31.59        90.90        95.74        43.43       103.10        65.49 
TCGA-D3-A2J9 TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH 
       23.77       168.00        69.90        48.76       113.52        42.08 
TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ 
       12.10       171.58        56.19        66.08        45.11       130.72 
TCGA-D3-A3C6 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF 
       58.06        46.32       166.52        86.93        60.23        24.53 
TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E 
       13.87         9.34       103.59        39.75        21.47       161.85 
TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R 
       43.69        40.14       131.90        18.38        10.03        51.68 
TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 
      135.75       137.92       166.19       125.19       151.53        54.67 
TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA 
        3.65         6.41        11.34         3.25         9.90        25.18 
TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 
       48.89        36.03       117.21        20.38       194.83       176.55 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC 
       35.93       107.34        53.92        65.92        23.44        68.09 
TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R 
       28.60        10.49       215.44        15.68        13.87        10.16 
TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17Y TCGA-EE-A17Z 
       45.11        35.01         3.55        52.01        27.22         8.65 
TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C 
       94.98        33.73        68.15         4.96       109.64       151.27 
TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D 
      168.26        13.55        63.35        80.61        47.84        13.97 
TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P 
       39.62        72.07        32.19         2.60        18.61        56.42 
TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X 
       37.35        14.47        55.92        25.87       171.55        17.92 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC 
       46.82       102.90        24.43        58.75        47.54        67.43 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
      314.56       135.95       208.04        89.33        54.74        79.66 
TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU 
       90.97        13.91        14.30        55.59        44.88        94.82 
TCGA-EE-A2M5 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG 
       21.67        28.83        19.76        47.28       103.27       103.20 
TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN 
       16.96       204.66       144.76       203.05       167.90        47.54 
TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA 
      248.65        43.23       136.47        41.59        53.26       124.31 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG 
      122.73        25.84         3.68        54.51        13.81        23.47 
TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 
      138.81       172.18       127.20        36.95        64.08        34.32 
TCGA-EE-A3JA TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 
       53.19        33.40       101.79       148.08        31.40        35.44 
TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D 
       13.94        50.76        77.75        98.40        48.89        12.59 
TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L 
       13.02        26.37       268.93       152.35         6.44       131.51 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W 
       61.05        44.05       162.08        50.89        37.25       148.18 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG 
       79.99        43.82        23.34        20.15        16.37        31.27 
TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN 
       32.05       247.04        80.32        46.98        33.21        92.98 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 
      174.21         4.90       216.92        48.59       228.59       202.65 
TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD 
       28.08         7.79        27.72        48.85       357.37        53.52 
TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZM 
       40.27        15.45         9.70        32.75        47.38       101.26 
TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU 
       74.73       133.55        11.41       148.80        53.16        26.56 
TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 
       49.48        27.09        27.02        77.82        66.67        28.73 
TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 
      174.84        12.43        26.73        49.45        77.88         0.20 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 
        0.16         2.40         9.90         7.23        14.04       120.46 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D 
      117.93        84.72        64.44        62.79        32.48        39.58 
TCGA-QB-A6FS 
        6.67 

  EPHA3 MUTATED EPHA3 WILD-TYPE 
           7.43            0.16 
  EPHA3 MUTATED EPHA3 WILD-TYPE 
         129.27          357.37 
  EPHA3 MUTATED EPHA3 WILD-TYPE 
         45.665          48.850 
[1] "7.4 - 129.3 (45.7)" "0.2 - 357.4 (48.9)"
[1] "hr=" "1.3"
D99V3, continuous
                 vv
clus              DISTANT METASTASIS PRIMARY TUMOR
  EPHA3 MUTATED                    4             1
  EPHA3 WILD-TYPE                 31             3
                 vv
clus              REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  EPHA3 MUTATED                                           7                  16
  EPHA3 WILD-TYPE                                        51                 154
D99V4, multiclass
                                           clus
vv                                          EPHA3 MUTATED EPHA3 WILD-TYPE
  DISTANT METASTASIS                                    4              31
  PRIMARY TUMOR                                         1               3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE             7              51
  REGIONAL LYMPH NODE                                  16             154
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  EPHA3 MUTATED             0       1       4        2        2        2
  EPHA3 WILD-TYPE          10       5      18        8       22       15
                 vv
clus              STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  EPHA3 MUTATED           0         0         1         5          2          1
  EPHA3 WILD-TYPE        10        14         8        26         11         21
                 vv
clus              STAGE IIIC STAGE IV
  EPHA3 MUTATED            4        2
  EPHA3 WILD-TYPE         40       10
D99V5, multiclass
             clus
vv            EPHA3 MUTATED EPHA3 WILD-TYPE
  I OR II NOS             0              10
  STAGE 0                 1               5
  STAGE I                 4              18
  STAGE IA                2               8
  STAGE IB                2              22
  STAGE II                2              15
  STAGE IIA               0              10
  STAGE IIB               0              14
  STAGE IIC               1               8
  STAGE III               5              26
  STAGE IIIA              2              11
  STAGE IIIB              1              21
  STAGE IIIC              4              40
  STAGE IV                2              10
[1] 14  2
[1] 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
  EPHA3 MUTATED       7  5  2  8
  EPHA3 WILD-TYPE    44 53 51 47
D99V6, multiclass
       clus
vv      EPHA3 MUTATED EPHA3 WILD-TYPE
  T0+T1             7              44
  T2                5              53
  T3                2              51
  T4                8              47
[1] 4 2
[1] TRUE
[1] "dimension 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
  EPHA3 MUTATED    14   8   3   1
  EPHA3 WILD-TYPE 124  40  29  32
D99V7, multiclass
    clus
vv   EPHA3 MUTATED EPHA3 WILD-TYPE
  N0            14             124
  N1             8              40
  N2             3              29
  N3             1              32
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               M0  M1 M1A M1B M1C
  EPHA3 MUTATED    24   1   0   0   1
  EPHA3 WILD-TYPE 216   3   2   2   4
D99V8, multiclass
     clus
vv    EPHA3 MUTATED EPHA3 WILD-TYPE
  M0             24             216
  M1              1               3
  M1A             0               2
  M1B             0               2
  M1C             1               4
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D99V9, binary
                 cls
clus               0  1
  EPHA3 MUTATED   12  5
  EPHA3 WILD-TYPE 90 62
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EPHA3 MUTATED     12    5
  EPHA3 WILD-TYPE   90   62
     clus
vv    EPHA3 MUTATED EPHA3 WILD-TYPE
  NO             12              90
  YES             5              62
[1] 2 2
[1] FALSE
D99V10, binary
                 cls
clus                0   1
  EPHA3 MUTATED     5  23
  EPHA3 WILD-TYPE  28 212
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EPHA3 MUTATED      5   23
  EPHA3 WILD-TYPE   28  212
     clus
vv    EPHA3 MUTATED EPHA3 WILD-TYPE
  NO              5              28
  YES            23             212
[1] 2 2
[1] FALSE
D99V11, continuous
D99V12, binary
                 cls
clus                0   1
  EPHA3 MUTATED    10  18
  EPHA3 WILD-TYPE  93 147
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EPHA3 MUTATED     10   18
  EPHA3 WILD-TYPE   93  147
        clus
vv       EPHA3 MUTATED EPHA3 WILD-TYPE
  FEMALE            10              93
  MALE              18             147
[1] 2 2
[1] FALSE
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  EPHA3 MUTATED       0                         0    28
  EPHA3 WILD-TYPE     3                         1   236
D99V13, multiclass
                           clus
vv                          EPHA3 MUTATED EPHA3 WILD-TYPE
  ASIAN                                 0               3
  BLACK OR AFRICAN AMERICAN             0               1
  WHITE                                28             236
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D99V14, binary
                 cls
clus                0   1
  EPHA3 MUTATED     0  27
  EPHA3 WILD-TYPE   3 234
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EPHA3 MUTATED      0   27
  EPHA3 WILD-TYPE    3  234
                        clus
vv                       EPHA3 MUTATED EPHA3 WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO            27             234
[1] 2 2
[1] FALSE

Clustering(100) Variable = ARL16 MUTATION ANALYSIS
D100V1, survival
                 sevent
clus2               0   1
  ARL16 MUTATED     4   3
  ARL16 WILD-TYPE 124 127
  ARL16 MUTATED ARL16 WILD-TYPE 
              7             251 
  ARL16 MUTATED ARL16 WILD-TYPE 
              3             127 
$`ARL16 MUTATED`
TCGA-D3-A2JF TCGA-EE-A29A TCGA-EE-A2GU TCGA-EE-A2MS TCGA-EE-A3JD TCGA-ER-A2NC 
       30.87         7.99        36.33        27.16        27.35        11.80 
TCGA-FS-A1ZT 
       40.64 

$`ARL16 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.47         8.52       111.09        32.42        70.16       110.79 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       28.08        22.55        45.83        81.24        10.29        85.32 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
        8.38        21.14        88.50        68.22        69.90        11.41 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO 
        7.50        36.16         6.31        92.42        56.19        64.44 
TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB 
       45.11       114.67        15.25        46.98        46.32        82.29 
TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR 
       61.38        13.32        24.00         6.31         9.34       103.59 
TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J 
       26.37         5.39        80.22        42.71        15.09        41.10 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO 
       17.72         8.84        20.48        13.94        52.01        47.87 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 
        1.55         6.97        23.11         4.01         2.89         9.90 
TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 
       11.31        13.22        48.79        35.80        51.12        10.03 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 
       39.19        13.68         9.99        44.52        36.69        25.15 
TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 
        4.93        22.36         6.64        19.36         7.00        17.56 
TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN 
       14.83        13.15         0.20         0.00         0.00        13.22 
TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 
       11.57        10.55         6.31         8.12         1.12         1.35 
TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F 
       12.20         5.13         4.31        36.07         4.34         5.13 
TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E 
        9.21         1.18         9.90        37.97        11.15        38.63 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P 
        8.55         4.41         1.08        27.12         9.50        12.03 
TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X 
        8.09         8.84         9.99         2.43         8.68         8.09 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB 
       11.31        49.22        23.90         9.67         8.94        39.39 
TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ 
       34.29        17.98        34.92        47.21        30.08        19.43 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP 
       16.01        35.54        28.31        33.83        30.84         5.42 
TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 
        1.15        13.02        34.98         8.84        98.27         2.70 
TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH 
        6.18        47.51         9.53        29.46        44.25         7.96 
TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN 
       14.56        63.42       111.78       111.91        56.02        25.08 
TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA 
       26.99        21.60        29.65        23.05         5.56       124.31 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG 
      122.73        25.84         3.68        30.15        13.81        15.95 
TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 
       12.72         3.22        22.92        21.60        21.60        16.14 
TCGA-EE-A3JA TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 
       22.22         0.46        13.94        33.60        31.40        18.61 
TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C 
       12.95        38.40         5.72        76.41        25.18         3.78 
TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J 
        3.52        11.90        11.11       114.15        34.88         4.21 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S 
       13.45        28.60        42.84        34.68         9.57        36.07 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG 
       17.72        78.44         1.87         1.51        13.08        12.62 
TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN 
       11.74         9.04         6.58        22.49         1.71        18.41 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 
       85.74         4.90        64.47         3.45        11.01        23.80 
TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC 
       14.24        15.52         7.33         7.30         3.39        20.38 
TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ 
        8.22        19.53        11.08         7.17        30.87        12.92 
TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS 
       12.89        47.38        52.08         8.65         8.81        49.15 
TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 
        8.68        27.39         0.82         5.23        53.85         7.36 
TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD 
       28.73        14.20        10.78         5.98         6.41         2.27 
TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
        0.20         0.99         0.13         0.16         0.43         9.90 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 
        7.23        12.85        24.85        31.33        84.72        10.13 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS 
       16.24        15.42        12.16        14.70         5.79 

  ARL16 MUTATED ARL16 WILD-TYPE 
           7.99            0.00 
  ARL16 MUTATED ARL16 WILD-TYPE 
          40.64          124.31 
  ARL16 MUTATED ARL16 WILD-TYPE 
          27.35           14.56 
[1] "8.0 - 40.6 (27.4)"  "0.0 - 124.3 (14.6)"
[1] "hr=" "1.4"
D100V2, survival
                 sevent
clus2               0   1
  ARL16 MUTATED     4   3
  ARL16 WILD-TYPE 128 128
  ARL16 MUTATED ARL16 WILD-TYPE 
              7             256 
  ARL16 MUTATED ARL16 WILD-TYPE 
              3             128 
$`ARL16 MUTATED`
TCGA-D3-A2JF TCGA-EE-A29A TCGA-EE-A2GU TCGA-EE-A2MS TCGA-EE-A3JD TCGA-ER-A2NC 
       48.76        63.35        94.82       136.47        27.35        43.82 
TCGA-FS-A1ZT 
       53.16 

$`ARL16 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.57        16.67       112.04       112.57        71.80       133.25 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       28.08        31.59        90.90        95.74        43.43       103.10 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
       65.49        23.77       115.53       168.00        69.90        11.87 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO 
      113.52        42.08        12.10       171.58        56.19        66.08 
TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB 
       45.11       130.72        58.06        46.98        46.32       166.52 
TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR 
       86.93        60.23        24.53        13.87         9.34       103.59 
TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J 
       39.75        21.47       161.85        43.69        40.14       131.90 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO 
       18.38        10.03        51.68        15.06       135.75       137.92 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW 
      166.19         7.43       125.19       151.53        54.67         3.65 
TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC 
        6.41        11.34         3.25         9.90        25.18        66.25 
TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 
       48.89        36.03       117.21        20.38       194.83       176.55 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB 
       35.93       107.34        61.18        53.92        65.92        23.44 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q 
       68.09        28.60        10.49       215.44        15.68        13.87 
TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X 
       10.16        45.11        35.01         3.55        52.01        29.82 
TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 
       27.22         8.65        94.98        33.73        14.70        26.89 
TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H 
       68.15         4.96       109.64       151.27        78.87       168.26 
TCGA-EE-A20I TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G 
       13.55        80.61        47.84        13.97        39.62        72.07 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
       32.19         2.60        44.35        18.61        56.42        37.35 
TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 
       14.47        55.92        25.87       171.55        17.92        46.82 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC 
      102.90        24.43        39.29        58.75        47.54        67.43 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK 
      314.56       135.95       208.04        48.72        89.33        54.74 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR 
       79.66        75.48        90.97       101.95        13.91        14.30 
TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 
       55.59        44.88        21.67       129.27        28.83        19.76 
TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI 
       61.51        47.28       103.27       103.20        16.96       204.66 
TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP 
       96.23       144.76       203.05       167.90        47.54       248.65 
TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB 
       43.23       103.56        41.59        53.26       124.31       122.73 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH 
       25.84         3.68        54.51        13.81        23.47       138.81 
TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA 
      172.18       127.20        36.95        64.08        34.32        53.19 
TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 
       33.40       101.79       148.08        31.40        35.44        13.94 
TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D 
       50.76         9.17        77.75        98.40        48.89        12.59 
TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L 
       13.02        26.37       268.93       152.35         6.44       131.51 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W 
       61.05        44.05       162.08        50.89        37.25       148.18 
TCGA-ER-A1A1 TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH 
       79.99        23.34        20.15        16.37        31.27        32.05 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A 
      247.04        80.32        46.98        33.21        92.98       174.21 
TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
        4.90       216.92        48.59       228.59       202.65        20.91 
TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD 
       28.08         7.79        27.72        48.85       357.37        53.52 
TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK 
       40.27        15.45         9.70        32.75        47.38        23.93 
TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZU 
      101.26        74.73       133.55        11.41       148.80        26.56 
TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 
       49.48        27.09        27.02        77.82        66.67        28.73 
TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 
      174.84        12.43        26.73        49.45        77.88         0.20 
TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
       22.92        47.54         0.16         2.40         9.90         7.23 
TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 
       14.04       120.46       117.93        84.72        10.13        64.44 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS 
       62.79        32.48        39.58         6.67 

  ARL16 MUTATED ARL16 WILD-TYPE 
          27.35            0.16 
  ARL16 MUTATED ARL16 WILD-TYPE 
         136.47          357.37 
  ARL16 MUTATED ARL16 WILD-TYPE 
          53.16           47.69 
[1] "27.4 - 136.5 (53.2)" "0.2 - 357.4 (47.7)" 
[1] "hr=" "1.1"
D100V3, continuous
                 vv
clus              DISTANT METASTASIS PRIMARY TUMOR
  ARL16 MUTATED                    4             0
  ARL16 WILD-TYPE                 31             4
                 vv
clus              REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  ARL16 MUTATED                                           0                   3
  ARL16 WILD-TYPE                                        58                 167
D100V4, multiclass
                                           clus
vv                                          ARL16 MUTATED ARL16 WILD-TYPE
  DISTANT METASTASIS                                    4              31
  PRIMARY TUMOR                                         0               4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE             0              58
  REGIONAL LYMPH NODE                                   3             167
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  ARL16 MUTATED             0       0       0        2        1        1
  ARL16 WILD-TYPE          10       6      22        8       23       16
                 vv
clus              STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  ARL16 MUTATED           0         0         0         2          1          0
  ARL16 WILD-TYPE        10        14         9        29         12         22
                 vv
clus              STAGE IIIC STAGE IV
  ARL16 MUTATED            0        0
  ARL16 WILD-TYPE         44       12
D100V5, multiclass
             clus
vv            ARL16 MUTATED ARL16 WILD-TYPE
  I OR II NOS             0              10
  STAGE 0                 0               6
  STAGE I                 0              22
  STAGE IA                2               8
  STAGE IB                1              23
  STAGE II                1              16
  STAGE IIA               0              10
  STAGE IIB               0              14
  STAGE IIC               0               9
  STAGE III               2              29
  STAGE IIIA              1              12
  STAGE IIIB              0              22
  STAGE IIIC              0              44
  STAGE IV                0              12
[1] 14  2
[1] 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
  ARL16 MUTATED       2  2  2  0
  ARL16 WILD-TYPE    49 56 51 55
D100V6, multiclass
       clus
vv      ARL16 MUTATED ARL16 WILD-TYPE
  T0+T1             2              49
  T2                2              56
  T3                2              51
  T4                0              55
[1] 4 2
[1] TRUE
[1] "dimension 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
  ARL16 MUTATED     4   2   1   0
  ARL16 WILD-TYPE 134  46  31  33
D100V7, multiclass
    clus
vv   ARL16 MUTATED ARL16 WILD-TYPE
  N0             4             134
  N1             2              46
  N2             1              31
  N3             0              33
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               M0  M1 M1A M1B M1C
  ARL16 MUTATED     7   0   0   0   0
  ARL16 WILD-TYPE 233   4   2   2   5
D100V8, multiclass
     clus
vv    ARL16 MUTATED ARL16 WILD-TYPE
  M0              7             233
  M1              0               4
  M1A             0               2
  M1B             0               2
  M1C             0               5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D100V9, binary
                 cls
clus               0  1
  ARL16 MUTATED    5  0
  ARL16 WILD-TYPE 97 67
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ARL16 MUTATED      5    0
  ARL16 WILD-TYPE   97   67
     clus
vv    ARL16 MUTATED ARL16 WILD-TYPE
  NO              5              97
  YES             0              67
[1] 2 2
[1] FALSE
D100V10, binary
                 cls
clus                0   1
  ARL16 MUTATED     1   6
  ARL16 WILD-TYPE  32 229
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ARL16 MUTATED      1    6
  ARL16 WILD-TYPE   32  229
     clus
vv    ARL16 MUTATED ARL16 WILD-TYPE
  NO              1              32
  YES             6             229
[1] 2 2
[1] FALSE
D100V11, continuous
D100V12, binary
                 cls
clus                0   1
  ARL16 MUTATED     1   6
  ARL16 WILD-TYPE 102 159
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ARL16 MUTATED      1    6
  ARL16 WILD-TYPE  102  159
        clus
vv       ARL16 MUTATED ARL16 WILD-TYPE
  FEMALE             1             102
  MALE               6             159
[1] 2 2
[1] FALSE
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ARL16 MUTATED       0                         0     7
  ARL16 WILD-TYPE     3                         1   257
D100V13, multiclass
                           clus
vv                          ARL16 MUTATED ARL16 WILD-TYPE
  ASIAN                                 0               3
  BLACK OR AFRICAN AMERICAN             0               1
  WHITE                                 7             257
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D100V14, binary
                 cls
clus                0   1
  ARL16 MUTATED     0   6
  ARL16 WILD-TYPE   3 255
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ARL16 MUTATED      0    6
  ARL16 WILD-TYPE    3  255
                        clus
vv                       ARL16 MUTATED ARL16 WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO             6             255
[1] 2 2
[1] FALSE

Clustering(101) Variable = DDX17 MUTATION ANALYSIS
D101V1, survival
                 sevent
clus2               0   1
  DDX17 MUTATED     5   6
  DDX17 WILD-TYPE 123 124
  DDX17 MUTATED DDX17 WILD-TYPE 
             11             247 
  DDX17 MUTATED DDX17 WILD-TYPE 
              6             124 
$`DDX17 MUTATED`
TCGA-D3-A1Q3 TCGA-D3-A5GR TCGA-DA-A1I4 TCGA-EE-A2A2 TCGA-EE-A2GI TCGA-EE-A2MD 
        8.52         1.55         9.99        23.90        30.08         9.53 
TCGA-EE-A3AB TCGA-ER-A195 TCGA-ER-A19F TCGA-FS-A1ZA TCGA-FW-A3R5 
      122.73        18.61        11.11         7.30         0.99 

$`DDX17 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       16.47       111.09        32.42        70.16       110.79        28.08 
TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 
       22.55        45.83        81.24        10.29        85.32         8.38 
TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF 
       21.14        88.50        68.22        69.90        11.41        30.87 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO 
        7.50        36.16         6.31        92.42        56.19        64.44 
TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB 
       45.11       114.67        15.25        46.98        46.32        82.29 
TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR 
       61.38        13.32        24.00         6.31         9.34       103.59 
TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J 
       26.37         5.39        80.22        42.71        15.09        41.10 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO 
       17.72         8.84        20.48        13.94        52.01        47.87 
TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA 
        6.97        23.11         4.01         2.89         9.90        11.31 
TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 
       13.22        48.79        35.80        51.12        10.03        39.19 
TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB 
       13.68        44.52        36.69        25.15         4.93        22.36 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q 
        6.64        19.36         7.00        17.56        14.83        13.15 
TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y 
        0.20         0.00         0.00        13.22        11.57        10.55 
TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 
        6.31         8.12         1.12         1.35        12.20         5.13 
TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I 
        4.31        36.07         4.34         5.13         9.21         1.18 
TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G 
        7.99         9.90        37.97        11.15        38.63         8.55 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
        4.41         1.08        27.12         9.50        12.03         8.09 
TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 
        8.84         9.99         2.43         8.68         8.09        11.31 
TCGA-EE-A2A1 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD 
       49.22         9.67         8.94        39.39        34.29        17.98 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM 
       34.92        47.21        19.43        16.01        35.54        28.31 
TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT 
       33.83        30.84         5.42         1.15        13.02        34.98 
TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC 
       36.33         8.84        98.27         2.70         6.18        47.51 
TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK 
       29.46        44.25         7.96        14.56        63.42       111.78 
TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR 
      111.91        56.02        25.08        26.99        21.60        29.65 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3AD 
       27.16        23.05         5.56       124.31        25.84         3.68 
TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 
       30.15        13.81        15.95        12.72         3.22        22.92 
TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE 
       21.60        21.60        16.14        22.22        27.35         0.46 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 
       13.94        33.60        31.40        12.95        38.40         5.72 
TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19G 
       76.41        25.18         3.78         3.52        11.90       114.15 
TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P 
       34.88         4.21        13.45        28.60        42.84        34.68 
TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
        9.57        36.07        17.72        78.44        11.80         1.87 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET 
        1.51        13.08        12.62        11.74         9.04         6.58 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW 
       22.49         1.71        18.41        85.74         4.90        64.47 
TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 
        3.45        11.01        23.80        14.24        15.52         7.33 
TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG 
        3.39        20.38         8.22        19.53        11.08         7.17 
TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ 
       30.87        12.92        12.89        47.38        52.08         8.65 
TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY 
        8.81        49.15        40.64         8.68        27.39         0.82 
TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 
        5.23        53.85         7.36        28.73        14.20        10.78 
TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV 
        5.98         6.41         2.27         0.20         0.13         0.16 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 
        0.43         9.90         7.23        12.85        24.85        31.33 
TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D 
       84.72        10.13        16.24        15.42        12.16        14.70 
TCGA-QB-A6FS 
        5.79 

  DDX17 MUTATED DDX17 WILD-TYPE 
           0.99            0.00 
  DDX17 MUTATED DDX17 WILD-TYPE 
         122.73          124.31 
  DDX17 MUTATED DDX17 WILD-TYPE 
           9.99           15.09 
[1] "1.0 - 122.7 (10.0)" "0.0 - 124.3 (15.1)"
[1] "hr=" "1.3"
D101V2, survival
                 sevent
clus2               0   1
  DDX17 MUTATED     5   6
  DDX17 WILD-TYPE 127 125
  DDX17 MUTATED DDX17 WILD-TYPE 
             11             252 
  DDX17 MUTATED DDX17 WILD-TYPE 
              6             125 
$`DDX17 MUTATED`
TCGA-D3-A1Q3 TCGA-D3-A5GR TCGA-DA-A1I4 TCGA-EE-A2A2 TCGA-EE-A2GI TCGA-EE-A2MD 
       16.67       166.19        35.93        24.43        48.72        47.28 
TCGA-EE-A3AB TCGA-ER-A195 TCGA-ER-A19F TCGA-FS-A1ZA TCGA-FW-A3R5 
      122.73        35.44        26.37        27.72        22.92 

$`DDX17 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       16.57       112.04       112.57        71.80       133.25        28.08 
TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 
       31.59        90.90        95.74        43.43       103.10        65.49 
TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF 
       23.77       115.53       168.00        69.90        11.87        48.76 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO 
      113.52        42.08        12.10       171.58        56.19        66.08 
TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB 
       45.11       130.72        58.06        46.98        46.32       166.52 
TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR 
       86.93        60.23        24.53        13.87         9.34       103.59 
TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J 
       39.75        21.47       161.85        43.69        40.14       131.90 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO 
       18.38        10.03        51.68        15.06       135.75       137.92 
TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX 
        7.43       125.19       151.53        54.67         3.65         6.41 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1HV 
       11.34         3.25         9.90        25.18        66.25        48.89 
TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I5 
       36.03       117.21        20.38       194.83       176.55       107.34 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
       61.18        53.92        65.92        23.44        68.09        28.60 
TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG 
       10.49       215.44        15.68        13.87        10.16        45.11 
TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z 
       35.01         3.55        52.01        29.82        27.22         8.65 
TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 
       94.98        33.73        14.70        26.89        68.15         4.96 
TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A 
      109.64       151.27        78.87       168.26        13.55        63.35 
TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H 
       80.61        47.84        13.97        39.62        72.07        32.19 
TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R 
        2.60        44.35        18.61        56.42        37.35        14.47 
TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 
       55.92        25.87       171.55        17.92        46.82       102.90 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE 
       39.29        58.75        47.54        67.43       314.56       135.95 
TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN 
      208.04        89.33        54.74        79.66        75.48        90.97 
TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU 
      101.95        13.91        14.30        55.59        44.88        94.82 
TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2ME 
       21.67       129.27        28.83        19.76        61.51       103.27 
TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML 
      103.20        16.96       204.66        96.23       144.76       203.05 
TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS 
      167.90        47.54       248.65        43.23       103.56       136.47 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE 
       41.59        53.26       124.31        25.84         3.68        54.51 
TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 
       13.81        23.47       138.81       172.18       127.20        36.95 
TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH 
       64.08        34.32        53.19        27.35        33.40       101.79 
TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A 
      148.08        31.40        13.94        50.76         9.17        77.75 
TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19G TCGA-ER-A19H 
       98.40        48.89        12.59        13.02       268.93       152.35 
TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q 
        6.44       131.51        61.05        44.05       162.08        50.89 
TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE 
       37.25       148.18        79.99        43.82        23.34        20.15 
TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV 
       16.37        31.27        32.05       247.04        80.32        46.98 
TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX 
       33.21        92.98       174.21         4.90       216.92        48.59 
TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZB 
      228.59       202.65        20.91        28.08         7.79        48.85 
TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH 
      357.37        53.52        40.27        15.45         9.70        32.75 
TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR 
       47.38        23.93       101.26        74.73       133.55        11.41 
TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ 
      148.80        53.16        26.56        49.48        27.09        27.02 
TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB 
       77.82        66.67        28.73       174.84        12.43        26.73 
TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY 
       49.45        77.88         0.20        47.54         0.16         2.40 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        9.90         7.23        14.04       120.46       117.93        84.72 
TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS 
       10.13        64.44        62.79        32.48        39.58         6.67 

  DDX17 MUTATED DDX17 WILD-TYPE 
          16.67            0.16 
  DDX17 MUTATED DDX17 WILD-TYPE 
         166.19          357.37 
  DDX17 MUTATED DDX17 WILD-TYPE 
          35.44           48.87 
[1] "16.7 - 166.2 (35.4)" "0.2 - 357.4 (48.9)" 
[1] "hr=" "1.5"
D101V3, continuous
                 vv
clus              DISTANT METASTASIS PRIMARY TUMOR
  DDX17 MUTATED                    1             0
  DDX17 WILD-TYPE                 34             4
                 vv
clus              REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  DDX17 MUTATED                                           1                   9
  DDX17 WILD-TYPE                                        57                 161
D101V4, multiclass
                                           clus
vv                                          DDX17 MUTATED DDX17 WILD-TYPE
  DISTANT METASTASIS                                    1              34
  PRIMARY TUMOR                                         0               4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE             1              57
  REGIONAL LYMPH NODE                                   9             161
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  DDX17 MUTATED             0       0       0        1        0        1
  DDX17 WILD-TYPE          10       6      22        9       24       16
                 vv
clus              STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DDX17 MUTATED           0         0         1         3          0          1
  DDX17 WILD-TYPE        10        14         8        28         13         21
                 vv
clus              STAGE IIIC STAGE IV
  DDX17 MUTATED            2        0
  DDX17 WILD-TYPE         42       12
D101V5, multiclass
             clus
vv            DDX17 MUTATED DDX17 WILD-TYPE
  I OR II NOS             0              10
  STAGE 0                 0               6
  STAGE I                 0              22
  STAGE IA                1               9
  STAGE IB                0              24
  STAGE II                1              16
  STAGE IIA               0              10
  STAGE IIB               0              14
  STAGE IIC               1               8
  STAGE III               3              28
  STAGE IIIA              0              13
  STAGE IIIB              1              21
  STAGE IIIC              2              42
  STAGE IV                0              12
[1] 14  2
[1] 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
  DDX17 MUTATED       3  0  2  3
  DDX17 WILD-TYPE    48 58 51 52
D101V6, multiclass
       clus
vv      DDX17 MUTATED DDX17 WILD-TYPE
  T0+T1             3              48
  T2                0              58
  T3                2              51
  T4                3              52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  DDX17 MUTATED     5   2   4   0
  DDX17 WILD-TYPE 133  46  28  33
D101V7, multiclass
    clus
vv   DDX17 MUTATED DDX17 WILD-TYPE
  N0             5             133
  N1             2              46
  N2             4              28
  N3             0              33
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               M0  M1 M1A M1B M1C
  DDX17 MUTATED    11   0   0   0   0
  DDX17 WILD-TYPE 229   4   2   2   5
D101V8, multiclass
     clus
vv    DDX17 MUTATED DDX17 WILD-TYPE
  M0             11             229
  M1              0               4
  M1A             0               2
  M1B             0               2
  M1C             0               5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D101V9, binary
                 cls
clus                0   1
  DDX17 MUTATED     1   5
  DDX17 WILD-TYPE 101  62
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX17 MUTATED      1    5
  DDX17 WILD-TYPE  101   62
     clus
vv    DDX17 MUTATED DDX17 WILD-TYPE
  NO              1             101
  YES             5              62
[1] 2 2
[1] FALSE
D101V10, binary
                 cls
clus                0   1
  DDX17 MUTATED     1  10
  DDX17 WILD-TYPE  32 225
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX17 MUTATED      1   10
  DDX17 WILD-TYPE   32  225
     clus
vv    DDX17 MUTATED DDX17 WILD-TYPE
  NO              1              32
  YES            10             225
[1] 2 2
[1] FALSE
D101V11, continuous
D101V12, binary
                 cls
clus                0   1
  DDX17 MUTATED     2   9
  DDX17 WILD-TYPE 101 156
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX17 MUTATED      2    9
  DDX17 WILD-TYPE  101  156
        clus
vv       DDX17 MUTATED DDX17 WILD-TYPE
  FEMALE             2             101
  MALE               9             156
[1] 2 2
[1] FALSE
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DDX17 MUTATED       0                         0    11
  DDX17 WILD-TYPE     3                         1   253
D101V13, multiclass
                           clus
vv                          DDX17 MUTATED DDX17 WILD-TYPE
  ASIAN                                 0               3
  BLACK OR AFRICAN AMERICAN             0               1
  WHITE                                11             253
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D101V14, binary
                 cls
clus                0   1
  DDX17 MUTATED     0  11
  DDX17 WILD-TYPE   3 250
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX17 MUTATED      0   11
  DDX17 WILD-TYPE    3  250
                        clus
vv                       DDX17 MUTATED DDX17 WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO            11             250
[1] 2 2
[1] FALSE

Clustering(102) Variable = MAN1A1 MUTATION ANALYSIS
D102V1, survival
                  sevent
clus2                0   1
  MAN1A1 MUTATED     4   8
  MAN1A1 WILD-TYPE 124 122
  MAN1A1 MUTATED MAN1A1 WILD-TYPE 
              12              246 
  MAN1A1 MUTATED MAN1A1 WILD-TYPE 
               8              122 
$`MAN1A1 MUTATED`
TCGA-D3-A2J8 TCGA-D3-A3C7 TCGA-D3-A3ML TCGA-EE-A29E TCGA-EE-A29N TCGA-EE-A2MR 
        8.38        46.98         6.31        38.63         9.50        29.65 
TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3JD TCGA-ER-A199 TCGA-FS-A1ZC TCGA-FW-A3R5 
       22.92        21.60        27.35         5.72        20.38         0.99 

$`MAN1A1 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.47         8.52       111.09        32.42        70.16       110.79 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       28.08        22.55        45.83        81.24        10.29        85.32 
TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF 
       21.14        88.50        68.22        69.90        11.41        30.87 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO 
        7.50        36.16         6.31        92.42        56.19        64.44 
TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC 
       45.11       114.67        15.25        46.32        82.29        61.38 
TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV 
       13.32        24.00         9.34       103.59        26.37         5.39 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N 
       80.22        42.71        15.09        41.10        17.72         8.84 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS 
       20.48        13.94        52.01        47.87         1.55         6.97 
TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC 
       23.11         4.01         2.89         9.90        11.31        13.22 
TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 
       48.79        35.80        51.12        10.03        39.19        13.68 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB 
        9.99        44.52        36.69        25.15         4.93        22.36 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q 
        6.64        19.36         7.00        17.56        14.83        13.15 
TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y 
        0.20         0.00         0.00        13.22        11.57        10.55 
TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 
        6.31         8.12         1.12         1.35        12.20         5.13 
TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I 
        4.31        36.07         4.34         5.13         9.21         1.18 
TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29H 
        7.99         9.90        37.97        11.15         8.55         4.41 
TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S 
        1.08        27.12        12.03         8.09         8.84         9.99 
TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 
        2.43         8.68         8.09        11.31        49.22        23.90 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE 
        9.67         8.94        39.39        34.29        17.98        34.92 
TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM 
       47.21        30.08        19.43        16.01        35.54        28.31 
TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT 
       33.83        30.84         5.42         1.15        13.02        34.98 
TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC 
       36.33         8.84        98.27         2.70         6.18        47.51 
TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ 
        9.53        29.46        44.25         7.96        14.56        63.42 
TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ 
      111.78       111.91        56.02        25.08        26.99        21.60 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC 
       27.16        23.05         5.56       124.31       122.73        25.84 
TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 
        3.68        30.15        13.81        15.95        12.72         3.22 
TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI 
       21.60        16.14        22.22         0.46        13.94        33.60 
TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19B 
       31.40        18.61        12.95        38.40        76.41        25.18 
TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H 
        3.78         3.52        11.90        11.11       114.15        34.88 
TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q 
        4.21        13.45        28.60        42.84        34.68         9.57 
TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE 
       36.07        17.72        78.44        11.80         1.87         1.51 
TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV 
       13.08        12.62        11.74         9.04         6.58        22.49 
TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX 
        1.71        18.41        85.74         4.90        64.47         3.45 
TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA 
       11.01        23.80        14.24        15.52         7.33         7.30 
TCGA-FS-A1ZB TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH 
        3.39         8.22        19.53        11.08         7.17        30.87 
TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR 
       12.92        12.89        47.38        52.08         8.65         8.81 
TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ 
       49.15        40.64         8.68        27.39         0.82         5.23 
TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB 
       53.85         7.36        28.73        14.20        10.78         5.98 
TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY 
        6.41         2.27         0.20         0.13         0.16         0.43 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        9.90         7.23        12.85        24.85        31.33        84.72 
TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS 
       10.13        16.24        15.42        12.16        14.70         5.79 

  MAN1A1 MUTATED MAN1A1 WILD-TYPE 
            0.99             0.00 
  MAN1A1 MUTATED MAN1A1 WILD-TYPE 
           46.98           124.31 
  MAN1A1 MUTATED MAN1A1 WILD-TYPE 
           20.99            14.63 
[1] "1.0 - 47.0 (21.0)"  "0.0 - 124.3 (14.6)"
[1] "hr=" "1.5"
D102V2, survival
                  sevent
clus2                0   1
  MAN1A1 MUTATED     4   8
  MAN1A1 WILD-TYPE 128 123
  MAN1A1 MUTATED MAN1A1 WILD-TYPE 
              12              251 
  MAN1A1 MUTATED MAN1A1 WILD-TYPE 
               8              123 
$`MAN1A1 MUTATED`
TCGA-D3-A2J8 TCGA-D3-A3C7 TCGA-D3-A3ML TCGA-EE-A29E TCGA-EE-A29N TCGA-EE-A2MR 
       65.49        46.98        13.87        39.62        18.61       103.56 
TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3JD TCGA-ER-A199 TCGA-FS-A1ZC TCGA-FW-A3R5 
      127.20        36.95        27.35         9.17       357.37        22.92 

$`MAN1A1 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.57        16.67       112.04       112.57        71.80       133.25 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       28.08        31.59        90.90        95.74        43.43       103.10 
TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF 
       23.77       115.53       168.00        69.90        11.87        48.76 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO 
      113.52        42.08        12.10       171.58        56.19        66.08 
TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC 
       45.11       130.72        58.06        46.32       166.52        86.93 
TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV 
       60.23        24.53         9.34       103.59        39.75        21.47 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N 
      161.85        43.69        40.14       131.90        18.38        10.03 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS 
       51.68        15.06       135.75       137.92       166.19         7.43 
TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 
      125.19       151.53        54.67         3.65         6.41        11.34 
TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1HW 
        3.25         9.90        25.18        66.25        48.89        36.03 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 
      117.21        20.38       194.83       176.55        35.93       107.34 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
       61.18        53.92        65.92        23.44        68.09        28.60 
TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG 
       10.49       215.44        15.68        13.87        10.16        45.11 
TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z 
       35.01         3.55        52.01        29.82        27.22         8.65 
TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 
       94.98        33.73        14.70        26.89        68.15         4.96 
TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A 
      109.64       151.27        78.87       168.26        13.55        63.35 
TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L 
       80.61        47.84        13.97        72.07        32.19         2.60 
TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V 
       44.35        56.42        37.35        14.47        55.92        25.87 
TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 
      171.55        17.92        46.82       102.90        24.43        39.29 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH 
       58.75        47.54        67.43       314.56       135.95       208.04 
TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN 
       48.72        89.33        54.74        79.66        75.48        90.97 
TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU 
      101.95        13.91        14.30        55.59        44.88        94.82 
TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD 
       21.67       129.27        28.83        19.76        61.51        47.28 
TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK 
      103.27       103.20        16.96       204.66        96.23       144.76 
TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MS 
      203.05       167.90        47.54       248.65        43.23       136.47 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD 
       41.59        53.26       124.31       122.73        25.84         3.68 
TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J7 
       54.51        13.81        23.47       138.81       172.18        64.08 
TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 
       34.32        53.19        33.40       101.79       148.08        31.40 
TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C 
       35.44        13.94        50.76        77.75        98.40        48.89 
TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J 
       12.59        13.02        26.37       268.93       152.35         6.44 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S 
      131.51        61.05        44.05       162.08        50.89        37.25 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF 
      148.18        79.99        43.82        23.34        20.15        16.37 
TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL 
       31.27        32.05       247.04        80.32        46.98        33.21 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY 
       92.98       174.21         4.90       216.92        48.59       228.59 
TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB 
      202.65        20.91        28.08         7.79        27.72        48.85 
TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ 
       53.52        40.27        15.45         9.70        32.75        47.38 
TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS 
       23.93       101.26        74.73       133.55        11.41       148.80 
TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 
       53.16        26.56        49.48        27.09        27.02        77.82 
TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC 
       66.67        28.73       174.84        12.43        26.73        49.45 
TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
       77.88         0.20        47.54         0.16         2.40         9.90 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 
        7.23        14.04       120.46       117.93        84.72        10.13 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS 
       64.44        62.79        32.48        39.58         6.67 

  MAN1A1 MUTATED MAN1A1 WILD-TYPE 
            9.17             0.16 
  MAN1A1 MUTATED MAN1A1 WILD-TYPE 
          357.37           314.56 
  MAN1A1 MUTATED MAN1A1 WILD-TYPE 
          38.285           48.760 
[1] "9.2 - 357.4 (38.3)" "0.2 - 314.6 (48.8)"
[1] "hr=" "1.2"
D102V3, continuous
                  vv
clus               DISTANT METASTASIS PRIMARY TUMOR
  MAN1A1 MUTATED                    1             0
  MAN1A1 WILD-TYPE                 34             4
                  vv
clus               REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  MAN1A1 MUTATED                                           2
  MAN1A1 WILD-TYPE                                        56
                  vv
clus               REGIONAL LYMPH NODE
  MAN1A1 MUTATED                     9
  MAN1A1 WILD-TYPE                 161
D102V4, multiclass
                                           clus
vv                                          MAN1A1 MUTATED MAN1A1 WILD-TYPE
  DISTANT METASTASIS                                     1               34
  PRIMARY TUMOR                                          0                4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE              2               56
  REGIONAL LYMPH NODE                                    9              161
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  MAN1A1 MUTATED             2       0       1        0        1        1
  MAN1A1 WILD-TYPE           8       6      21       10       23       16
                  vv
clus               STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  MAN1A1 MUTATED           0         0         0         4          1
  MAN1A1 WILD-TYPE        10        14         9        27         12
                  vv
clus               STAGE IIIB STAGE IIIC STAGE IV
  MAN1A1 MUTATED            1          1        0
  MAN1A1 WILD-TYPE         21         43       12
D102V5, multiclass
             clus
vv            MAN1A1 MUTATED MAN1A1 WILD-TYPE
  I OR II NOS              2                8
  STAGE 0                  0                6
  STAGE I                  1               21
  STAGE IA                 0               10
  STAGE IB                 1               23
  STAGE II                 1               16
  STAGE IIA                0               10
  STAGE IIB                0               14
  STAGE IIC                0                9
  STAGE III                4               27
  STAGE IIIA               1               12
  STAGE IIIB               1               21
  STAGE IIIC               1               43
  STAGE IV                 0               12
[1] 14  2
[1] 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
  MAN1A1 MUTATED       1  2  3  2
  MAN1A1 WILD-TYPE    50 56 50 53
D102V6, multiclass
       clus
vv      MAN1A1 MUTATED MAN1A1 WILD-TYPE
  T0+T1              1               50
  T2                 2               56
  T3                 3               50
  T4                 2               53
[1] 4 2
[1] TRUE
[1] "dimension 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
  MAN1A1 MUTATED     5   3   3   1
  MAN1A1 WILD-TYPE 133  45  29  32
D102V7, multiclass
    clus
vv   MAN1A1 MUTATED MAN1A1 WILD-TYPE
  N0              5              133
  N1              3               45
  N2              3               29
  N3              1               32
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                M0  M1 M1A M1B M1C
  MAN1A1 MUTATED    12   0   0   0   0
  MAN1A1 WILD-TYPE 228   4   2   2   5
D102V8, multiclass
     clus
vv    MAN1A1 MUTATED MAN1A1 WILD-TYPE
  M0              12              228
  M1               0                4
  M1A              0                2
  M1B              0                2
  M1C              0                5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D102V9, binary
                  cls
clus                0  1
  MAN1A1 MUTATED    5  2
  MAN1A1 WILD-TYPE 97 65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAN1A1 MUTATED      5    2
  MAN1A1 WILD-TYPE   97   65
     clus
vv    MAN1A1 MUTATED MAN1A1 WILD-TYPE
  NO               5               97
  YES              2               65
[1] 2 2
[1] FALSE
D102V10, binary
                  cls
clus                 0   1
  MAN1A1 MUTATED     2  10
  MAN1A1 WILD-TYPE  31 225
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAN1A1 MUTATED      2   10
  MAN1A1 WILD-TYPE   31  225
     clus
vv    MAN1A1 MUTATED MAN1A1 WILD-TYPE
  NO               2               31
  YES             10              225
[1] 2 2
[1] FALSE
D102V11, continuous
D102V12, binary
                  cls
clus                 0   1
  MAN1A1 MUTATED     2  10
  MAN1A1 WILD-TYPE 101 155
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAN1A1 MUTATED      2   10
  MAN1A1 WILD-TYPE  101  155
        clus
vv       MAN1A1 MUTATED MAN1A1 WILD-TYPE
  FEMALE              2              101
  MALE               10              155
[1] 2 2
[1] FALSE
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MAN1A1 MUTATED       0                         0    12
  MAN1A1 WILD-TYPE     3                         1   252
D102V13, multiclass
                           clus
vv                          MAN1A1 MUTATED MAN1A1 WILD-TYPE
  ASIAN                                  0                3
  BLACK OR AFRICAN AMERICAN              0                1
  WHITE                                 12              252
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D102V14, binary
                  cls
clus                 0   1
  MAN1A1 MUTATED     0  12
  MAN1A1 WILD-TYPE   3 249
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAN1A1 MUTATED      0   12
  MAN1A1 WILD-TYPE    3  249
                        clus
vv                       MAN1A1 MUTATED MAN1A1 WILD-TYPE
  HISPANIC OR LATINO                  0                3
  NOT HISPANIC OR LATINO             12              249
[1] 2 2
[1] FALSE

Clustering(103) Variable = ADAM30 MUTATION ANALYSIS
D103V1, survival
                  sevent
clus2                0   1
  ADAM30 MUTATED     9  17
  ADAM30 WILD-TYPE 119 113
  ADAM30 MUTATED ADAM30 WILD-TYPE 
              26              232 
  ADAM30 MUTATED ADAM30 WILD-TYPE 
              17              113 
$`ADAM30 MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1QA TCGA-D3-A2J6 TCGA-D3-A2JO TCGA-D3-A3C6 
       16.47         8.52        45.83        10.29        64.44        15.25 
TCGA-DA-A1I4 TCGA-EB-A44R TCGA-EE-A183 TCGA-EE-A29E TCGA-EE-A29Q TCGA-EE-A2GI 
        9.99         0.20        12.20        38.63         8.09        30.08 
TCGA-EE-A2MD TCGA-EE-A2MR TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3JA TCGA-EE-A3JD 
        9.53        29.65        23.05       124.31        22.22        27.35 
TCGA-ER-A19E TCGA-ER-A19P TCGA-FS-A1ZK TCGA-FS-A1ZQ TCGA-FS-A1ZZ TCGA-FW-A3R5 
       11.90        34.68        12.89         8.65         5.23         0.99 
TCGA-GN-A262 TCGA-GN-A266 
       24.85        10.13 

$`ADAM30 WILD-TYPE`
TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 
      111.09        32.42        70.16       110.79        28.08        22.55 
TCGA-D3-A1QB TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB 
       81.24        85.32         8.38        21.14        88.50        68.22 
TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK 
       69.90        11.41        30.87         7.50        36.16         6.31 
TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C7 TCGA-D3-A3C8 
       92.42        56.19        45.11       114.67        46.98        46.32 
TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO 
       82.29        61.38        13.32        24.00         6.31         9.34 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H 
      103.59        26.37         5.39        80.22        42.71        15.09 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN 
       41.10        17.72         8.84        20.48        13.94        52.01 
TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 
       47.87         1.55         6.97        23.11         4.01         2.89 
TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY 
        9.90        11.31        13.22        48.79        35.80        51.12 
TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 
       10.03        39.19        13.68        44.52        36.69        25.15 
TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 
        4.93        22.36         6.64        19.36         7.00        17.56 
TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EE-A17X 
       14.83        13.15         0.00         0.00        13.22        11.57 
TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A184 
       10.55         6.31         8.12         1.12         1.35         5.13 
TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I 
        4.31        36.07         4.34         5.13         9.21         1.18 
TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29H 
        7.99         9.90        37.97        11.15         8.55         4.41 
TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29R TCGA-EE-A29S 
        1.08        27.12         9.50        12.03         8.84         9.99 
TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 
        2.43         8.68         8.09        11.31        49.22        23.90 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE 
        9.67         8.94        39.39        34.29        17.98        34.92 
TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN 
       47.21        19.43        16.01        35.54        28.31        33.83 
TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU 
       30.84         5.42         1.15        13.02        34.98        36.33 
TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2ME 
        8.84        98.27         2.70         6.18        47.51        29.46 
TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML 
       44.25         7.96        14.56        63.42       111.78       111.91 
TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MS TCGA-EE-A2MU 
       56.02        25.08        26.99        21.60        27.16         5.56 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG 
      122.73        25.84         3.68        30.15        13.81        15.95 
TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 
       12.72         3.22        22.92        21.60        21.60        16.14 
TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 
        0.46        13.94        33.60        31.40        18.61        12.95 
TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D 
       38.40         5.72        76.41        25.18         3.78         3.52 
TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M 
       11.11       114.15        34.88         4.21        13.45        28.60 
TCGA-ER-A19N TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
       42.84         9.57        36.07        17.72        78.44        11.80 
TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES 
        1.87         1.51        13.08        12.62        11.74         9.04 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
        6.58        22.49         1.71        18.41        85.74         4.90 
TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 
       64.47         3.45        11.01        23.80        14.24        15.52 
TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE 
        7.33         7.30         3.39        20.38         8.22        19.53 
TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZP 
       11.08         7.17        30.87        12.92        47.38        52.08 
TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY 
        8.81        49.15        40.64         8.68        27.39         0.82 
TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB 
       53.85         7.36        28.73        14.20        10.78         5.98 
TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY 
        6.41         2.27         0.20         0.13         0.16         0.43 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 
        9.90         7.23        12.85        31.33        84.72        16.24 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS 
       15.42        12.16        14.70         5.79 

  ADAM30 MUTATED ADAM30 WILD-TYPE 
             0.2              0.0 
  ADAM30 MUTATED ADAM30 WILD-TYPE 
          124.31           122.73 
  ADAM30 MUTATED ADAM30 WILD-TYPE 
          14.070           14.765 
[1] "0.2 - 124.3 (14.1)" "0.0 - 122.7 (14.8)"
[1] "hr=" "1.4"
D103V2, survival
                  sevent
clus2                0   1
  ADAM30 MUTATED     9  17
  ADAM30 WILD-TYPE 123 114
  ADAM30 MUTATED ADAM30 WILD-TYPE 
              26              237 
  ADAM30 MUTATED ADAM30 WILD-TYPE 
              17              114 
$`ADAM30 MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1QA TCGA-D3-A2J6 TCGA-D3-A2JO TCGA-D3-A3C6 
       16.57        16.67        90.90        43.43        66.08        58.06 
TCGA-DA-A1I4 TCGA-EB-A44R TCGA-EE-A183 TCGA-EE-A29E TCGA-EE-A29Q TCGA-EE-A2GI 
       35.93        10.16        26.89        39.62        37.35        48.72 
TCGA-EE-A2MD TCGA-EE-A2MR TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3JA TCGA-EE-A3JD 
       47.28       103.56        41.59       124.31        53.19        27.35 
TCGA-ER-A19E TCGA-ER-A19P TCGA-FS-A1ZK TCGA-FS-A1ZQ TCGA-FS-A1ZZ TCGA-FW-A3R5 
       13.02       162.08        23.93       133.55        27.02        22.92 
TCGA-GN-A262 TCGA-GN-A266 
      120.46        10.13 

$`ADAM30 WILD-TYPE`
TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 
      112.04       112.57        71.80       133.25        28.08        31.59 
TCGA-D3-A1QB TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB 
       95.74       103.10        65.49        23.77       115.53       168.00 
TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK 
       69.90        11.87        48.76       113.52        42.08        12.10 
TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C7 TCGA-D3-A3C8 
      171.58        56.19        45.11       130.72        46.98        46.32 
TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO 
      166.52        86.93        60.23        24.53        13.87         9.34 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H 
      103.59        39.75        21.47       161.85        43.69        40.14 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN 
      131.90        18.38        10.03        51.68        15.06       135.75 
TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 
      137.92       166.19         7.43       125.19       151.53        54.67 
TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA 
        3.65         6.41        11.34         3.25         9.90        25.18 
TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 
       66.25        48.89        36.03       117.21        20.38       194.83 
TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB 
      176.55       107.34        61.18        53.92        65.92        23.44 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q 
       68.09        28.60        10.49       215.44        15.68        13.87 
TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y 
       45.11        35.01         3.55        52.01        29.82        27.22 
TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A184 TCGA-EE-A185 
        8.65        94.98        33.73        14.70        68.15         4.96 
TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A 
      109.64       151.27        78.87       168.26        13.55        63.35 
TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L 
       80.61        47.84        13.97        72.07        32.19         2.60 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V 
       44.35        18.61        56.42        14.47        55.92        25.87 
TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 
      171.55        17.92        46.82       102.90        24.43        39.29 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH 
       58.75        47.54        67.43       314.56       135.95       208.04 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO 
       89.33        54.74        79.66        75.48        90.97       101.95 
TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 
       13.91        14.30        55.59        44.88        94.82        21.67 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2ME TCGA-EE-A2MG 
      129.27        28.83        19.76        61.51       103.27       103.20 
TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM 
       16.96       204.66        96.23       144.76       203.05       167.90 
TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3AB 
       47.54       248.65        43.23       136.47        53.26       122.73 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH 
       25.84         3.68        54.51        13.81        23.47       138.81 
TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JE 
      172.18       127.20        36.95        64.08        34.32        33.40 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 
      101.79       148.08        31.40        35.44        13.94        50.76 
TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19F 
        9.17        77.75        98.40        48.89        12.59        26.37 
TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N 
      268.93       152.35         6.44       131.51        61.05        44.05 
TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
       50.89        37.25       148.18        79.99        43.82        23.34 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET 
       20.15        16.37        31.27        32.05       247.04        80.32 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW 
       46.98        33.21        92.98       174.21         4.90       216.92 
TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 
       48.59       228.59       202.65        20.91        28.08         7.79 
TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF 
       27.72        48.85       357.37        53.52        40.27        15.45 
TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZR 
        9.70        32.75        47.38       101.26        74.73        11.41 
TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A4F0 
      148.80        53.16        26.56        49.48        27.09        77.82 
TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC 
       66.67        28.73       174.84        12.43        26.73        49.45 
TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
       77.88         0.20        47.54         0.16         2.40         9.90 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 
        7.23        14.04       117.93        84.72        64.44        62.79 
TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS 
       32.48        39.58         6.67 

  ADAM30 MUTATED ADAM30 WILD-TYPE 
           10.13             0.16 
  ADAM30 MUTATED ADAM30 WILD-TYPE 
          162.08           357.37 
  ADAM30 MUTATED ADAM30 WILD-TYPE 
          40.605           48.890 
[1] "10.1 - 162.1 (40.6)" "0.2 - 357.4 (48.9)" 
[1] "hr=" "1.8"
D103V3, continuous
                  vv
clus               DISTANT METASTASIS PRIMARY TUMOR
  ADAM30 MUTATED                    3             0
  ADAM30 WILD-TYPE                 32             4
                  vv
clus               REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  ADAM30 MUTATED                                           5
  ADAM30 WILD-TYPE                                        53
                  vv
clus               REGIONAL LYMPH NODE
  ADAM30 MUTATED                    18
  ADAM30 WILD-TYPE                 152
D103V4, multiclass
                                           clus
vv                                          ADAM30 MUTATED ADAM30 WILD-TYPE
  DISTANT METASTASIS                                     3               32
  PRIMARY TUMOR                                          0                4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE              5               53
  REGIONAL LYMPH NODE                                   18              152
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  ADAM30 MUTATED             1       1       1        1        5        2
  ADAM30 WILD-TYPE           9       5      21        9       19       15
                  vv
clus               STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  ADAM30 MUTATED           0         3         1         3          0
  ADAM30 WILD-TYPE        10        11         8        28         13
                  vv
clus               STAGE IIIB STAGE IIIC STAGE IV
  ADAM30 MUTATED            2          3        0
  ADAM30 WILD-TYPE         20         41       12
D103V5, multiclass
             clus
vv            ADAM30 MUTATED ADAM30 WILD-TYPE
  I OR II NOS              1                9
  STAGE 0                  1                5
  STAGE I                  1               21
  STAGE IA                 1                9
  STAGE IB                 5               19
  STAGE II                 2               15
  STAGE IIA                0               10
  STAGE IIB                3               11
  STAGE IIC                1                8
  STAGE III                3               28
  STAGE IIIA               0               13
  STAGE IIIB               2               20
  STAGE IIIC               3               41
  STAGE IV                 0               12
[1] 14  2
[1] 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
  ADAM30 MUTATED       3  6  6  2
  ADAM30 WILD-TYPE    48 52 47 53
D103V6, multiclass
       clus
vv      ADAM30 MUTATED ADAM30 WILD-TYPE
  T0+T1              3               48
  T2                 6               52
  T3                 6               47
  T4                 2               53
[1] 4 2
[1] TRUE
[1] "dimension 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
  ADAM30 MUTATED    16   2   4   2
  ADAM30 WILD-TYPE 122  46  28  31
D103V7, multiclass
    clus
vv   ADAM30 MUTATED ADAM30 WILD-TYPE
  N0             16              122
  N1              2               46
  N2              4               28
  N3              2               31
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                M0  M1 M1A M1B M1C
  ADAM30 MUTATED    24   0   0   0   0
  ADAM30 WILD-TYPE 216   4   2   2   5
D103V8, multiclass
     clus
vv    ADAM30 MUTATED ADAM30 WILD-TYPE
  M0              24              216
  M1               0                4
  M1A              0                2
  M1B              0                2
  M1C              0                5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D103V9, binary
                  cls
clus                0  1
  ADAM30 MUTATED    9  7
  ADAM30 WILD-TYPE 93 60
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ADAM30 MUTATED      9    7
  ADAM30 WILD-TYPE   93   60
     clus
vv    ADAM30 MUTATED ADAM30 WILD-TYPE
  NO               9               93
  YES              7               60
[1] 2 2
[1] FALSE
D103V10, binary
                  cls
clus                 0   1
  ADAM30 MUTATED     3  23
  ADAM30 WILD-TYPE  30 212
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ADAM30 MUTATED      3   23
  ADAM30 WILD-TYPE   30  212
     clus
vv    ADAM30 MUTATED ADAM30 WILD-TYPE
  NO               3               30
  YES             23              212
[1] 2 2
[1] FALSE
D103V11, continuous
D103V12, binary
                  cls
clus                 0   1
  ADAM30 MUTATED     8  18
  ADAM30 WILD-TYPE  95 147
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ADAM30 MUTATED      8   18
  ADAM30 WILD-TYPE   95  147
        clus
vv       ADAM30 MUTATED ADAM30 WILD-TYPE
  FEMALE              8               95
  MALE               18              147
[1] 2 2
[1] FALSE
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ADAM30 MUTATED       1                         0    25
  ADAM30 WILD-TYPE     2                         1   239
D103V13, multiclass
                           clus
vv                          ADAM30 MUTATED ADAM30 WILD-TYPE
  ASIAN                                  1                2
  BLACK OR AFRICAN AMERICAN              0                1
  WHITE                                 25              239
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D103V14, binary
                  cls
clus                 0   1
  ADAM30 MUTATED     1  25
  ADAM30 WILD-TYPE   2 236
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ADAM30 MUTATED      1   25
  ADAM30 WILD-TYPE    2  236
                        clus
vv                       ADAM30 MUTATED ADAM30 WILD-TYPE
  HISPANIC OR LATINO                  1                2
  NOT HISPANIC OR LATINO             25              236
[1] 2 2
[1] FALSE

Clustering(104) Variable = NBEAL1 MUTATION ANALYSIS
D104V1, survival
                  sevent
clus2                0   1
  NBEAL1 MUTATED    14  14
  NBEAL1 WILD-TYPE 114 116
  NBEAL1 MUTATED NBEAL1 WILD-TYPE 
              28              230 
  NBEAL1 MUTATED NBEAL1 WILD-TYPE 
              14              116 
$`NBEAL1 MUTATED`
TCGA-D3-A1Q6 TCGA-D3-A1QA TCGA-D3-A2J6 TCGA-D3-A2JC TCGA-D3-A3C6 TCGA-D3-A3C8 
       70.16        45.83        10.29        69.90        15.25        46.32 
TCGA-D3-A3CE TCGA-EE-A183 TCGA-EE-A29E TCGA-EE-A2GC TCGA-EE-A2GE TCGA-EE-A2GI 
       13.32        12.20        38.63        34.29        34.92        30.08 
TCGA-EE-A2MD TCGA-EE-A2MG TCGA-EE-A2MJ TCGA-EE-A2MR TCGA-EE-A2MU TCGA-EE-A3AA 
        9.53        44.25        63.42        29.65         5.56       124.31 
TCGA-EE-A3AD TCGA-EE-A3AG TCGA-ER-A19F TCGA-ER-A19Q TCGA-FR-A3YN TCGA-FS-A4FC 
        3.68        15.95        11.11         9.57        18.41         6.41 
TCGA-GN-A262 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A26A 
       24.85        84.72        10.13        12.16 

$`NBEAL1 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       16.47         8.52       111.09        32.42       110.79        28.08 
TCGA-D3-A1Q9 TCGA-D3-A1QB TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA 
       22.55        81.24        85.32         8.38        21.14        88.50 
TCGA-D3-A2JB TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK 
       68.22        11.41        30.87         7.50        36.16         6.31 
TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C7 
       92.42        56.19        64.44        45.11       114.67        46.98 
TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR 
       82.29        61.38        24.00         6.31         9.34       103.59 
TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J 
       26.37         5.39        80.22        42.71        15.09        41.10 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO 
       17.72         8.84        20.48        13.94        52.01        47.87 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 
        1.55         6.97        23.11         4.01         2.89         9.90 
TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 
       11.31        13.22        48.79        35.80        51.12        10.03 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 
       39.19        13.68         9.99        44.52        36.69        25.15 
TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 
        4.93        22.36         6.64        19.36         7.00        17.56 
TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN 
       14.83        13.15         0.20         0.00         0.00        13.22 
TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 
       11.57        10.55         6.31         8.12         1.12         1.35 
TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H 
        5.13         4.31        36.07         4.34         5.13         9.21 
TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29G 
        1.18         7.99         9.90        37.97        11.15         8.55 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
        4.41         1.08        27.12         9.50        12.03         8.09 
TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 
        8.84         9.99         2.43         8.68         8.09        11.31 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD 
       49.22        23.90         9.67         8.94        39.39        17.98 
TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN 
       47.21        19.43        16.01        35.54        28.31        33.83 
TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU 
       30.84         5.42         1.15        13.02        34.98        36.33 
TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2ME 
        8.84        98.27         2.70         6.18        47.51        29.46 
TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN 
        7.96        14.56       111.78       111.91        56.02        25.08 
TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AB TCGA-EE-A3AC 
       26.99        21.60        27.16        23.05       122.73        25.84 
TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 
       30.15        13.81        12.72         3.22        22.92        21.60 
TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH 
       21.60        16.14        22.22        27.35         0.46        13.94 
TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 
       33.60        31.40        18.61        12.95        38.40         5.72 
TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19G 
       76.41        25.18         3.78         3.52        11.90       114.15 
TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P 
       34.88         4.21        13.45        28.60        42.84        34.68 
TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE 
       36.07        17.72        78.44        11.80         1.87         1.51 
TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV 
       13.08        12.62        11.74         9.04         6.58        22.49 
TCGA-ER-A3PL TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY 
        1.71        85.74         4.90        64.47         3.45        11.01 
TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB 
       23.80        14.24        15.52         7.33         7.30         3.39 
TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH 
       20.38         8.22        19.53        11.08         7.17        30.87 
TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR 
       12.92        12.89        47.38        52.08         8.65         8.81 
TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ 
       49.15        40.64         8.68        27.39         0.82         5.23 
TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB 
       53.85         7.36        28.73        14.20        10.78         5.98 
TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY 
        2.27         0.20         0.99         0.13         0.16         0.43 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A268 
        9.90         7.23        12.85        31.33        16.24        15.42 
TCGA-GN-A26D TCGA-QB-A6FS 
       14.70         5.79 

  NBEAL1 MUTATED NBEAL1 WILD-TYPE 
            3.68             0.00 
  NBEAL1 MUTATED NBEAL1 WILD-TYPE 
          124.31           122.73 
  NBEAL1 MUTATED NBEAL1 WILD-TYPE 
           21.63            14.22 
[1] "3.7 - 124.3 (21.6)" "0.0 - 122.7 (14.2)"
[1] "hr=" "1.3"
D104V2, survival
                  sevent
clus2                0   1
  NBEAL1 MUTATED    15  14
  NBEAL1 WILD-TYPE 117 117
  NBEAL1 MUTATED NBEAL1 WILD-TYPE 
              29              234 
  NBEAL1 MUTATED NBEAL1 WILD-TYPE 
              14              117 
$`NBEAL1 MUTATED`
TCGA-D3-A1Q6 TCGA-D3-A1QA TCGA-D3-A2J6 TCGA-D3-A2JC TCGA-D3-A3C6 TCGA-D3-A3C8 
       71.80        90.90        43.43        69.90        58.06        46.32 
TCGA-D3-A3CE TCGA-D9-A149 TCGA-EE-A183 TCGA-EE-A29E TCGA-EE-A2GC TCGA-EE-A2GE 
       60.23        54.67        26.89        39.62        67.43       135.95 
TCGA-EE-A2GI TCGA-EE-A2MD TCGA-EE-A2MG TCGA-EE-A2MJ TCGA-EE-A2MR TCGA-EE-A2MU 
       48.72        47.28       103.20        96.23       103.56        53.26 
TCGA-EE-A3AA TCGA-EE-A3AD TCGA-EE-A3AG TCGA-ER-A19F TCGA-ER-A19Q TCGA-FR-A3YN 
      124.31         3.68        23.47        26.37        50.89        92.98 
TCGA-FS-A4FC TCGA-GN-A262 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A26A 
       49.45       120.46        84.72        10.13        32.48 

$`NBEAL1 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       16.57        16.67       112.04       112.57       133.25        28.08 
TCGA-D3-A1Q9 TCGA-D3-A1QB TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA 
       31.59        95.74       103.10        65.49        23.77       115.53 
TCGA-D3-A2JB TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK 
      168.00        11.87        48.76       113.52        42.08        12.10 
TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C7 
      171.58        56.19        66.08        45.11       130.72        46.98 
TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR 
      166.52        86.93        24.53        13.87         9.34       103.59 
TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J 
       39.75        21.47       161.85        43.69        40.14       131.90 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO 
       18.38        10.03        51.68        15.06       135.75       137.92 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A1JW TCGA-D9-A1JX 
      166.19         7.43       125.19       151.53         3.65         6.41 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1HV 
       11.34         3.25         9.90        25.18        66.25        48.89 
TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 
       36.03       117.21        20.38       194.83       176.55        35.93 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC 
      107.34        61.18        53.92        65.92        23.44        68.09 
TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R 
       28.60        10.49       215.44        15.68        13.87        10.16 
TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y 
       45.11        35.01         3.55        52.01        29.82        27.22 
TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A184 TCGA-EE-A185 
        8.65        94.98        33.73        14.70        68.15         4.96 
TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A 
      109.64       151.27        78.87       168.26        13.55        63.35 
TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L 
       80.61        47.84        13.97        72.07        32.19         2.60 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S 
       44.35        18.61        56.42        37.35        14.47        55.92 
TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 
       25.87       171.55        17.92        46.82       102.90        24.43 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GH TCGA-EE-A2GJ 
       39.29        58.75        47.54       314.56       208.04        89.33 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP 
       54.74        79.66        75.48        90.97       101.95        13.91 
TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 
       14.30        55.59        44.88        94.82        21.67       129.27 
TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2ME TCGA-EE-A2MH TCGA-EE-A2MI 
       28.83        19.76        61.51       103.27        16.96       204.66 
TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ 
      144.76       203.05       167.90        47.54       248.65        43.23 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AE TCGA-EE-A3AF 
      136.47        41.59       122.73        25.84        54.51        13.81 
TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 
      138.81       172.18       127.20        36.95        64.08        34.32 
TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 
       53.19        27.35        33.40       101.79       148.08        31.40 
TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B 
       35.44        13.94        50.76         9.17        77.75        98.40 
TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J 
       48.89        12.59        13.02       268.93       152.35         6.44 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19S TCGA-ER-A19W 
      131.51        61.05        44.05       162.08        37.25       148.18 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG 
       79.99        43.82        23.34        20.15        16.37        31.27 
TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A44A 
       32.05       247.04        80.32        46.98        33.21       174.21 
TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
        4.90       216.92        48.59       228.59       202.65        20.91 
TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD 
       28.08         7.79        27.72        48.85       357.37        53.52 
TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK 
       40.27        15.45         9.70        32.75        47.38        23.93 
TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT 
      101.26        74.73       133.55        11.41       148.80        53.16 
TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 
       26.56        49.48        27.09        27.02        77.82        66.67 
TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FD TCGA-FW-A3I3 
       28.73       174.84        12.43        26.73        77.88         0.20 
TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
       22.92        47.54         0.16         2.40         9.90         7.23 
TCGA-GF-A6C8 TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26D TCGA-QB-A6FS 
       14.04       117.93        64.44        62.79        39.58         6.67 

  NBEAL1 MUTATED NBEAL1 WILD-TYPE 
            3.68             0.16 
  NBEAL1 MUTATED NBEAL1 WILD-TYPE 
          135.95           357.37 
  NBEAL1 MUTATED NBEAL1 WILD-TYPE 
           54.67            47.46 
[1] "3.7 - 135.9 (54.7)" "0.2 - 357.4 (47.5)"
[1] "hr=" "1"  
D104V3, continuous
                  vv
clus               DISTANT METASTASIS PRIMARY TUMOR
  NBEAL1 MUTATED                    0             0
  NBEAL1 WILD-TYPE                 35             4
                  vv
clus               REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  NBEAL1 MUTATED                                          10
  NBEAL1 WILD-TYPE                                        48
                  vv
clus               REGIONAL LYMPH NODE
  NBEAL1 MUTATED                    20
  NBEAL1 WILD-TYPE                 150
D104V4, multiclass
                                           clus
vv                                          NBEAL1 MUTATED NBEAL1 WILD-TYPE
  DISTANT METASTASIS                                     0               35
  PRIMARY TUMOR                                          0                4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE             10               48
  REGIONAL LYMPH NODE                                   20              150
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  NBEAL1 MUTATED             0       2       3        2        3        1
  NBEAL1 WILD-TYPE          10       4      19        8       21       16
                  vv
clus               STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  NBEAL1 MUTATED           1         2         0         7          1
  NBEAL1 WILD-TYPE         9        12         9        24         12
                  vv
clus               STAGE IIIB STAGE IIIC STAGE IV
  NBEAL1 MUTATED            1          1        0
  NBEAL1 WILD-TYPE         21         43       12
D104V5, multiclass
             clus
vv            NBEAL1 MUTATED NBEAL1 WILD-TYPE
  I OR II NOS              0               10
  STAGE 0                  2                4
  STAGE I                  3               19
  STAGE IA                 2                8
  STAGE IB                 3               21
  STAGE II                 1               16
  STAGE IIA                1                9
  STAGE IIB                2               12
  STAGE IIC                0                9
  STAGE III                7               24
  STAGE IIIA               1               12
  STAGE IIIB               1               21
  STAGE IIIC               1               43
  STAGE IV                 0               12
[1] 14  2
[1] 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
  NBEAL1 MUTATED       7  6  6  2
  NBEAL1 WILD-TYPE    44 52 47 53
D104V6, multiclass
       clus
vv      NBEAL1 MUTATED NBEAL1 WILD-TYPE
  T0+T1              7               44
  T2                 6               52
  T3                 6               47
  T4                 2               53
[1] 4 2
[1] TRUE
[1] "dimension 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
  NBEAL1 MUTATED    17   7   2   1
  NBEAL1 WILD-TYPE 121  41  30  32
D104V7, multiclass
    clus
vv   NBEAL1 MUTATED NBEAL1 WILD-TYPE
  N0             17              121
  N1              7               41
  N2              2               30
  N3              1               32
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                M0  M1 M1A M1B M1C
  NBEAL1 MUTATED    27   0   0   0   0
  NBEAL1 WILD-TYPE 213   4   2   2   5
D104V8, multiclass
     clus
vv    NBEAL1 MUTATED NBEAL1 WILD-TYPE
  M0              27              213
  M1               0                4
  M1A              0                2
  M1B              0                2
  M1C              0                5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D104V9, binary
                  cls
clus                0  1
  NBEAL1 MUTATED   13  3
  NBEAL1 WILD-TYPE 89 64
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NBEAL1 MUTATED     13    3
  NBEAL1 WILD-TYPE   89   64
     clus
vv    NBEAL1 MUTATED NBEAL1 WILD-TYPE
  NO              13               89
  YES              3               64
[1] 2 2
[1] FALSE
D104V10, binary
                  cls
clus                 0   1
  NBEAL1 MUTATED     7  23
  NBEAL1 WILD-TYPE  26 212
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NBEAL1 MUTATED      7   23
  NBEAL1 WILD-TYPE   26  212
     clus
vv    NBEAL1 MUTATED NBEAL1 WILD-TYPE
  NO               7               26
  YES             23              212
[1] 2 2
[1] FALSE
D104V11, continuous
D104V12, binary
                  cls
clus                 0   1
  NBEAL1 MUTATED     9  21
  NBEAL1 WILD-TYPE  94 144
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NBEAL1 MUTATED      9   21
  NBEAL1 WILD-TYPE   94  144
        clus
vv       NBEAL1 MUTATED NBEAL1 WILD-TYPE
  FEMALE              9               94
  MALE               21              144
[1] 2 2
[1] FALSE
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  NBEAL1 MUTATED       0                         0    30
  NBEAL1 WILD-TYPE     3                         1   234
D104V13, multiclass
                           clus
vv                          NBEAL1 MUTATED NBEAL1 WILD-TYPE
  ASIAN                                  0                3
  BLACK OR AFRICAN AMERICAN              0                1
  WHITE                                 30              234
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D104V14, binary
                  cls
clus                 0   1
  NBEAL1 MUTATED     0  30
  NBEAL1 WILD-TYPE   3 231
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NBEAL1 MUTATED      0   30
  NBEAL1 WILD-TYPE    3  231
                        clus
vv                       NBEAL1 MUTATED NBEAL1 WILD-TYPE
  HISPANIC OR LATINO                  0                3
  NOT HISPANIC OR LATINO             30              231
[1] 2 2
[1] FALSE

Clustering(105) Variable = WDR65 MUTATION ANALYSIS
D105V1, survival
                 sevent
clus2               0   1
  WDR65 MUTATED    15   5
  WDR65 WILD-TYPE 113 125
  WDR65 MUTATED WDR65 WILD-TYPE 
             20             238 
  WDR65 MUTATED WDR65 WILD-TYPE 
              5             125 
$`WDR65 MUTATED`
TCGA-D3-A2JL TCGA-D3-A3C7 TCGA-D3-A3CB TCGA-D9-A6EC TCGA-DA-A3F5 TCGA-EE-A20C 
       92.42        46.98        82.29        13.22        17.56         4.34 
TCGA-EE-A29M TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A3AA 
       27.12        39.39        17.98        30.84        29.65       124.31 
TCGA-EE-A3AB TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-ER-A198 TCGA-ER-A19E TCGA-ER-A3PL 
      122.73        21.60        21.60        38.40        11.90         1.71 
TCGA-FS-A1ZK TCGA-FS-A4F9 
       12.89        10.78 

$`WDR65 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.47         8.52       111.09        32.42        70.16       110.79 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       28.08        22.55        45.83        81.24        10.29        85.32 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
        8.38        21.14        88.50        68.22        69.90        11.41 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JN TCGA-D3-A2JO 
       30.87         7.50        36.16         6.31        56.19        64.44 
TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C8 TCGA-D3-A3CC TCGA-D3-A3CE 
       45.11       114.67        15.25        46.32        61.38        13.32 
TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV 
       24.00         6.31         9.34       103.59        26.37         5.39 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N 
       80.22        42.71        15.09        41.10        17.72         8.84 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS 
       20.48        13.94        52.01        47.87         1.55         6.97 
TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-DA-A1HV 
       23.11         4.01         2.89         9.90        11.31        48.79 
TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 
       35.80        51.12        10.03        39.19        13.68         9.99 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC 
       44.52        36.69        25.15         4.93        22.36         6.64 
TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG 
       19.36         7.00        14.83        13.15         0.20         0.00 
TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 
        0.00        13.22        11.57        10.55         6.31         8.12 
TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B 
        1.12         1.35        12.20         5.13         4.31        36.07 
TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C 
        5.13         9.21         1.18         7.99         9.90        37.97 
TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29N 
       11.15        38.63         8.55         4.41         1.08         9.50 
TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W 
       12.03         8.09         8.84         9.99         2.43         8.68 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 
        8.09        11.31        49.22        23.90         9.67         8.94 
TCGA-EE-A2GC TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK 
       34.29        34.92        47.21        30.08        19.43        16.01 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS 
       35.54        28.31        33.83         5.42         1.15        13.02 
TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 
       34.98        36.33         8.84        98.27         2.70         6.18 
TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI 
       47.51         9.53        29.46        44.25         7.96        14.56 
TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP 
       63.42       111.78       111.91        56.02        25.08        26.99 
TCGA-EE-A2MQ TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AC TCGA-EE-A3AD 
       21.60        27.16        23.05         5.56        25.84         3.68 
TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 
       30.15        13.81        15.95        12.72         3.22        22.92 
TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI 
       16.14        22.22        27.35         0.46        13.94        33.60 
TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B 
       31.40        18.61        12.95         5.72        76.41        25.18 
TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J 
        3.78         3.52        11.11       114.15        34.88         4.21 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S 
       13.45        28.60        42.84        34.68         9.57        36.07 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF 
       17.72        78.44        11.80         1.87         1.51        13.08 
TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-FR-A3YN 
       12.62        11.74         9.04         6.58        22.49        18.41 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 
       85.74         4.90        64.47         3.45        11.01        23.80 
TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC 
       14.24        15.52         7.33         7.30         3.39        20.38 
TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ 
        8.22        19.53        11.08         7.17        30.87        12.92 
TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT 
       47.38        52.08         8.65         8.81        49.15        40.64 
TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 
        8.68        27.39         0.82         5.23        53.85         7.36 
TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 
       28.73        14.20         5.98         6.41         2.27         0.20 
TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
        0.99         0.13         0.16         0.43         9.90         7.23 
TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 
       12.85        24.85        31.33        84.72        10.13        16.24 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS 
       15.42        12.16        14.70         5.79 

  WDR65 MUTATED WDR65 WILD-TYPE 
           1.71            0.00 
  WDR65 MUTATED WDR65 WILD-TYPE 
         124.31          114.67 
  WDR65 MUTATED WDR65 WILD-TYPE 
          24.36           14.07 
[1] "1.7 - 124.3 (24.4)" "0.0 - 114.7 (14.1)"
[1] "hr=" "2.9"
D105V2, survival
                 sevent
clus2               0   1
  WDR65 MUTATED    15   6
  WDR65 WILD-TYPE 117 125
  WDR65 MUTATED WDR65 WILD-TYPE 
             21             242 
  WDR65 MUTATED WDR65 WILD-TYPE 
              6             125 
$`WDR65 MUTATED`
TCGA-D3-A2JL TCGA-D3-A3C7 TCGA-D3-A3CB TCGA-D9-A1JX TCGA-D9-A6EC TCGA-DA-A3F5 
      171.58        46.98       166.52         6.41        66.25       215.44 
TCGA-EE-A20C TCGA-EE-A29M TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A2MR 
      151.27        44.35        47.54       314.56       101.95       103.56 
TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-ER-A198 TCGA-ER-A19E 
      124.31       122.73        36.95        64.08        50.76        13.02 
TCGA-ER-A3PL TCGA-FS-A1ZK TCGA-FS-A4F9 
       33.21        23.93        12.43 

$`WDR65 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.57        16.67       112.04       112.57        71.80       133.25 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       28.08        31.59        90.90        95.74        43.43       103.10 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
       65.49        23.77       115.53       168.00        69.90        11.87 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JN TCGA-D3-A2JO 
       48.76       113.52        42.08        12.10        56.19        66.08 
TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C8 TCGA-D3-A3CC TCGA-D3-A3CE 
       45.11       130.72        58.06        46.32        86.93        60.23 
TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV 
       24.53        13.87         9.34       103.59        39.75        21.47 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N 
      161.85        43.69        40.14       131.90        18.38        10.03 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS 
       51.68        15.06       135.75       137.92       166.19         7.43 
TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A3Z1 TCGA-D9-A3Z3 
      125.19       151.53        54.67         3.65        11.34         3.25 
TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 
        9.90        25.18        48.89        36.03       117.21        20.38 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 
      194.83       176.55        35.93       107.34        61.18        53.92 
TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F8 
       65.92        23.44        68.09        28.60        10.49        15.68 
TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN 
       13.87        10.16        45.11        35.01         3.55        52.01 
TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 
       29.82        27.22         8.65        94.98        33.73        14.70 
TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H 
       26.89        68.15         4.96       109.64        78.87       168.26 
TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E 
       13.55        63.35        80.61        47.84        13.97        39.62 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
       72.07        32.19         2.60        18.61        56.42        37.35 
TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 
       14.47        55.92        25.87       171.55        17.92        46.82 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GC TCGA-EE-A2GE 
      102.90        24.43        39.29        58.75        67.43       135.95 
TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM 
      208.04        48.72        89.33        54.74        79.66        75.48 
TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU 
       90.97        13.91        14.30        55.59        44.88        94.82 
TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD 
       21.67       129.27        28.83        19.76        61.51        47.28 
TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK 
      103.27       103.20        16.96       204.66        96.23       144.76 
TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MS 
      203.05       167.90        47.54       248.65        43.23       136.47 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF 
       41.59        53.26        25.84         3.68        54.51        13.81 
TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J8 TCGA-EE-A3JA 
       23.47       138.81       172.18       127.20        34.32        53.19 
TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 
       27.35        33.40       101.79       148.08        31.40        35.44 
TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D 
       13.94         9.17        77.75        98.40        48.89        12.59 
TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M 
       26.37       268.93       152.35         6.44       131.51        61.05 
TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 
       44.05       162.08        50.89        37.25       148.18        79.99 
TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH 
       43.82        23.34        20.15        16.37        31.27        32.05 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
      247.04        80.32        46.98        92.98       174.21         4.90 
TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 
      216.92        48.59       228.59       202.65        20.91        28.08 
TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE 
        7.79        27.72        48.85       357.37        53.52        40.27 
TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZP 
       15.45         9.70        32.75        47.38       101.26        74.73 
TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW 
      133.55        11.41       148.80        53.16        26.56        49.48 
TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 
       27.09        27.02        77.82        66.67        28.73       174.84 
TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU 
       26.73        49.45        77.88         0.20        22.92        47.54 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 
        0.16         2.40         9.90         7.23        14.04       120.46 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
      117.93        84.72        10.13        64.44        62.79        32.48 
TCGA-GN-A26D TCGA-QB-A6FS 
       39.58         6.67 

  WDR65 MUTATED WDR65 WILD-TYPE 
           6.41            0.16 
  WDR65 MUTATED WDR65 WILD-TYPE 
         314.56          357.37 
  WDR65 MUTATED WDR65 WILD-TYPE 
          64.08           47.69 
[1] "6.4 - 314.6 (64.1)" "0.2 - 357.4 (47.7)"
[1] "hr=" "2.4"
D105V3, continuous
                 vv
clus              DISTANT METASTASIS PRIMARY TUMOR
  WDR65 MUTATED                    2             1
  WDR65 WILD-TYPE                 33             3
                 vv
clus              REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  WDR65 MUTATED                                           6                  12
  WDR65 WILD-TYPE                                        52                 158
D105V4, multiclass
                                           clus
vv                                          WDR65 MUTATED WDR65 WILD-TYPE
  DISTANT METASTASIS                                    2              33
  PRIMARY TUMOR                                         1               3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE             6              52
  REGIONAL LYMPH NODE                                  12             158
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  WDR65 MUTATED             2       1       2        0        2        2
  WDR65 WILD-TYPE           8       5      20       10       22       15
                 vv
clus              STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  WDR65 MUTATED           0         1         0         4          1          1
  WDR65 WILD-TYPE        10        13         9        27         12         21
                 vv
clus              STAGE IIIC STAGE IV
  WDR65 MUTATED            2        1
  WDR65 WILD-TYPE         42       11
D105V5, multiclass
             clus
vv            WDR65 MUTATED WDR65 WILD-TYPE
  I OR II NOS             2               8
  STAGE 0                 1               5
  STAGE I                 2              20
  STAGE IA                0              10
  STAGE IB                2              22
  STAGE II                2              15
  STAGE IIA               0              10
  STAGE IIB               1              13
  STAGE IIC               0               9
  STAGE III               4              27
  STAGE IIIA              1              12
  STAGE IIIB              1              21
  STAGE IIIC              2              42
  STAGE IV                1              11
[1] 14  2
[1] 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
  WDR65 MUTATED       4  6  3  4
  WDR65 WILD-TYPE    47 52 50 51
D105V6, multiclass
       clus
vv      WDR65 MUTATED WDR65 WILD-TYPE
  T0+T1             4              47
  T2                6              52
  T3                3              50
  T4                4              51
[1] 4 2
[1] TRUE
[1] "dimension 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
  WDR65 MUTATED    11   5   1   2
  WDR65 WILD-TYPE 127  43  31  31
D105V7, multiclass
    clus
vv   WDR65 MUTATED WDR65 WILD-TYPE
  N0            11             127
  N1             5              43
  N2             1              31
  N3             2              31
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               M0  M1 M1A M1B M1C
  WDR65 MUTATED    20   0   1   0   0
  WDR65 WILD-TYPE 220   4   1   2   5
D105V8, multiclass
     clus
vv    WDR65 MUTATED WDR65 WILD-TYPE
  M0             20             220
  M1              0               4
  M1A             1               1
  M1B             0               2
  M1C             0               5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D105V9, binary
                 cls
clus               0  1
  WDR65 MUTATED    7  6
  WDR65 WILD-TYPE 95 61
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WDR65 MUTATED      7    6
  WDR65 WILD-TYPE   95   61
     clus
vv    WDR65 MUTATED WDR65 WILD-TYPE
  NO              7              95
  YES             6              61
[1] 2 2
[1] FALSE
D105V10, binary
                 cls
clus                0   1
  WDR65 MUTATED     3  18
  WDR65 WILD-TYPE  30 217
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WDR65 MUTATED      3   18
  WDR65 WILD-TYPE   30  217
     clus
vv    WDR65 MUTATED WDR65 WILD-TYPE
  NO              3              30
  YES            18             217
[1] 2 2
[1] FALSE
D105V11, continuous
D105V12, binary
                 cls
clus                0   1
  WDR65 MUTATED     8  13
  WDR65 WILD-TYPE  95 152
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WDR65 MUTATED      8   13
  WDR65 WILD-TYPE   95  152
        clus
vv       WDR65 MUTATED WDR65 WILD-TYPE
  FEMALE             8              95
  MALE              13             152
[1] 2 2
[1] FALSE
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  WDR65 MUTATED       0                         0    21
  WDR65 WILD-TYPE     3                         1   243
D105V13, multiclass
                           clus
vv                          WDR65 MUTATED WDR65 WILD-TYPE
  ASIAN                                 0               3
  BLACK OR AFRICAN AMERICAN             0               1
  WHITE                                21             243
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D105V14, binary
                 cls
clus                0   1
  WDR65 MUTATED     0  21
  WDR65 WILD-TYPE   3 240
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WDR65 MUTATED      0   21
  WDR65 WILD-TYPE    3  240
                        clus
vv                       WDR65 MUTATED WDR65 WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO            21             240
[1] 2 2
[1] FALSE

Clustering(106) Variable = C6ORF165 MUTATION ANALYSIS
D106V1, survival
                    sevent
clus2                  0   1
  C6ORF165 MUTATED     7   9
  C6ORF165 WILD-TYPE 121 121
  C6ORF165 MUTATED C6ORF165 WILD-TYPE 
                16                242 
  C6ORF165 MUTATED C6ORF165 WILD-TYPE 
                 9                121 
$`C6ORF165 MUTATED`
TCGA-D3-A2JG TCGA-DA-A1I5 TCGA-EE-A17X TCGA-EE-A20C TCGA-EE-A29D TCGA-EE-A2GC 
        7.50        44.52        11.57         4.34        11.15        34.29 
TCGA-EE-A2GI TCGA-EE-A2GO TCGA-EE-A2MR TCGA-ER-A19F TCGA-ER-A19H TCGA-FS-A1ZK 
       30.08        30.84        29.65        11.11        34.88        12.89 
TCGA-FS-A1ZZ TCGA-FW-A3R5 TCGA-FW-A3TV TCGA-GN-A266 
        5.23         0.99         0.16        10.13 

$`C6ORF165 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.47         8.52       111.09        32.42        70.16       110.79 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       28.08        22.55        45.83        81.24        10.29        85.32 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
        8.38        21.14        88.50        68.22        69.90        11.41 
TCGA-D3-A2JF TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO 
       30.87        36.16         6.31        92.42        56.19        64.44 
TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB 
       45.11       114.67        15.25        46.98        46.32        82.29 
TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR 
       61.38        13.32        24.00         6.31         9.34       103.59 
TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J 
       26.37         5.39        80.22        42.71        15.09        41.10 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO 
       17.72         8.84        20.48        13.94        52.01        47.87 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 
        1.55         6.97        23.11         4.01         2.89         9.90 
TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 
       11.31        13.22        48.79        35.80        51.12        10.03 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA 
       39.19        13.68         9.99        36.69        25.15         4.93 
TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 
       22.36         6.64        19.36         7.00        17.56        14.83 
TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EE-A17Y 
       13.15         0.20         0.00         0.00        13.22        10.55 
TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 
        6.31         8.12         1.12         1.35        12.20         5.13 
TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A 
        4.31        36.07         5.13         9.21         1.18         7.99 
TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L 
        9.90        37.97        38.63         8.55         4.41         1.08 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S 
       27.12         9.50        12.03         8.09         8.84         9.99 
TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 
        2.43         8.68         8.09        11.31        49.22        23.90 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH 
        9.67         8.94        39.39        17.98        34.92        47.21 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP 
       19.43        16.01        35.54        28.31        33.83         5.42 
TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 
        1.15        13.02        34.98        36.33         8.84        98.27 
TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG 
        2.70         6.18        47.51         9.53        29.46        44.25 
TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM 
        7.96        14.56        63.42       111.78       111.91        56.02 
TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU 
       25.08        26.99        21.60        27.16        23.05         5.56 
TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF 
      124.31       122.73        25.84         3.68        30.15        13.81 
TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 
       15.95        12.72         3.22        22.92        21.60        21.60 
TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI 
       16.14        22.22        27.35         0.46        13.94        33.60 
TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A 
       31.40        18.61        12.95        38.40         5.72        76.41 
TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19G TCGA-ER-A19J 
       25.18         3.78         3.52        11.90       114.15         4.21 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S 
       13.45        28.60        42.84        34.68         9.57        36.07 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF 
       17.72        78.44        11.80         1.87         1.51        13.08 
TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL 
       12.62        11.74         9.04         6.58        22.49         1.71 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY 
       18.41        85.74         4.90        64.47         3.45        11.01 
TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB 
       23.80        14.24        15.52         7.33         7.30         3.39 
TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH 
       20.38         8.22        19.53        11.08         7.17        30.87 
TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS 
       12.92        47.38        52.08         8.65         8.81        49.15 
TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A4F0 TCGA-FS-A4F4 
       40.64         8.68        27.39         0.82        53.85         7.36 
TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD 
       28.73        14.20        10.78         5.98         6.41         2.27 
TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 
        0.20         0.13         0.43         9.90         7.23        12.85 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
       24.85        31.33        84.72        16.24        15.42        12.16 
TCGA-GN-A26D TCGA-QB-A6FS 
       14.70         5.79 

  C6ORF165 MUTATED C6ORF165 WILD-TYPE 
              0.16               0.00 
  C6ORF165 MUTATED C6ORF165 WILD-TYPE 
             44.52             124.31 
  C6ORF165 MUTATED C6ORF165 WILD-TYPE 
             11.36              15.17 
[1] "0.2 - 44.5 (11.4)"  "0.0 - 124.3 (15.2)"
[1] "hr=" "1.4"
D106V2, survival
                    sevent
clus2                  0   1
  C6ORF165 MUTATED     7   9
  C6ORF165 WILD-TYPE 125 122
  C6ORF165 MUTATED C6ORF165 WILD-TYPE 
                16                247 
  C6ORF165 MUTATED C6ORF165 WILD-TYPE 
                 9                122 
$`C6ORF165 MUTATED`
TCGA-D3-A2JG TCGA-DA-A1I5 TCGA-EE-A17X TCGA-EE-A20C TCGA-EE-A29D TCGA-EE-A2GC 
      113.52       107.34        29.82       151.27        13.97        67.43 
TCGA-EE-A2GI TCGA-EE-A2GO TCGA-EE-A2MR TCGA-ER-A19F TCGA-ER-A19H TCGA-FS-A1ZK 
       48.72       101.95       103.56        26.37       152.35        23.93 
TCGA-FS-A1ZZ TCGA-FW-A3R5 TCGA-FW-A3TV TCGA-GN-A266 
       27.02        22.92         0.16        10.13 

$`C6ORF165 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.57        16.67       112.04       112.57        71.80       133.25 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       28.08        31.59        90.90        95.74        43.43       103.10 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
       65.49        23.77       115.53       168.00        69.90        11.87 
TCGA-D3-A2JF TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO 
       48.76        42.08        12.10       171.58        56.19        66.08 
TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB 
       45.11       130.72        58.06        46.98        46.32       166.52 
TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR 
       86.93        60.23        24.53        13.87         9.34       103.59 
TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J 
       39.75        21.47       161.85        43.69        40.14       131.90 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO 
       18.38        10.03        51.68        15.06       135.75       137.92 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW 
      166.19         7.43       125.19       151.53        54.67         3.65 
TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC 
        6.41        11.34         3.25         9.90        25.18        66.25 
TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 
       48.89        36.03       117.21        20.38       194.83       176.55 
TCGA-DA-A1I4 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC 
       35.93        61.18        53.92        65.92        23.44        68.09 
TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R 
       28.60        10.49       215.44        15.68        13.87        10.16 
TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17Y TCGA-EE-A17Z 
       45.11        35.01         3.55        52.01        27.22         8.65 
TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 
       94.98        33.73        14.70        26.89        68.15         4.96 
TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B 
      109.64        78.87       168.26        13.55        63.35        80.61 
TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M 
       47.84        39.62        72.07        32.19         2.60        44.35 
TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V 
       18.61        56.42        37.35        14.47        55.92        25.87 
TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 
      171.55        17.92        46.82       102.90        24.43        39.29 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ 
       58.75        47.54       314.56       135.95       208.04        89.33 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR 
       54.74        79.66        75.48        90.97        13.91        14.30 
TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 
       55.59        44.88        94.82        21.67       129.27        28.83 
TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH 
       19.76        61.51        47.28       103.27       103.20        16.96 
TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN 
      204.66        96.23       144.76       203.05       167.90        47.54 
TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA 
      248.65        43.23       136.47        41.59        53.26       124.31 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG 
      122.73        25.84         3.68        54.51        13.81        23.47 
TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 
      138.81       172.18       127.20        36.95        64.08        34.32 
TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 
       53.19        27.35        33.40       101.79       148.08        31.40 
TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B 
       35.44        13.94        50.76         9.17        77.75        98.40 
TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19G TCGA-ER-A19J TCGA-ER-A19L 
       48.89        12.59        13.02       268.93         6.44       131.51 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W 
       61.05        44.05       162.08        50.89        37.25       148.18 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG 
       79.99        43.82        23.34        20.15        16.37        31.27 
TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN 
       32.05       247.04        80.32        46.98        33.21        92.98 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 
      174.21         4.90       216.92        48.59       228.59       202.65 
TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC 
       20.91        28.08         7.79        27.72        48.85       357.37 
TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ 
       53.52        40.27        15.45         9.70        32.75        47.38 
TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT 
      101.26        74.73       133.55        11.41       148.80        53.16 
TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 
       26.56        49.48        27.09        77.82        66.67        28.73 
TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 
      174.84        12.43        26.73        49.45        77.88         0.20 
TCGA-FW-A3TU TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 
       47.54         2.40         9.90         7.23        14.04       120.46 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D 
      117.93        84.72        64.44        62.79        32.48        39.58 
TCGA-QB-A6FS 
        6.67 

  C6ORF165 MUTATED C6ORF165 WILD-TYPE 
              0.16               0.20 
  C6ORF165 MUTATED C6ORF165 WILD-TYPE 
            152.35             357.37 
  C6ORF165 MUTATED C6ORF165 WILD-TYPE 
             39.27              48.59 
[1] "0.2 - 152.3 (39.3)" "0.2 - 357.4 (48.6)"
[1] "hr=" "1.3"
D106V3, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  C6ORF165 MUTATED                    4             0
  C6ORF165 WILD-TYPE                 31             4
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  C6ORF165 MUTATED                                           3
  C6ORF165 WILD-TYPE                                        55
                    vv
clus                 REGIONAL LYMPH NODE
  C6ORF165 MUTATED                     9
  C6ORF165 WILD-TYPE                 161
D106V4, multiclass
                                           clus
vv                                          C6ORF165 MUTATED C6ORF165 WILD-TYPE
  DISTANT METASTASIS                                       4                 31
  PRIMARY TUMOR                                            0                  4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                3                 55
  REGIONAL LYMPH NODE                                      9                161
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  C6ORF165 MUTATED             0       1       1        2        0        2
  C6ORF165 WILD-TYPE          10       5      21        8       24       15
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  C6ORF165 MUTATED           0         2         0         2          1
  C6ORF165 WILD-TYPE        10        12         9        29         12
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  C6ORF165 MUTATED            0          1        1
  C6ORF165 WILD-TYPE         22         43       11
D106V5, multiclass
             clus
vv            C6ORF165 MUTATED C6ORF165 WILD-TYPE
  I OR II NOS                0                 10
  STAGE 0                    1                  5
  STAGE I                    1                 21
  STAGE IA                   2                  8
  STAGE IB                   0                 24
  STAGE II                   2                 15
  STAGE IIA                  0                 10
  STAGE IIB                  2                 12
  STAGE IIC                  0                  9
  STAGE III                  2                 29
  STAGE IIIA                 1                 12
  STAGE IIIB                 0                 22
  STAGE IIIC                 1                 43
  STAGE IV                   1                 11
[1] 14  2
[1] 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
  C6ORF165 MUTATED       4  1  5  1
  C6ORF165 WILD-TYPE    47 57 48 54
D106V6, multiclass
       clus
vv      C6ORF165 MUTATED C6ORF165 WILD-TYPE
  T0+T1                4                 47
  T2                   1                 57
  T3                   5                 48
  T4                   1                 54
[1] 4 2
[1] TRUE
[1] "dimension 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
  C6ORF165 MUTATED    11   2   2   0
  C6ORF165 WILD-TYPE 127  46  30  33
D106V7, multiclass
    clus
vv   C6ORF165 MUTATED C6ORF165 WILD-TYPE
  N0               11                127
  N1                2                 46
  N2                2                 30
  N3                0                 33
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1 M1A M1B M1C
  C6ORF165 MUTATED    14   0   0   0   1
  C6ORF165 WILD-TYPE 226   4   2   2   4
D106V8, multiclass
     clus
vv    C6ORF165 MUTATED C6ORF165 WILD-TYPE
  M0                14                226
  M1                 0                  4
  M1A                0                  2
  M1B                0                  2
  M1C                1                  4
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D106V9, binary
                    cls
clus                  0  1
  C6ORF165 MUTATED    6  3
  C6ORF165 WILD-TYPE 96 64
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C6ORF165 MUTATED      6    3
  C6ORF165 WILD-TYPE   96   64
     clus
vv    C6ORF165 MUTATED C6ORF165 WILD-TYPE
  NO                 6                 96
  YES                3                 64
[1] 2 2
[1] FALSE
D106V10, binary
                    cls
clus                   0   1
  C6ORF165 MUTATED     1  15
  C6ORF165 WILD-TYPE  32 220
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C6ORF165 MUTATED      1   15
  C6ORF165 WILD-TYPE   32  220
     clus
vv    C6ORF165 MUTATED C6ORF165 WILD-TYPE
  NO                 1                 32
  YES               15                220
[1] 2 2
[1] FALSE
D106V11, continuous
D106V12, binary
                    cls
clus                   0   1
  C6ORF165 MUTATED     5  11
  C6ORF165 WILD-TYPE  98 154
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C6ORF165 MUTATED      5   11
  C6ORF165 WILD-TYPE   98  154
        clus
vv       C6ORF165 MUTATED C6ORF165 WILD-TYPE
  FEMALE                5                 98
  MALE                 11                154
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  C6ORF165 MUTATED       0                         0    16
  C6ORF165 WILD-TYPE     3                         1   248
D106V13, multiclass
                           clus
vv                          C6ORF165 MUTATED C6ORF165 WILD-TYPE
  ASIAN                                    0                  3
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                   16                248
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D106V14, binary
                    cls
clus                   0   1
  C6ORF165 MUTATED     1  14
  C6ORF165 WILD-TYPE   2 247
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C6ORF165 MUTATED      1   14
  C6ORF165 WILD-TYPE    2  247
                        clus
vv                       C6ORF165 MUTATED C6ORF165 WILD-TYPE
  HISPANIC OR LATINO                    1                  2
  NOT HISPANIC OR LATINO               14                247
[1] 2 2
[1] FALSE

Clustering(107) Variable = RNF133 MUTATION ANALYSIS
D107V1, survival
                  sevent
clus2                0   1
  RNF133 MUTATED     5   3
  RNF133 WILD-TYPE 123 127
  RNF133 MUTATED RNF133 WILD-TYPE 
               8              250 
  RNF133 MUTATED RNF133 WILD-TYPE 
               3              127 
$`RNF133 MUTATED`
TCGA-DA-A1I5 TCGA-DA-A3F5 TCGA-EE-A182 TCGA-EE-A2MD TCGA-EE-A3AA TCGA-EE-A3JI 
       44.52        17.56         1.35         9.53       124.31        33.60 
TCGA-FW-A3R5 TCGA-GN-A266 
        0.99        10.13 

$`RNF133 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.47         8.52       111.09        32.42        70.16       110.79 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       28.08        22.55        45.83        81.24        10.29        85.32 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
        8.38        21.14        88.50        68.22        69.90        11.41 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       30.87         7.50        36.16         6.31        92.42        56.19 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 
       64.44        45.11       114.67        15.25        46.98        46.32 
TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO 
       82.29        61.38        13.32        24.00         6.31         9.34 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H 
      103.59        26.37         5.39        80.22        42.71        15.09 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN 
       41.10        17.72         8.84        20.48        13.94        52.01 
TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 
       47.87         1.55         6.97        23.11         4.01         2.89 
TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY 
        9.90        11.31        13.22        48.79        35.80        51.12 
TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I7 TCGA-DA-A1I8 
       10.03        39.19        13.68         9.99        36.69        25.15 
TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F8 
        4.93        22.36         6.64        19.36         7.00        14.83 
TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EE-A17X 
       13.15         0.20         0.00         0.00        13.22        11.57 
TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A184 
       10.55         6.31         8.12         1.12        12.20         5.13 
TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I 
        4.31        36.07         4.34         5.13         9.21         1.18 
TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G 
        7.99         9.90        37.97        11.15        38.63         8.55 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
        4.41         1.08        27.12         9.50        12.03         8.09 
TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 
        8.84         9.99         2.43         8.68         8.09        11.31 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC 
       49.22        23.90         9.67         8.94        39.39        34.29 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK 
       17.98        34.92        47.21        30.08        19.43        16.01 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR 
       35.54        28.31        33.83        30.84         5.42         1.15 
TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 
       13.02        34.98        36.33         8.84        98.27         2.70 
TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI 
        6.18        47.51        29.46        44.25         7.96        14.56 
TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP 
       63.42       111.78       111.91        56.02        25.08        26.99 
TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AB 
       21.60        29.65        27.16        23.05         5.56       122.73 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH 
       25.84         3.68        30.15        13.81        15.95        12.72 
TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA 
        3.22        22.92        21.60        21.60        16.14        22.22 
TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 
       27.35         0.46        13.94        31.40        18.61        12.95 
TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D 
       38.40         5.72        76.41        25.18         3.78         3.52 
TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L 
       11.90        11.11       114.15        34.88         4.21        13.45 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W 
       28.60        42.84        34.68         9.57        36.07        17.72 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG 
       78.44        11.80         1.87         1.51        13.08        12.62 
TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN 
       11.74         9.04         6.58        22.49         1.71        18.41 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 
       85.74         4.90        64.47         3.45        11.01        23.80 
TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC 
       14.24        15.52         7.33         7.30         3.39        20.38 
TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ 
        8.22        19.53        11.08         7.17        30.87        12.92 
TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS 
       12.89        47.38        52.08         8.65         8.81        49.15 
TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 
       40.64         8.68        27.39         0.82         5.23        53.85 
TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC 
        7.36        28.73        14.20        10.78         5.98         6.41 
TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
        2.27         0.20         0.13         0.16         0.43         9.90 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 
        7.23        12.85        24.85        31.33        84.72        16.24 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS 
       15.42        12.16        14.70         5.79 

  RNF133 MUTATED RNF133 WILD-TYPE 
            0.99             0.00 
  RNF133 MUTATED RNF133 WILD-TYPE 
          124.31           122.73 
  RNF133 MUTATED RNF133 WILD-TYPE 
          13.845           14.765 
[1] "1.0 - 124.3 (13.8)" "0.0 - 122.7 (14.8)"
[1] "hr=" "1.4"
D107V2, survival
                  sevent
clus2                0   1
  RNF133 MUTATED     5   3
  RNF133 WILD-TYPE 127 128
  RNF133 MUTATED RNF133 WILD-TYPE 
               8              255 
  RNF133 MUTATED RNF133 WILD-TYPE 
               3              128 
$`RNF133 MUTATED`
TCGA-DA-A1I5 TCGA-DA-A3F5 TCGA-EE-A182 TCGA-EE-A2MD TCGA-EE-A3AA TCGA-EE-A3JI 
      107.34       215.44        14.70        47.28       124.31       148.08 
TCGA-FW-A3R5 TCGA-GN-A266 
       22.92        10.13 

$`RNF133 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.57        16.67       112.04       112.57        71.80       133.25 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       28.08        31.59        90.90        95.74        43.43       103.10 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
       65.49        23.77       115.53       168.00        69.90        11.87 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       48.76       113.52        42.08        12.10       171.58        56.19 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 
       66.08        45.11       130.72        58.06        46.98        46.32 
TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO 
      166.52        86.93        60.23        24.53        13.87         9.34 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H 
      103.59        39.75        21.47       161.85        43.69        40.14 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN 
      131.90        18.38        10.03        51.68        15.06       135.75 
TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 
      137.92       166.19         7.43       125.19       151.53        54.67 
TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA 
        3.65         6.41        11.34         3.25         9.90        25.18 
TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 
       66.25        48.89        36.03       117.21        20.38       194.83 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB 
      176.55        35.93        61.18        53.92        65.92        23.44 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R 
       68.09        28.60        10.49        15.68        13.87        10.16 
TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y 
       45.11        35.01         3.55        52.01        29.82        27.22 
TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 
        8.65        94.98        33.73        26.89        68.15         4.96 
TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A 
      109.64       151.27        78.87       168.26        13.55        63.35 
TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H 
       80.61        47.84        13.97        39.62        72.07        32.19 
TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R 
        2.60        44.35        18.61        56.42        37.35        14.47 
TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 
       55.92        25.87       171.55        17.92        46.82       102.90 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD 
       24.43        39.29        58.75        47.54        67.43       314.56 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
      135.95       208.04        48.72        89.33        54.74        79.66 
TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS 
       75.48        90.97       101.95        13.91        14.30        55.59 
TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 
       44.88        94.82        21.67       129.27        28.83        19.76 
TCGA-EE-A2MC TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ 
       61.51       103.27       103.20        16.96       204.66        96.23 
TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ 
      144.76       203.05       167.90        47.54       248.65        43.23 
TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AC 
      103.56       136.47        41.59        53.26       122.73        25.84 
TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 
        3.68        54.51        13.81        23.47       138.81       172.18 
TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JD 
      127.20        36.95        64.08        34.32        53.19        27.35 
TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 
       33.40       101.79        31.40        35.44        13.94        50.76 
TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E 
        9.17        77.75        98.40        48.89        12.59        13.02 
TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M 
       26.37       268.93       152.35         6.44       131.51        61.05 
TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 
       44.05       162.08        50.89        37.25       148.18        79.99 
TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH 
       43.82        23.34        20.15        16.37        31.27        32.05 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A 
      247.04        80.32        46.98        33.21        92.98       174.21 
TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
        4.90       216.92        48.59       228.59       202.65        20.91 
TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD 
       28.08         7.79        27.72        48.85       357.37        53.52 
TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK 
       40.27        15.45         9.70        32.75        47.38        23.93 
TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT 
      101.26        74.73       133.55        11.41       148.80        53.16 
TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 
       26.56        49.48        27.09        27.02        77.82        66.67 
TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD 
       28.73       174.84        12.43        26.73        49.45        77.88 
TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
        0.20        47.54         0.16         2.40         9.90         7.23 
TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 
       14.04       120.46       117.93        84.72        64.44        62.79 
TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS 
       32.48        39.58         6.67 

  RNF133 MUTATED RNF133 WILD-TYPE 
           10.13             0.16 
  RNF133 MUTATED RNF133 WILD-TYPE 
          215.44           357.37 
  RNF133 MUTATED RNF133 WILD-TYPE 
           77.31            48.59 
[1] "10.1 - 215.4 (77.3)" "0.2 - 357.4 (48.6)" 
[1] "hr=" "1.6"
D107V3, continuous
                  vv
clus               DISTANT METASTASIS PRIMARY TUMOR
  RNF133 MUTATED                    2             0
  RNF133 WILD-TYPE                 33             4
                  vv
clus               REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  RNF133 MUTATED                                           1
  RNF133 WILD-TYPE                                        57
                  vv
clus               REGIONAL LYMPH NODE
  RNF133 MUTATED                     5
  RNF133 WILD-TYPE                 165
D107V4, multiclass
                                           clus
vv                                          RNF133 MUTATED RNF133 WILD-TYPE
  DISTANT METASTASIS                                     2               33
  PRIMARY TUMOR                                          0                4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE              1               57
  REGIONAL LYMPH NODE                                    5              165
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  RNF133 MUTATED             0       0       1        0        0        1
  RNF133 WILD-TYPE          10       6      21       10       24       16
                  vv
clus               STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  RNF133 MUTATED           0         0         0         2          0
  RNF133 WILD-TYPE        10        14         9        29         13
                  vv
clus               STAGE IIIB STAGE IIIC STAGE IV
  RNF133 MUTATED            0          2        1
  RNF133 WILD-TYPE         22         42       11
D107V5, multiclass
             clus
vv            RNF133 MUTATED RNF133 WILD-TYPE
  I OR II NOS              0               10
  STAGE 0                  0                6
  STAGE I                  1               21
  STAGE IA                 0               10
  STAGE IB                 0               24
  STAGE II                 1               16
  STAGE IIA                0               10
  STAGE IIB                0               14
  STAGE IIC                0                9
  STAGE III                2               29
  STAGE IIIA               0               13
  STAGE IIIB               0               22
  STAGE IIIC               2               42
  STAGE IV                 1               11
[1] 14  2
[1] 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
  RNF133 MUTATED       3  1  1  1
  RNF133 WILD-TYPE    48 57 52 54
D107V6, multiclass
       clus
vv      RNF133 MUTATED RNF133 WILD-TYPE
  T0+T1              3               48
  T2                 1               57
  T3                 1               52
  T4                 1               54
[1] 4 2
[1] TRUE
[1] "dimension 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
  RNF133 MUTATED     3   2   1   1
  RNF133 WILD-TYPE 135  46  31  32
D107V7, multiclass
    clus
vv   RNF133 MUTATED RNF133 WILD-TYPE
  N0              3              135
  N1              2               46
  N2              1               31
  N3              1               32
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                M0  M1 M1A M1B M1C
  RNF133 MUTATED     6   0   0   0   1
  RNF133 WILD-TYPE 234   4   2   2   4
D107V8, multiclass
     clus
vv    RNF133 MUTATED RNF133 WILD-TYPE
  M0               6              234
  M1               0                4
  M1A              0                2
  M1B              0                2
  M1C              1                4
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D107V9, binary
                  cls
clus                 0   1
  RNF133 MUTATED     2   2
  RNF133 WILD-TYPE 100  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RNF133 MUTATED      2    2
  RNF133 WILD-TYPE  100   65
     clus
vv    RNF133 MUTATED RNF133 WILD-TYPE
  NO               2              100
  YES              2               65
[1] 2 2
[1] FALSE
D107V10, binary
                  cls
clus                 0   1
  RNF133 MUTATED     2   6
  RNF133 WILD-TYPE  31 229
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RNF133 MUTATED      2    6
  RNF133 WILD-TYPE   31  229
     clus
vv    RNF133 MUTATED RNF133 WILD-TYPE
  NO               2               31
  YES              6              229
[1] 2 2
[1] FALSE
D107V11, continuous
D107V12, binary
                  cls
clus                 0   1
  RNF133 MUTATED     2   6
  RNF133 WILD-TYPE 101 159
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RNF133 MUTATED      2    6
  RNF133 WILD-TYPE  101  159
        clus
vv       RNF133 MUTATED RNF133 WILD-TYPE
  FEMALE              2              101
  MALE                6              159
[1] 2 2
[1] FALSE
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RNF133 MUTATED       0                         0     8
  RNF133 WILD-TYPE     3                         1   256
D107V13, multiclass
                           clus
vv                          RNF133 MUTATED RNF133 WILD-TYPE
  ASIAN                                  0                3
  BLACK OR AFRICAN AMERICAN              0                1
  WHITE                                  8              256
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D107V14, binary
                  cls
clus                 0   1
  RNF133 MUTATED     0   8
  RNF133 WILD-TYPE   3 253
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RNF133 MUTATED      0    8
  RNF133 WILD-TYPE    3  253
                        clus
vv                       RNF133 MUTATED RNF133 WILD-TYPE
  HISPANIC OR LATINO                  0                3
  NOT HISPANIC OR LATINO              8              253
[1] 2 2
[1] FALSE

Clustering(108) Variable = GTPBP4 MUTATION ANALYSIS
D108V1, survival
                  sevent
clus2                0   1
  GTPBP4 MUTATED     5   3
  GTPBP4 WILD-TYPE 123 127
  GTPBP4 MUTATED GTPBP4 WILD-TYPE 
               8              250 
  GTPBP4 MUTATED GTPBP4 WILD-TYPE 
               3              127 
$`GTPBP4 MUTATED`
TCGA-D3-A2JA TCGA-D3-A2JF TCGA-EE-A29A TCGA-EE-A2A1 TCGA-EE-A3AA TCGA-EE-A3AG 
       88.50        30.87         7.99        49.22       124.31        15.95 
TCGA-EE-A3JA TCGA-FW-A3R5 
       22.22         0.99 

$`GTPBP4 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.47         8.52       111.09        32.42        70.16       110.79 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       28.08        22.55        45.83        81.24        10.29        85.32 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JG 
        8.38        21.14        68.22        69.90        11.41         7.50 
TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP 
       36.16         6.31        92.42        56.19        64.44        45.11 
TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC 
      114.67        15.25        46.98        46.32        82.29        61.38 
TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU 
       13.32        24.00         6.31         9.34       103.59        26.37 
TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K 
        5.39        80.22        42.71        15.09        41.10        17.72 
TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR 
        8.84        20.48        13.94        52.01        47.87         1.55 
TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA 
        6.97        23.11         4.01         2.89         9.90        11.31 
TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 
       13.22        48.79        35.80        51.12        10.03        39.19 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA 
       13.68         9.99        44.52        36.69        25.15         4.93 
TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 
       22.36         6.64        19.36         7.00        17.56        14.83 
TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EE-A17X 
       13.15         0.20         0.00         0.00        13.22        11.57 
TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 
       10.55         6.31         8.12         1.12         1.35        12.20 
TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H 
        5.13         4.31        36.07         4.34         5.13         9.21 
TCGA-EE-A20I TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G 
        1.18         9.90        37.97        11.15        38.63         8.55 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
        4.41         1.08        27.12         9.50        12.03         8.09 
TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 
        8.84         9.99         2.43         8.68         8.09        11.31 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD 
       23.90         9.67         8.94        39.39        34.29        17.98 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
       34.92        47.21        30.08        19.43        16.01        35.54 
TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS 
       28.31        33.83        30.84         5.42         1.15        13.02 
TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 
       34.98        36.33         8.84        98.27         2.70         6.18 
TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI 
       47.51         9.53        29.46        44.25         7.96        14.56 
TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP 
       63.42       111.78       111.91        56.02        25.08        26.99 
TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AB 
       21.60        29.65        27.16        23.05         5.56       122.73 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AH TCGA-EE-A3J3 
       25.84         3.68        30.15        13.81        12.72         3.22 
TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JD TCGA-EE-A3JE 
       22.92        21.60        21.60        16.14        27.35         0.46 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 
       13.94        33.60        31.40        18.61        12.95        38.40 
TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E 
        5.72        76.41        25.18         3.78         3.52        11.90 
TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M 
       11.11       114.15        34.88         4.21        13.45        28.60 
TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 
       42.84        34.68         9.57        36.07        17.72        78.44 
TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH 
       11.80         1.87         1.51        13.08        12.62        11.74 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A 
        9.04         6.58        22.49         1.71        18.41        85.74 
TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
        4.90        64.47         3.45        11.01        23.80        14.24 
TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD 
       15.52         7.33         7.30         3.39        20.38         8.22 
TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK 
       19.53        11.08         7.17        30.87        12.92        12.89 
TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT 
       47.38        52.08         8.65         8.81        49.15        40.64 
TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 
        8.68        27.39         0.82         5.23        53.85         7.36 
TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD 
       28.73        14.20        10.78         5.98         6.41         2.27 
TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
        0.20         0.13         0.16         0.43         9.90         7.23 
TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 
       12.85        24.85        31.33        84.72        10.13        16.24 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS 
       15.42        12.16        14.70         5.79 

  GTPBP4 MUTATED GTPBP4 WILD-TYPE 
            0.99             0.00 
  GTPBP4 MUTATED GTPBP4 WILD-TYPE 
          124.31           122.73 
  GTPBP4 MUTATED GTPBP4 WILD-TYPE 
          26.545           14.400 
[1] "1.0 - 124.3 (26.5)" "0.0 - 122.7 (14.4)"
[1] "hr=" "1.9"
D108V2, survival
                  sevent
clus2                0   1
  GTPBP4 MUTATED     5   3
  GTPBP4 WILD-TYPE 127 128
  GTPBP4 MUTATED GTPBP4 WILD-TYPE 
               8              255 
  GTPBP4 MUTATED GTPBP4 WILD-TYPE 
               3              128 
$`GTPBP4 MUTATED`
TCGA-D3-A2JA TCGA-D3-A2JF TCGA-EE-A29A TCGA-EE-A2A1 TCGA-EE-A3AA TCGA-EE-A3AG 
      115.53        48.76        63.35       102.90       124.31        23.47 
TCGA-EE-A3JA TCGA-FW-A3R5 
       53.19        22.92 

$`GTPBP4 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.57        16.67       112.04       112.57        71.80       133.25 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       28.08        31.59        90.90        95.74        43.43       103.10 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JG 
       65.49        23.77       168.00        69.90        11.87       113.52 
TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP 
       42.08        12.10       171.58        56.19        66.08        45.11 
TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC 
      130.72        58.06        46.98        46.32       166.52        86.93 
TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU 
       60.23        24.53        13.87         9.34       103.59        39.75 
TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K 
       21.47       161.85        43.69        40.14       131.90        18.38 
TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR 
       10.03        51.68        15.06       135.75       137.92       166.19 
TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX 
        7.43       125.19       151.53        54.67         3.65         6.41 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1HV 
       11.34         3.25         9.90        25.18        66.25        48.89 
TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 
       36.03       117.21        20.38       194.83       176.55        35.93 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC 
      107.34        61.18        53.92        65.92        23.44        68.09 
TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R 
       28.60        10.49       215.44        15.68        13.87        10.16 
TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y 
       45.11        35.01         3.55        52.01        29.82        27.22 
TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 
        8.65        94.98        33.73        14.70        26.89        68.15 
TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I 
        4.96       109.64       151.27        78.87       168.26        13.55 
TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H 
       80.61        47.84        13.97        39.62        72.07        32.19 
TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R 
        2.60        44.35        18.61        56.42        37.35        14.47 
TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A2 
       55.92        25.87       171.55        17.92        46.82        24.43 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE 
       39.29        58.75        47.54        67.43       314.56       135.95 
TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM 
      208.04        48.72        89.33        54.74        79.66        75.48 
TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT 
       90.97       101.95        13.91        14.30        55.59        44.88 
TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC 
       94.82        21.67       129.27        28.83        19.76        61.51 
TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ 
       47.28       103.27       103.20        16.96       204.66        96.23 
TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ 
      144.76       203.05       167.90        47.54       248.65        43.23 
TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AC 
      103.56       136.47        41.59        53.26       122.73        25.84 
TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 
        3.68        54.51        13.81       138.81       172.18       127.20 
TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH 
       36.95        64.08        34.32        27.35        33.40       101.79 
TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 
      148.08        31.40        35.44        13.94        50.76         9.17 
TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F 
       77.75        98.40        48.89        12.59        13.02        26.37 
TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N 
      268.93       152.35         6.44       131.51        61.05        44.05 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
      162.08        50.89        37.25       148.18        79.99        43.82 
TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES 
       23.34        20.15        16.37        31.27        32.05       247.04 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
       80.32        46.98        33.21        92.98       174.21         4.90 
TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 
      216.92        48.59       228.59       202.65        20.91        28.08 
TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE 
        7.79        27.72        48.85       357.37        53.52        40.27 
TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM 
       15.45         9.70        32.75        47.38        23.93       101.26 
TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU 
       74.73       133.55        11.41       148.80        53.16        26.56 
TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 
       49.48        27.09        27.02        77.82        66.67        28.73 
TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 
      174.84        12.43        26.73        49.45        77.88         0.20 
TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 
       47.54         0.16         2.40         9.90         7.23        14.04 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 
      120.46       117.93        84.72        10.13        64.44        62.79 
TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS 
       32.48        39.58         6.67 

  GTPBP4 MUTATED GTPBP4 WILD-TYPE 
           22.92             0.16 
  GTPBP4 MUTATED GTPBP4 WILD-TYPE 
          124.31           357.37 
  GTPBP4 MUTATED GTPBP4 WILD-TYPE 
           58.27            47.54 
[1] "22.9 - 124.3 (58.3)" "0.2 - 357.4 (47.5)" 
[1] "hr=" "1.3"
D108V3, continuous
                  vv
clus               DISTANT METASTASIS PRIMARY TUMOR
  GTPBP4 MUTATED                    2             0
  GTPBP4 WILD-TYPE                 33             4
                  vv
clus               REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  GTPBP4 MUTATED                                           2
  GTPBP4 WILD-TYPE                                        56
                  vv
clus               REGIONAL LYMPH NODE
  GTPBP4 MUTATED                     4
  GTPBP4 WILD-TYPE                 166
D108V4, multiclass
                                           clus
vv                                          GTPBP4 MUTATED GTPBP4 WILD-TYPE
  DISTANT METASTASIS                                     2               33
  PRIMARY TUMOR                                          0                4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE              2               56
  REGIONAL LYMPH NODE                                    4              166
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  GTPBP4 MUTATED             0       0       0        1        2        0
  GTPBP4 WILD-TYPE          10       6      22        9       22       17
                  vv
clus               STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  GTPBP4 MUTATED           0         0         0         3          2
  GTPBP4 WILD-TYPE        10        14         9        28         11
                  vv
clus               STAGE IIIB STAGE IIIC STAGE IV
  GTPBP4 MUTATED            0          0        0
  GTPBP4 WILD-TYPE         22         44       12
D108V5, multiclass
             clus
vv            GTPBP4 MUTATED GTPBP4 WILD-TYPE
  I OR II NOS              0               10
  STAGE 0                  0                6
  STAGE I                  0               22
  STAGE IA                 1                9
  STAGE IB                 2               22
  STAGE II                 0               17
  STAGE IIA                0               10
  STAGE IIB                0               14
  STAGE IIC                0                9
  STAGE III                3               28
  STAGE IIIA               2               11
  STAGE IIIB               0               22
  STAGE IIIC               0               44
  STAGE IV                 0               12
[1] 14  2
[1] 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
  GTPBP4 MUTATED       3  3  1  0
  GTPBP4 WILD-TYPE    48 55 52 55
D108V6, multiclass
       clus
vv      GTPBP4 MUTATED GTPBP4 WILD-TYPE
  T0+T1              3               48
  T2                 3               55
  T3                 1               52
  T4                 0               55
[1] 4 2
[1] TRUE
[1] "dimension 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
  GTPBP4 MUTATED     3   3   2   0
  GTPBP4 WILD-TYPE 135  45  30  33
D108V7, multiclass
    clus
vv   GTPBP4 MUTATED GTPBP4 WILD-TYPE
  N0              3              135
  N1              3               45
  N2              2               30
  N3              0               33
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                M0  M1 M1A M1B M1C
  GTPBP4 MUTATED     8   0   0   0   0
  GTPBP4 WILD-TYPE 232   4   2   2   5
D108V8, multiclass
     clus
vv    GTPBP4 MUTATED GTPBP4 WILD-TYPE
  M0               8              232
  M1               0                4
  M1A              0                2
  M1B              0                2
  M1C              0                5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D108V9, binary
                  cls
clus                0  1
  GTPBP4 MUTATED    5  0
  GTPBP4 WILD-TYPE 97 67
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GTPBP4 MUTATED      5    0
  GTPBP4 WILD-TYPE   97   67
     clus
vv    GTPBP4 MUTATED GTPBP4 WILD-TYPE
  NO               5               97
  YES              0               67
[1] 2 2
[1] FALSE
D108V10, binary
                  cls
clus                 0   1
  GTPBP4 MUTATED     2   6
  GTPBP4 WILD-TYPE  31 229
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GTPBP4 MUTATED      2    6
  GTPBP4 WILD-TYPE   31  229
     clus
vv    GTPBP4 MUTATED GTPBP4 WILD-TYPE
  NO               2               31
  YES              6              229
[1] 2 2
[1] FALSE
D108V11, continuous
D108V12, binary
                  cls
clus                 0   1
  GTPBP4 MUTATED     0   8
  GTPBP4 WILD-TYPE 103 157
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GTPBP4 MUTATED      0    8
  GTPBP4 WILD-TYPE  103  157
        clus
vv       GTPBP4 MUTATED GTPBP4 WILD-TYPE
  FEMALE              0              103
  MALE                8              157
[1] 2 2
[1] FALSE
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  GTPBP4 MUTATED       0                         0     8
  GTPBP4 WILD-TYPE     3                         1   256
D108V13, multiclass
                           clus
vv                          GTPBP4 MUTATED GTPBP4 WILD-TYPE
  ASIAN                                  0                3
  BLACK OR AFRICAN AMERICAN              0                1
  WHITE                                  8              256
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D108V14, binary
                  cls
clus                 0   1
  GTPBP4 MUTATED     0   7
  GTPBP4 WILD-TYPE   3 254
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GTPBP4 MUTATED      0    7
  GTPBP4 WILD-TYPE    3  254
                        clus
vv                       GTPBP4 MUTATED GTPBP4 WILD-TYPE
  HISPANIC OR LATINO                  0                3
  NOT HISPANIC OR LATINO              7              254
[1] 2 2
[1] FALSE

Clustering(109) Variable = ACSBG1 MUTATION ANALYSIS
D109V1, survival
                  sevent
clus2                0   1
  ACSBG1 MUTATED     7   3
  ACSBG1 WILD-TYPE 121 127
  ACSBG1 MUTATED ACSBG1 WILD-TYPE 
              10              248 
  ACSBG1 MUTATED ACSBG1 WILD-TYPE 
               3              127 
$`ACSBG1 MUTATED`
TCGA-DA-A1HY TCGA-EB-A5SG TCGA-EE-A29M TCGA-EE-A2A0 TCGA-EE-A2GL TCGA-EE-A2GO 
       51.12         0.00        27.12        11.31        35.54        30.84 
TCGA-EE-A2MG TCGA-EE-A2MR TCGA-EE-A3AG TCGA-FW-A3R5 
       44.25        29.65        15.95         0.99 

$`ACSBG1 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.47         8.52       111.09        32.42        70.16       110.79 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       28.08        22.55        45.83        81.24        10.29        85.32 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
        8.38        21.14        88.50        68.22        69.90        11.41 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       30.87         7.50        36.16         6.31        92.42        56.19 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 
       64.44        45.11       114.67        15.25        46.98        46.32 
TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO 
       82.29        61.38        13.32        24.00         6.31         9.34 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H 
      103.59        26.37         5.39        80.22        42.71        15.09 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN 
       41.10        17.72         8.84        20.48        13.94        52.01 
TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 
       47.87         1.55         6.97        23.11         4.01         2.89 
TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1I0 
        9.90        11.31        13.22        48.79        35.80        10.03 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 
       39.19        13.68         9.99        44.52        36.69        25.15 
TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 
        4.93        22.36         6.64        19.36         7.00        17.56 
TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EE-A17X 
       14.83        13.15         0.20         0.00        13.22        11.57 
TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 
       10.55         6.31         8.12         1.12         1.35        12.20 
TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H 
        5.13         4.31        36.07         4.34         5.13         9.21 
TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E 
        1.18         7.99         9.90        37.97        11.15        38.63 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
        8.55         4.41         1.08         9.50        12.03         8.09 
TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A1 
        8.84         9.99         2.43         8.68         8.09        49.22 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD 
       23.90         9.67         8.94        39.39        34.29        17.98 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GM 
       34.92        47.21        30.08        19.43        16.01        28.31 
TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU 
       33.83         5.42         1.15        13.02        34.98        36.33 
TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD 
        8.84        98.27         2.70         6.18        47.51         9.53 
TCGA-EE-A2ME TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML 
       29.46         7.96        14.56        63.42       111.78       111.91 
TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MS TCGA-EE-A2MT 
       56.02        25.08        26.99        21.60        27.16        23.05 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE 
        5.56       124.31       122.73        25.84         3.68        30.15 
TCGA-EE-A3AF TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 
       13.81        12.72         3.22        22.92        21.60        21.60 
TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI 
       16.14        22.22        27.35         0.46        13.94        33.60 
TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A 
       31.40        18.61        12.95        38.40         5.72        76.41 
TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G 
       25.18         3.78         3.52        11.90        11.11       114.15 
TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P 
       34.88         4.21        13.45        28.60        42.84        34.68 
TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
        9.57        36.07        17.72        78.44        11.80         1.87 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET 
        1.51        13.08        12.62        11.74         9.04         6.58 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW 
       22.49         1.71        18.41        85.74         4.90        64.47 
TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 
        3.45        11.01        23.80        14.24        15.52         7.33 
TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF 
        7.30         3.39        20.38         8.22        19.53        11.08 
TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP 
        7.17        30.87        12.92        12.89        47.38        52.08 
TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW 
        8.65         8.81        49.15        40.64         8.68        27.39 
TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 
        0.82         5.23        53.85         7.36        28.73        14.20 
TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU 
       10.78         5.98         6.41         2.27         0.20         0.13 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 
        0.16         0.43         9.90         7.23        12.85        24.85 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
       31.33        84.72        10.13        16.24        15.42        12.16 
TCGA-GN-A26D TCGA-QB-A6FS 
       14.70         5.79 

  ACSBG1 MUTATED ACSBG1 WILD-TYPE 
               0                0 
  ACSBG1 MUTATED ACSBG1 WILD-TYPE 
           51.12           124.31 
  ACSBG1 MUTATED ACSBG1 WILD-TYPE 
          28.385           14.400 
[1] "0.0 - 51.1 (28.4)"  "0.0 - 124.3 (14.4)"
[1] "hr=" "1.9"
D109V2, survival
                  sevent
clus2                0   1
  ACSBG1 MUTATED     7   3
  ACSBG1 WILD-TYPE 125 128
  ACSBG1 MUTATED ACSBG1 WILD-TYPE 
              10              253 
  ACSBG1 MUTATED ACSBG1 WILD-TYPE 
               3              128 
$`ACSBG1 MUTATED`
TCGA-DA-A1HY TCGA-EB-A5SG TCGA-EE-A29M TCGA-EE-A2A0 TCGA-EE-A2GL TCGA-EE-A2GO 
      117.21        45.11        44.35        46.82        79.66       101.95 
TCGA-EE-A2MG TCGA-EE-A2MR TCGA-EE-A3AG TCGA-FW-A3R5 
      103.20       103.56        23.47        22.92 

$`ACSBG1 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.57        16.67       112.04       112.57        71.80       133.25 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       28.08        31.59        90.90        95.74        43.43       103.10 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
       65.49        23.77       115.53       168.00        69.90        11.87 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       48.76       113.52        42.08        12.10       171.58        56.19 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 
       66.08        45.11       130.72        58.06        46.98        46.32 
TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO 
      166.52        86.93        60.23        24.53        13.87         9.34 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H 
      103.59        39.75        21.47       161.85        43.69        40.14 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN 
      131.90        18.38        10.03        51.68        15.06       135.75 
TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 
      137.92       166.19         7.43       125.19       151.53        54.67 
TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA 
        3.65         6.41        11.34         3.25         9.90        25.18 
TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 
       66.25        48.89        36.03        20.38       194.83       176.55 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB 
       35.93       107.34        61.18        53.92        65.92        23.44 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q 
       68.09        28.60        10.49       215.44        15.68        13.87 
TCGA-EB-A44R TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y 
       10.16        35.01         3.55        52.01        29.82        27.22 
TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 
        8.65        94.98        33.73        14.70        26.89        68.15 
TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I 
        4.96       109.64       151.27        78.87       168.26        13.55 
TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G 
       63.35        80.61        47.84        13.97        39.62        72.07 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R 
       32.19         2.60        18.61        56.42        37.35        14.47 
TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A1 TCGA-EE-A2A2 
       55.92        25.87       171.55        17.92       102.90        24.43 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE 
       39.29        58.75        47.54        67.43       314.56       135.95 
TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GM TCGA-EE-A2GN 
      208.04        48.72        89.33        54.74        75.48        90.97 
TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 
       13.91        14.30        55.59        44.88        94.82        21.67 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME 
      129.27        28.83        19.76        61.51        47.28       103.27 
TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM 
       16.96       204.66        96.23       144.76       203.05       167.90 
TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU 
       47.54       248.65        43.23       136.47        41.59        53.26 
TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF 
      124.31       122.73        25.84         3.68        54.51        13.81 
TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 
      138.81       172.18       127.20        36.95        64.08        34.32 
TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 
       53.19        27.35        33.40       101.79       148.08        31.40 
TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B 
       35.44        13.94        50.76         9.17        77.75        98.40 
TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H 
       48.89        12.59        13.02        26.37       268.93       152.35 
TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q 
        6.44       131.51        61.05        44.05       162.08        50.89 
TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE 
       37.25       148.18        79.99        43.82        23.34        20.15 
TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV 
       16.37        31.27        32.05       247.04        80.32        46.98 
TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX 
       33.21        92.98       174.21         4.90       216.92        48.59 
TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA 
      228.59       202.65        20.91        28.08         7.79        27.72 
TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG 
       48.85       357.37        53.52        40.27        15.45         9.70 
TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ 
       32.75        47.38        23.93       101.26        74.73       133.55 
TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY 
       11.41       148.80        53.16        26.56        49.48        27.09 
TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 
       27.02        77.82        66.67        28.73       174.84        12.43 
TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV 
       26.73        49.45        77.88         0.20        47.54         0.16 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 
        2.40         9.90         7.23        14.04       120.46       117.93 
TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D 
       84.72        10.13        64.44        62.79        32.48        39.58 
TCGA-QB-A6FS 
        6.67 

  ACSBG1 MUTATED ACSBG1 WILD-TYPE 
           22.92             0.16 
  ACSBG1 MUTATED ACSBG1 WILD-TYPE 
          117.21           357.37 
  ACSBG1 MUTATED ACSBG1 WILD-TYPE 
           63.24            48.59 
[1] "22.9 - 117.2 (63.2)" "0.2 - 357.4 (48.6)" 
[1] "hr=" "1.7"
D109V3, continuous
                  vv
clus               DISTANT METASTASIS PRIMARY TUMOR
  ACSBG1 MUTATED                    0             0
  ACSBG1 WILD-TYPE                 35             4
                  vv
clus               REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  ACSBG1 MUTATED                                           2
  ACSBG1 WILD-TYPE                                        56
                  vv
clus               REGIONAL LYMPH NODE
  ACSBG1 MUTATED                     8
  ACSBG1 WILD-TYPE                 162
D109V4, multiclass
                                           clus
vv                                          ACSBG1 MUTATED ACSBG1 WILD-TYPE
  DISTANT METASTASIS                                     0               35
  PRIMARY TUMOR                                          0                4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE              2               56
  REGIONAL LYMPH NODE                                    8              162
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  ACSBG1 MUTATED             0       0       2        0        1        1
  ACSBG1 WILD-TYPE          10       6      20       10       23       16
                  vv
clus               STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  ACSBG1 MUTATED           2         0         0         2          0
  ACSBG1 WILD-TYPE         8        14         9        29         13
                  vv
clus               STAGE IIIB STAGE IIIC STAGE IV
  ACSBG1 MUTATED            0          1        0
  ACSBG1 WILD-TYPE         22         43       12
D109V5, multiclass
             clus
vv            ACSBG1 MUTATED ACSBG1 WILD-TYPE
  I OR II NOS              0               10
  STAGE 0                  0                6
  STAGE I                  2               20
  STAGE IA                 0               10
  STAGE IB                 1               23
  STAGE II                 1               16
  STAGE IIA                2                8
  STAGE IIB                0               14
  STAGE IIC                0                9
  STAGE III                2               29
  STAGE IIIA               0               13
  STAGE IIIB               0               22
  STAGE IIIC               1               43
  STAGE IV                 0               12
[1] 14  2
[1] 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
  ACSBG1 MUTATED       1  4  3  0
  ACSBG1 WILD-TYPE    50 54 50 55
D109V6, multiclass
       clus
vv      ACSBG1 MUTATED ACSBG1 WILD-TYPE
  T0+T1              1               50
  T2                 4               54
  T3                 3               50
  T4                 0               55
[1] 4 2
[1] TRUE
[1] "dimension 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
  ACSBG1 MUTATED     6   0   2   1
  ACSBG1 WILD-TYPE 132  48  30  32
D109V7, multiclass
    clus
vv   ACSBG1 MUTATED ACSBG1 WILD-TYPE
  N0              6              132
  N1              0               48
  N2              2               30
  N3              1               32
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                M0  M1 M1A M1B M1C
  ACSBG1 MUTATED     9   0   0   0   0
  ACSBG1 WILD-TYPE 231   4   2   2   5
D109V8, multiclass
     clus
vv    ACSBG1 MUTATED ACSBG1 WILD-TYPE
  M0               9              231
  M1               0                4
  M1A              0                2
  M1B              0                2
  M1C              0                5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D109V9, binary
                  cls
clus                0  1
  ACSBG1 MUTATED    6  1
  ACSBG1 WILD-TYPE 96 66
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ACSBG1 MUTATED      6    1
  ACSBG1 WILD-TYPE   96   66
     clus
vv    ACSBG1 MUTATED ACSBG1 WILD-TYPE
  NO               6               96
  YES              1               66
[1] 2 2
[1] FALSE
D109V10, binary
                  cls
clus                 0   1
  ACSBG1 MUTATED     1   9
  ACSBG1 WILD-TYPE  32 226
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ACSBG1 MUTATED      1    9
  ACSBG1 WILD-TYPE   32  226
     clus
vv    ACSBG1 MUTATED ACSBG1 WILD-TYPE
  NO               1               32
  YES              9              226
[1] 2 2
[1] FALSE
D109V11, continuous
D109V12, binary
                  cls
clus                 0   1
  ACSBG1 MUTATED     5   5
  ACSBG1 WILD-TYPE  98 160
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ACSBG1 MUTATED      5    5
  ACSBG1 WILD-TYPE   98  160
        clus
vv       ACSBG1 MUTATED ACSBG1 WILD-TYPE
  FEMALE              5               98
  MALE                5              160
[1] 2 2
[1] FALSE
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ACSBG1 MUTATED       0                         0    10
  ACSBG1 WILD-TYPE     3                         1   254
D109V13, multiclass
                           clus
vv                          ACSBG1 MUTATED ACSBG1 WILD-TYPE
  ASIAN                                  0                3
  BLACK OR AFRICAN AMERICAN              0                1
  WHITE                                 10              254
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D109V14, binary
                  cls
clus                 0   1
  ACSBG1 MUTATED     0  10
  ACSBG1 WILD-TYPE   3 251
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ACSBG1 MUTATED      0   10
  ACSBG1 WILD-TYPE    3  251
                        clus
vv                       ACSBG1 MUTATED ACSBG1 WILD-TYPE
  HISPANIC OR LATINO                  0                3
  NOT HISPANIC OR LATINO             10              251
[1] 2 2
[1] FALSE

Clustering(110) Variable = TPTE MUTATION ANALYSIS
D110V1, survival
                sevent
clus2              0   1
  TPTE MUTATED    26  31
  TPTE WILD-TYPE 102  99
  TPTE MUTATED TPTE WILD-TYPE 
            57            201 
  TPTE MUTATED TPTE WILD-TYPE 
            31             99 
$`TPTE MUTATED`
TCGA-D3-A1Q3 TCGA-D3-A1Q5 TCGA-D3-A2JN TCGA-D3-A3C7 TCGA-D3-A3MV TCGA-D3-A51T 
        8.52        32.42        56.19        46.98         5.39        13.94 
TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY 
       52.01        47.87        13.22        48.79        35.80        51.12 
TCGA-DA-A1I1 TCGA-EE-A182 TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29L 
       39.19         1.35         7.99        37.97        11.15         1.08 
TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A2A0 TCGA-EE-A2GJ TCGA-EE-A2GO TCGA-EE-A2GP 
        9.50        12.03        11.31        19.43        30.84         5.42 
TCGA-EE-A2GR TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2MG 
        1.15         8.84        98.27        47.51         9.53        44.25 
TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AE 
       63.42       111.91        26.99        27.16        23.05        30.15 
TCGA-EE-A3AF TCGA-EE-A3J5 TCGA-EE-A3JA TCGA-ER-A193 TCGA-ER-A199 TCGA-ER-A2NC 
       13.81        21.60        22.22        31.40         5.72        11.80 
TCGA-ER-A3PL TCGA-FS-A1Z3 TCGA-FS-A1ZA TCGA-FS-A1ZC TCGA-FS-A1ZP TCGA-FS-A1ZW 
        1.71        14.24         7.30        20.38        52.08        27.39 
TCGA-FS-A1ZZ TCGA-FS-A4F5 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FW-A3R5 TCGA-FW-A3TU 
        5.23        28.73         5.98         6.41         0.99         0.13 
TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A266 
       12.85        24.85        10.13 

$`TPTE WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 
       16.47       111.09        70.16       110.79        28.08        22.55 
TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 
       45.83        81.24        10.29        85.32         8.38        21.14 
TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JG 
       88.50        68.22        69.90        11.41        30.87         7.50 
TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ 
       36.16         6.31        92.42        64.44        45.11       114.67 
TCGA-D3-A3C6 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF 
       15.25        46.32        82.29        61.38        13.32        24.00 
TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F 
        6.31         9.34       103.59        26.37        80.22        42.71 
TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A5GR 
       15.09        41.10        17.72         8.84        20.48         1.55 
TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA 
        6.97        23.11         4.01         2.89         9.90        11.31 
TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 
       10.03        13.68         9.99        44.52        36.69        25.15 
TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 
        4.93        22.36         6.64        19.36         7.00        17.56 
TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN 
       14.83        13.15         0.20         0.00         0.00        13.22 
TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A183 
       11.57        10.55         6.31         8.12         1.12        12.20 
TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H 
        5.13         4.31        36.07         4.34         5.13         9.21 
TCGA-EE-A20I TCGA-EE-A29B TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M 
        1.18         9.90        38.63         8.55         4.41        27.12 
TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X 
        8.09         8.84         9.99         2.43         8.68         8.09 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC 
       49.22        23.90         9.67         8.94        39.39        34.29 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GK TCGA-EE-A2GL 
       17.98        34.92        47.21        30.08        16.01        35.54 
TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M7 
       28.31        33.83        13.02        34.98        36.33         2.70 
TCGA-EE-A2M8 TCGA-EE-A2ME TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2MM 
        6.18        29.46         7.96        14.56       111.78        56.02 
TCGA-EE-A2MN TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB 
       25.08        21.60        29.65         5.56       124.31       122.73 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 
       25.84         3.68        15.95        12.72         3.22        22.92 
TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI 
       21.60        16.14        27.35         0.46        13.94        33.60 
TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C 
       18.61        12.95        38.40        76.41        25.18         3.78 
TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J 
        3.52        11.90        11.11       114.15        34.88         4.21 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S 
       13.45        28.60        42.84        34.68         9.57        36.07 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG 
       17.72        78.44         1.87         1.51        13.08        12.62 
TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-FR-A3YN TCGA-FR-A44A 
       11.74         9.04         6.58        22.49        18.41        85.74 
TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z4 
        4.90        64.47         3.45        11.01        23.80        15.52 
TCGA-FS-A1Z7 TCGA-FS-A1ZB TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG 
        7.33         3.39         8.22        19.53        11.08         7.17 
TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZR 
       30.87        12.92        12.89        47.38         8.65         8.81 
TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZY TCGA-FS-A4F0 TCGA-FS-A4F4 
       49.15        40.64         8.68         0.82        53.85         7.36 
TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TV TCGA-FW-A5DY 
       14.20        10.78         2.27         0.20         0.16         0.43 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 
        9.90         7.23        31.33        84.72        16.24        15.42 
TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS 
       12.16        14.70         5.79 

  TPTE MUTATED TPTE WILD-TYPE 
          0.13           0.00 
  TPTE MUTATED TPTE WILD-TYPE 
        111.91         124.31 
  TPTE MUTATED TPTE WILD-TYPE 
         19.43          14.70 
[1] "0.1 - 111.9 (19.4)" "0.0 - 124.3 (14.7)"
[1] "hr=" "1.1"
D110V2, survival
                sevent
clus2              0   1
  TPTE MUTATED    27  31
  TPTE WILD-TYPE 105 100
  TPTE MUTATED TPTE WILD-TYPE 
            58            205 
  TPTE MUTATED TPTE WILD-TYPE 
            31            100 
$`TPTE MUTATED`
TCGA-D3-A1Q3 TCGA-D3-A1Q5 TCGA-D3-A2JN TCGA-D3-A3C7 TCGA-D3-A3MV TCGA-D3-A51T 
       16.67       112.57        56.19        46.98        21.47        15.06 
TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D9-A1JW TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1HW 
      135.75       137.92         3.65        66.25        48.89        36.03 
TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-EE-A182 TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29D 
      117.21       194.83        14.70        63.35        47.84        13.97 
TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A2A0 TCGA-EE-A2GJ TCGA-EE-A2GO 
        2.60        18.61        56.42        46.82        89.33       101.95 
TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2MC TCGA-EE-A2MD 
       13.91        14.30        21.67       129.27        61.51        47.28 
TCGA-EE-A2MG TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MT 
      103.20        96.23       203.05       248.65       136.47        41.59 
TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J5 TCGA-EE-A3JA TCGA-ER-A193 TCGA-ER-A199 
       54.51        13.81        36.95        53.19        31.40         9.17 
TCGA-ER-A2NC TCGA-ER-A3PL TCGA-FS-A1Z3 TCGA-FS-A1ZA TCGA-FS-A1ZC TCGA-FS-A1ZP 
       43.82        33.21        20.91        27.72       357.37        74.73 
TCGA-FS-A1ZW TCGA-FS-A1ZZ TCGA-FS-A4F5 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FW-A3R5 
       49.48        27.02        28.73        26.73        49.45        22.92 
TCGA-FW-A3TU TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A266 
       47.54        14.04       120.46        10.13 

$`TPTE WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 
       16.57       112.04        71.80       133.25        28.08        31.59 
TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 
       90.90        95.74        43.43       103.10        65.49        23.77 
TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JG 
      115.53       168.00        69.90        11.87        48.76       113.52 
TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ 
       42.08        12.10       171.58        66.08        45.11       130.72 
TCGA-D3-A3C6 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF 
       58.06        46.32       166.52        86.93        60.23        24.53 
TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F 
       13.87         9.34       103.59        39.75       161.85        43.69 
TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A5GR 
       40.14       131.90        18.38        10.03        51.68       166.19 
TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JX TCGA-D9-A3Z1 
        7.43       125.19       151.53        54.67         6.41        11.34 
TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 
        3.25         9.90        25.18        20.38       176.55        35.93 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC 
      107.34        61.18        53.92        65.92        23.44        68.09 
TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R 
       28.60        10.49       215.44        15.68        13.87        10.16 
TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y 
       45.11        35.01         3.55        52.01        29.82        27.22 
TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 
        8.65        94.98        33.73        26.89        68.15         4.96 
TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29B 
      109.64       151.27        78.87       168.26        13.55        80.61 
TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29Q TCGA-EE-A29R 
       39.62        72.07        32.19        44.35        37.35        14.47 
TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A1 TCGA-EE-A2A2 
       55.92        25.87       171.55        17.92       102.90        24.43 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE 
       39.29        58.75        47.54        67.43       314.56       135.95 
TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN 
      208.04        48.72        54.74        79.66        75.48        90.97 
TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2ME 
       55.59        44.88        94.82        28.83        19.76       103.27 
TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MQ 
       16.96       204.66       144.76       167.90        47.54        43.23 
TCGA-EE-A2MR TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD 
      103.56        53.26       124.31       122.73        25.84         3.68 
TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 
       23.47       138.81       172.18       127.20        64.08        34.32 
TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 
       27.35        33.40       101.79       148.08        35.44        13.94 
TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E 
       50.76        77.75        98.40        48.89        12.59        13.02 
TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M 
       26.37       268.93       152.35         6.44       131.51        61.05 
TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 
       44.05       162.08        50.89        37.25       148.18        79.99 
TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES 
       23.34        20.15        16.37        31.27        32.05       247.04 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW 
       80.32        46.98        92.98       174.21         4.90       216.92 
TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZB 
       48.59       228.59       202.65        28.08         7.79        48.85 
TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ 
       53.52        40.27        15.45         9.70        32.75        47.38 
TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT 
       23.93       101.26       133.55        11.41       148.80        53.16 
TCGA-FS-A1ZU TCGA-FS-A1ZY TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 
       26.56        27.09        77.82        66.67       174.84        12.43 
TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
       77.88         0.20         0.16         2.40         9.90         7.23 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D 
      117.93        84.72        64.44        62.79        32.48        39.58 
TCGA-QB-A6FS 
        6.67 

  TPTE MUTATED TPTE WILD-TYPE 
          2.60           0.16 
  TPTE MUTATED TPTE WILD-TYPE 
        357.37         314.56 
  TPTE MUTATED TPTE WILD-TYPE 
         47.13          48.85 
[1] "2.6 - 357.4 (47.1)" "0.2 - 314.6 (48.9)"
[1] "hr=" "1.1"
D110V3, continuous
                vv
clus             DISTANT METASTASIS PRIMARY TUMOR
  TPTE MUTATED                    9             1
  TPTE WILD-TYPE                 26             3
                vv
clus             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  TPTE MUTATED                                          11                  37
  TPTE WILD-TYPE                                        47                 133
D110V4, multiclass
                                           clus
vv                                          TPTE MUTATED TPTE WILD-TYPE
  DISTANT METASTASIS                                   9             26
  PRIMARY TUMOR                                        1              3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE           11             47
  REGIONAL LYMPH NODE                                 37            133
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  TPTE MUTATED             3       0       6        2        5        7
  TPTE WILD-TYPE           7       6      16        8       19       10
                vv
clus             STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  TPTE MUTATED           2         3         2         6          2          6
  TPTE WILD-TYPE         8        11         7        25         11         16
                vv
clus             STAGE IIIC STAGE IV
  TPTE MUTATED            8        2
  TPTE WILD-TYPE         36       10
D110V5, multiclass
             clus
vv            TPTE MUTATED TPTE WILD-TYPE
  I OR II NOS            3              7
  STAGE 0                0              6
  STAGE I                6             16
  STAGE IA               2              8
  STAGE IB               5             19
  STAGE II               7             10
  STAGE IIA              2              8
  STAGE IIB              3             11
  STAGE IIC              2              7
  STAGE III              6             25
  STAGE IIIA             2             11
  STAGE IIIB             6             16
  STAGE IIIC             8             36
  STAGE IV               2             10
[1] 14  2
[1] 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
  TPTE MUTATED      11 13 14 12
  TPTE WILD-TYPE    40 45 39 43
D110V6, multiclass
       clus
vv      TPTE MUTATED TPTE WILD-TYPE
  T0+T1           11             40
  T2              13             45
  T3              14             39
  T4              12             43
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  TPTE MUTATED    32  12   5   5
  TPTE WILD-TYPE 106  36  27  28
D110V7, multiclass
    clus
vv   TPTE MUTATED TPTE WILD-TYPE
  N0           32            106
  N1           12             36
  N2            5             27
  N3            5             28
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              M0  M1 M1A M1B M1C
  TPTE MUTATED    53   1   1   0   0
  TPTE WILD-TYPE 187   3   1   2   5
D110V8, multiclass
     clus
vv    TPTE MUTATED TPTE WILD-TYPE
  M0            53            187
  M1             1              3
  M1A            1              1
  M1B            0              2
  M1C            0              5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D110V9, binary
                cls
clus              0  1
  TPTE MUTATED   22 16
  TPTE WILD-TYPE 80 51
[1] "tbl2"
                cls
clus             [,1] [,2]
  TPTE MUTATED     22   16
  TPTE WILD-TYPE   80   51
     clus
vv    TPTE MUTATED TPTE WILD-TYPE
  NO            22             80
  YES           16             51
[1] 2 2
[1] FALSE
D110V10, binary
                cls
clus               0   1
  TPTE MUTATED     7  51
  TPTE WILD-TYPE  26 184
[1] "tbl2"
                cls
clus             [,1] [,2]
  TPTE MUTATED      7   51
  TPTE WILD-TYPE   26  184
     clus
vv    TPTE MUTATED TPTE WILD-TYPE
  NO             7             26
  YES           51            184
[1] 2 2
[1] FALSE
D110V11, continuous
D110V12, binary
                cls
clus               0   1
  TPTE MUTATED    25  33
  TPTE WILD-TYPE  78 132
[1] "tbl2"
                cls
clus             [,1] [,2]
  TPTE MUTATED     25   33
  TPTE WILD-TYPE   78  132
        clus
vv       TPTE MUTATED TPTE WILD-TYPE
  FEMALE           25             78
  MALE             33            132
[1] 2 2
[1] FALSE
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TPTE MUTATED       0                         0    58
  TPTE WILD-TYPE     3                         1   206
D110V13, multiclass
                           clus
vv                          TPTE MUTATED TPTE WILD-TYPE
  ASIAN                                0              3
  BLACK OR AFRICAN AMERICAN            0              1
  WHITE                               58            206
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D110V14, binary
                cls
clus               0   1
  TPTE MUTATED     1  56
  TPTE WILD-TYPE   2 205
[1] "tbl2"
                cls
clus             [,1] [,2]
  TPTE MUTATED      1   56
  TPTE WILD-TYPE    2  205
                        clus
vv                       TPTE MUTATED TPTE WILD-TYPE
  HISPANIC OR LATINO                1              2
  NOT HISPANIC OR LATINO           56            205
[1] 2 2
[1] FALSE

Clustering(111) Variable = CLCC1 MUTATION ANALYSIS
D111V1, survival
                 sevent
clus2               0   1
  CLCC1 MUTATED     5   8
  CLCC1 WILD-TYPE 123 122
  CLCC1 MUTATED CLCC1 WILD-TYPE 
             13             245 
  CLCC1 MUTATED CLCC1 WILD-TYPE 
              8             122 
$`CLCC1 MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q6 TCGA-D3-A2J6 TCGA-D3-A3CE TCGA-D3-A3ML 
       16.47         8.52        70.16        10.29        13.32         6.31 
TCGA-EE-A29E TCGA-EE-A29L TCGA-EE-A2A2 TCGA-EE-A2GE TCGA-EE-A2GK TCGA-EE-A2MQ 
       38.63         1.08        23.90        34.92        16.01        21.60 
TCGA-EE-A3JI 
       33.60 

$`CLCC1 WILD-TYPE`
TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA 
      111.09        32.42       110.79        28.08        22.55        45.83 
TCGA-D3-A1QB TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB 
       81.24        85.32         8.38        21.14        88.50        68.22 
TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK 
       69.90        11.41        30.87         7.50        36.16         6.31 
TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 
       92.42        56.19        64.44        45.11       114.67        15.25 
TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3MO 
       46.98        46.32        82.29        61.38        24.00         9.34 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H 
      103.59        26.37         5.39        80.22        42.71        15.09 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN 
       41.10        17.72         8.84        20.48        13.94        52.01 
TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 
       47.87         1.55         6.97        23.11         4.01         2.89 
TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY 
        9.90        11.31        13.22        48.79        35.80        51.12 
TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 
       10.03        39.19        13.68         9.99        44.52        36.69 
TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 
       25.15         4.93        22.36         6.64        19.36         7.00 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH 
       17.56        14.83        13.15         0.20         0.00         0.00 
TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 
       13.22        11.57        10.55         6.31         8.12         1.12 
TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C 
        1.35        12.20         5.13         4.31        36.07         4.34 
TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C 
        5.13         9.21         1.18         7.99         9.90        37.97 
TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P 
       11.15         8.55         4.41        27.12         9.50        12.03 
TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X 
        8.09         8.84         9.99         2.43         8.68         8.09 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC 
       11.31        49.22         9.67         8.94        39.39        34.29 
TCGA-EE-A2GD TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GL TCGA-EE-A2GM 
       17.98        47.21        30.08        19.43        35.54        28.31 
TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT 
       33.83        30.84         5.42         1.15        13.02        34.98 
TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC 
       36.33         8.84        98.27         2.70         6.18        47.51 
TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ 
        9.53        29.46        44.25         7.96        14.56        63.42 
TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MR 
      111.78       111.91        56.02        25.08        26.99        29.65 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC 
       27.16        23.05         5.56       124.31       122.73        25.84 
TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 
        3.68        30.15        13.81        15.95        12.72         3.22 
TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JD 
       22.92        21.60        21.60        16.14        22.22        27.35 
TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 
        0.46        13.94        31.40        18.61        12.95        38.40 
TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E 
        5.72        76.41        25.18         3.78         3.52        11.90 
TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M 
       11.11       114.15        34.88         4.21        13.45        28.60 
TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 
       42.84        34.68         9.57        36.07        17.72        78.44 
TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH 
       11.80         1.87         1.51        13.08        12.62        11.74 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A 
        9.04         6.58        22.49         1.71        18.41        85.74 
TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
        4.90        64.47         3.45        11.01        23.80        14.24 
TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD 
       15.52         7.33         7.30         3.39        20.38         8.22 
TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK 
       19.53        11.08         7.17        30.87        12.92        12.89 
TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT 
       47.38        52.08         8.65         8.81        49.15        40.64 
TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 
        8.68        27.39         0.82         5.23        53.85         7.36 
TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD 
       28.73        14.20        10.78         5.98         6.41         2.27 
TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
        0.20         0.99         0.13         0.16         0.43         9.90 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 
        7.23        12.85        24.85        31.33        84.72        10.13 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS 
       16.24        15.42        12.16        14.70         5.79 

  CLCC1 MUTATED CLCC1 WILD-TYPE 
           1.08            0.00 
  CLCC1 MUTATED CLCC1 WILD-TYPE 
          70.16          124.31 
  CLCC1 MUTATED CLCC1 WILD-TYPE 
          16.47           14.56 
[1] "1.1 - 70.2 (16.5)"  "0.0 - 124.3 (14.6)"
[1] "hr=" "1.2"
D111V2, survival
                 sevent
clus2               0   1
  CLCC1 MUTATED     5   8
  CLCC1 WILD-TYPE 127 123
  CLCC1 MUTATED CLCC1 WILD-TYPE 
             13             250 
  CLCC1 MUTATED CLCC1 WILD-TYPE 
              8             123 
$`CLCC1 MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q6 TCGA-D3-A2J6 TCGA-D3-A3CE TCGA-D3-A3ML 
       16.57        16.67        71.80        43.43        60.23        13.87 
TCGA-EE-A29E TCGA-EE-A29L TCGA-EE-A2A2 TCGA-EE-A2GE TCGA-EE-A2GK TCGA-EE-A2MQ 
       39.62         2.60        24.43       135.95        54.74        43.23 
TCGA-EE-A3JI 
      148.08 

$`CLCC1 WILD-TYPE`
TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA 
      112.04       112.57       133.25        28.08        31.59        90.90 
TCGA-D3-A1QB TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB 
       95.74       103.10        65.49        23.77       115.53       168.00 
TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK 
       69.90        11.87        48.76       113.52        42.08        12.10 
TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 
      171.58        56.19        66.08        45.11       130.72        58.06 
TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3MO 
       46.98        46.32       166.52        86.93        24.53         9.34 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H 
      103.59        39.75        21.47       161.85        43.69        40.14 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN 
      131.90        18.38        10.03        51.68        15.06       135.75 
TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 
      137.92       166.19         7.43       125.19       151.53        54.67 
TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA 
        3.65         6.41        11.34         3.25         9.90        25.18 
TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 
       66.25        48.89        36.03       117.21        20.38       194.83 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA 
      176.55        35.93       107.34        61.18        53.92        65.92 
TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 
       23.44        68.09        28.60        10.49       215.44        15.68 
TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN 
       13.87        10.16        45.11        35.01         3.55        52.01 
TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 
       29.82        27.22         8.65        94.98        33.73        14.70 
TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F 
       26.89        68.15         4.96       109.64       151.27        78.87 
TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D 
      168.26        13.55        63.35        80.61        47.84        13.97 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
       72.07        32.19        44.35        18.61        56.42        37.35 
TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 
       14.47        55.92        25.87       171.55        17.92        46.82 
TCGA-EE-A2A1 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD 
      102.90        39.29        58.75        47.54        67.43       314.56 
TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN 
      208.04        48.72        89.33        79.66        75.48        90.97 
TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU 
      101.95        13.91        14.30        55.59        44.88        94.82 
TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD 
       21.67       129.27        28.83        19.76        61.51        47.28 
TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK 
      103.27       103.20        16.96       204.66        96.23       144.76 
TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MR TCGA-EE-A2MS 
      203.05       167.90        47.54       248.65       103.56       136.47 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD 
       41.59        53.26       124.31       122.73        25.84         3.68 
TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 
       54.51        13.81        23.47       138.81       172.18       127.20 
TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE 
       36.95        64.08        34.32        53.19        27.35        33.40 
TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 
      101.79        31.40        35.44        13.94        50.76         9.17 
TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F 
       77.75        98.40        48.89        12.59        13.02        26.37 
TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N 
      268.93       152.35         6.44       131.51        61.05        44.05 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
      162.08        50.89        37.25       148.18        79.99        43.82 
TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES 
       23.34        20.15        16.37        31.27        32.05       247.04 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
       80.32        46.98        33.21        92.98       174.21         4.90 
TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 
      216.92        48.59       228.59       202.65        20.91        28.08 
TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE 
        7.79        27.72        48.85       357.37        53.52        40.27 
TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM 
       15.45         9.70        32.75        47.38        23.93       101.26 
TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU 
       74.73       133.55        11.41       148.80        53.16        26.56 
TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 
       49.48        27.09        27.02        77.82        66.67        28.73 
TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 
      174.84        12.43        26.73        49.45        77.88         0.20 
TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
       22.92        47.54         0.16         2.40         9.90         7.23 
TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 
       14.04       120.46       117.93        84.72        10.13        64.44 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS 
       62.79        32.48        39.58         6.67 

  CLCC1 MUTATED CLCC1 WILD-TYPE 
           2.60            0.16 
  CLCC1 MUTATED CLCC1 WILD-TYPE 
         148.08          357.37 
  CLCC1 MUTATED CLCC1 WILD-TYPE 
          43.23           48.74 
[1] "2.6 - 148.1 (43.2)" "0.2 - 357.4 (48.7)"
[1] "hr=" "1.7"
D111V3, continuous
                 vv
clus              DISTANT METASTASIS PRIMARY TUMOR
  CLCC1 MUTATED                    0             0
  CLCC1 WILD-TYPE                 35             4
                 vv
clus              REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  CLCC1 MUTATED                                           1                  12
  CLCC1 WILD-TYPE                                        57                 158
D111V4, multiclass
                                           clus
vv                                          CLCC1 MUTATED CLCC1 WILD-TYPE
  DISTANT METASTASIS                                    0              35
  PRIMARY TUMOR                                         0               4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE             1              57
  REGIONAL LYMPH NODE                                  12             158
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  CLCC1 MUTATED             0       0       3        0        0        0
  CLCC1 WILD-TYPE          10       6      19       10       24       17
                 vv
clus              STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  CLCC1 MUTATED           0         1         1         2          2          1
  CLCC1 WILD-TYPE        10        13         8        29         11         21
                 vv
clus              STAGE IIIC STAGE IV
  CLCC1 MUTATED            3        0
  CLCC1 WILD-TYPE         41       12
D111V5, multiclass
             clus
vv            CLCC1 MUTATED CLCC1 WILD-TYPE
  I OR II NOS             0              10
  STAGE 0                 0               6
  STAGE I                 3              19
  STAGE IA                0              10
  STAGE IB                0              24
  STAGE II                0              17
  STAGE IIA               0              10
  STAGE IIB               1              13
  STAGE IIC               1               8
  STAGE III               2              29
  STAGE IIIA              2              11
  STAGE IIIB              1              21
  STAGE IIIC              3              41
  STAGE IV                0              12
[1] 14  2
[1] 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
  CLCC1 MUTATED       3  2  4  4
  CLCC1 WILD-TYPE    48 56 49 51
D111V6, multiclass
       clus
vv      CLCC1 MUTATED CLCC1 WILD-TYPE
  T0+T1             3              48
  T2                2              56
  T3                4              49
  T4                4              51
[1] 4 2
[1] TRUE
[1] "dimension 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
  CLCC1 MUTATED     5   4   2   2
  CLCC1 WILD-TYPE 133  44  30  31
D111V7, multiclass
    clus
vv   CLCC1 MUTATED CLCC1 WILD-TYPE
  N0             5             133
  N1             4              44
  N2             2              30
  N3             2              31
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               M0  M1 M1A M1B M1C
  CLCC1 MUTATED    13   0   0   0   0
  CLCC1 WILD-TYPE 227   4   2   2   5
D111V8, multiclass
     clus
vv    CLCC1 MUTATED CLCC1 WILD-TYPE
  M0             13             227
  M1              0               4
  M1A             0               2
  M1B             0               2
  M1C             0               5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D111V9, binary
                 cls
clus               0  1
  CLCC1 MUTATED    6  4
  CLCC1 WILD-TYPE 96 63
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CLCC1 MUTATED      6    4
  CLCC1 WILD-TYPE   96   63
     clus
vv    CLCC1 MUTATED CLCC1 WILD-TYPE
  NO              6              96
  YES             4              63
[1] 2 2
[1] FALSE
D111V10, binary
                 cls
clus                0   1
  CLCC1 MUTATED     1  12
  CLCC1 WILD-TYPE  32 223
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CLCC1 MUTATED      1   12
  CLCC1 WILD-TYPE   32  223
     clus
vv    CLCC1 MUTATED CLCC1 WILD-TYPE
  NO              1              32
  YES            12             223
[1] 2 2
[1] FALSE
D111V11, continuous
D111V12, binary
                 cls
clus                0   1
  CLCC1 MUTATED     4   9
  CLCC1 WILD-TYPE  99 156
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CLCC1 MUTATED      4    9
  CLCC1 WILD-TYPE   99  156
        clus
vv       CLCC1 MUTATED CLCC1 WILD-TYPE
  FEMALE             4              99
  MALE               9             156
[1] 2 2
[1] FALSE
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CLCC1 MUTATED       0                         0    13
  CLCC1 WILD-TYPE     3                         1   251
D111V13, multiclass
                           clus
vv                          CLCC1 MUTATED CLCC1 WILD-TYPE
  ASIAN                                 0               3
  BLACK OR AFRICAN AMERICAN             0               1
  WHITE                                13             251
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D111V14, binary
                 cls
clus                0   1
  CLCC1 MUTATED     0  13
  CLCC1 WILD-TYPE   3 248
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CLCC1 MUTATED      0   13
  CLCC1 WILD-TYPE    3  248
                        clus
vv                       CLCC1 MUTATED CLCC1 WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO            13             248
[1] 2 2
[1] FALSE

Clustering(112) Variable = PPAP2B MUTATION ANALYSIS
D112V1, survival
                  sevent
clus2                0   1
  PPAP2B MUTATED     5   4
  PPAP2B WILD-TYPE 123 126
  PPAP2B MUTATED PPAP2B WILD-TYPE 
               9              249 
  PPAP2B MUTATED PPAP2B WILD-TYPE 
               4              126 
$`PPAP2B MUTATED`
TCGA-D3-A2JF TCGA-D3-A5GO TCGA-EE-A2A0 TCGA-EE-A2MI TCGA-EE-A2MS TCGA-EE-A3JD 
       30.87        47.87        11.31        14.56        27.16        27.35 
TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FW-A3R5 
       53.85         7.36         0.99 

$`PPAP2B WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.47         8.52       111.09        32.42        70.16       110.79 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       28.08        22.55        45.83        81.24        10.29        85.32 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
        8.38        21.14        88.50        68.22        69.90        11.41 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO 
        7.50        36.16         6.31        92.42        56.19        64.44 
TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB 
       45.11       114.67        15.25        46.98        46.32        82.29 
TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR 
       61.38        13.32        24.00         6.31         9.34       103.59 
TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J 
       26.37         5.39        80.22        42.71        15.09        41.10 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GR 
       17.72         8.84        20.48        13.94        52.01         1.55 
TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA 
        6.97        23.11         4.01         2.89         9.90        11.31 
TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 
       13.22        48.79        35.80        51.12        10.03        39.19 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA 
       13.68         9.99        44.52        36.69        25.15         4.93 
TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 
       22.36         6.64        19.36         7.00        17.56        14.83 
TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EE-A17X 
       13.15         0.20         0.00         0.00        13.22        11.57 
TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 
       10.55         6.31         8.12         1.12         1.35        12.20 
TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H 
        5.13         4.31        36.07         4.34         5.13         9.21 
TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E 
        1.18         7.99         9.90        37.97        11.15        38.63 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P 
        8.55         4.41         1.08        27.12         9.50        12.03 
TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X 
        8.09         8.84         9.99         2.43         8.68         8.09 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC 
       49.22        23.90         9.67         8.94        39.39        34.29 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK 
       17.98        34.92        47.21        30.08        19.43        16.01 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR 
       35.54        28.31        33.83        30.84         5.42         1.15 
TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 
       13.02        34.98        36.33         8.84        98.27         2.70 
TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH 
        6.18        47.51         9.53        29.46        44.25         7.96 
TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP 
       63.42       111.78       111.91        56.02        25.08        26.99 
TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB 
       21.60        29.65        23.05         5.56       124.31       122.73 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH 
       25.84         3.68        30.15        13.81        15.95        12.72 
TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA 
        3.22        22.92        21.60        21.60        16.14        22.22 
TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 
        0.46        13.94        33.60        31.40        18.61        12.95 
TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D 
       38.40         5.72        76.41        25.18         3.78         3.52 
TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L 
       11.90        11.11       114.15        34.88         4.21        13.45 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W 
       28.60        42.84        34.68         9.57        36.07        17.72 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG 
       78.44        11.80         1.87         1.51        13.08        12.62 
TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN 
       11.74         9.04         6.58        22.49         1.71        18.41 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 
       85.74         4.90        64.47         3.45        11.01        23.80 
TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC 
       14.24        15.52         7.33         7.30         3.39        20.38 
TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ 
        8.22        19.53        11.08         7.17        30.87        12.92 
TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS 
       12.89        47.38        52.08         8.65         8.81        49.15 
TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F5 
       40.64         8.68        27.39         0.82         5.23        28.73 
TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 
       14.20        10.78         5.98         6.41         2.27         0.20 
TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 
        0.13         0.16         0.43         9.90         7.23        12.85 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 
       24.85        31.33        84.72        10.13        16.24        15.42 
TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS 
       12.16        14.70         5.79 

  PPAP2B MUTATED PPAP2B WILD-TYPE 
            0.99             0.00 
  PPAP2B MUTATED PPAP2B WILD-TYPE 
           53.85           124.31 
  PPAP2B MUTATED PPAP2B WILD-TYPE 
           27.16            14.70 
[1] "1.0 - 53.9 (27.2)"  "0.0 - 124.3 (14.7)"
[1] "hr=" "1.2"
D112V2, survival
                  sevent
clus2                0   1
  PPAP2B MUTATED     5   4
  PPAP2B WILD-TYPE 127 127
  PPAP2B MUTATED PPAP2B WILD-TYPE 
               9              254 
  PPAP2B MUTATED PPAP2B WILD-TYPE 
               4              127 
$`PPAP2B MUTATED`
TCGA-D3-A2JF TCGA-D3-A5GO TCGA-EE-A2A0 TCGA-EE-A2MI TCGA-EE-A2MS TCGA-EE-A3JD 
       48.76       137.92        46.82       204.66       136.47        27.35 
TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FW-A3R5 
       77.82        66.67        22.92 

$`PPAP2B WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.57        16.67       112.04       112.57        71.80       133.25 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       28.08        31.59        90.90        95.74        43.43       103.10 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
       65.49        23.77       115.53       168.00        69.90        11.87 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO 
      113.52        42.08        12.10       171.58        56.19        66.08 
TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB 
       45.11       130.72        58.06        46.98        46.32       166.52 
TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR 
       86.93        60.23        24.53        13.87         9.34       103.59 
TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J 
       39.75        21.47       161.85        43.69        40.14       131.90 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GR 
       18.38        10.03        51.68        15.06       135.75       166.19 
TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX 
        7.43       125.19       151.53        54.67         3.65         6.41 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1HV 
       11.34         3.25         9.90        25.18        66.25        48.89 
TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 
       36.03       117.21        20.38       194.83       176.55        35.93 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC 
      107.34        61.18        53.92        65.92        23.44        68.09 
TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R 
       28.60        10.49       215.44        15.68        13.87        10.16 
TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y 
       45.11        35.01         3.55        52.01        29.82        27.22 
TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 
        8.65        94.98        33.73        14.70        26.89        68.15 
TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I 
        4.96       109.64       151.27        78.87       168.26        13.55 
TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G 
       63.35        80.61        47.84        13.97        39.62        72.07 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
       32.19         2.60        44.35        18.61        56.42        37.35 
TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A1 
       14.47        55.92        25.87       171.55        17.92       102.90 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD 
       24.43        39.29        58.75        47.54        67.43       314.56 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
      135.95       208.04        48.72        89.33        54.74        79.66 
TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS 
       75.48        90.97       101.95        13.91        14.30        55.59 
TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 
       44.88        94.82        21.67       129.27        28.83        19.76 
TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MJ 
       61.51        47.28       103.27       103.20        16.96        96.23 
TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ 
      144.76       203.05       167.90        47.54       248.65        43.23 
TCGA-EE-A2MR TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC 
      103.56        41.59        53.26       124.31       122.73        25.84 
TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 
        3.68        54.51        13.81        23.47       138.81       172.18 
TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JE 
      127.20        36.95        64.08        34.32        53.19        33.40 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 
      101.79       148.08        31.40        35.44        13.94        50.76 
TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E 
        9.17        77.75        98.40        48.89        12.59        13.02 
TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M 
       26.37       268.93       152.35         6.44       131.51        61.05 
TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 
       44.05       162.08        50.89        37.25       148.18        79.99 
TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH 
       43.82        23.34        20.15        16.37        31.27        32.05 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A 
      247.04        80.32        46.98        33.21        92.98       174.21 
TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
        4.90       216.92        48.59       228.59       202.65        20.91 
TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD 
       28.08         7.79        27.72        48.85       357.37        53.52 
TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK 
       40.27        15.45         9.70        32.75        47.38        23.93 
TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT 
      101.26        74.73       133.55        11.41       148.80        53.16 
TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F5 TCGA-FS-A4F8 
       26.56        49.48        27.09        27.02        28.73       174.84 
TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU 
       12.43        26.73        49.45        77.88         0.20        47.54 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 
        0.16         2.40         9.90         7.23        14.04       120.46 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
      117.93        84.72        10.13        64.44        62.79        32.48 
TCGA-GN-A26D TCGA-QB-A6FS 
       39.58         6.67 

  PPAP2B MUTATED PPAP2B WILD-TYPE 
           22.92             0.16 
  PPAP2B MUTATED PPAP2B WILD-TYPE 
          204.66           357.37 
  PPAP2B MUTATED PPAP2B WILD-TYPE 
           66.67            47.69 
[1] "22.9 - 204.7 (66.7)" "0.2 - 357.4 (47.7)" 
[1] "hr=" "1.4"
D112V3, continuous
                  vv
clus               DISTANT METASTASIS PRIMARY TUMOR
  PPAP2B MUTATED                    2             0
  PPAP2B WILD-TYPE                 33             4
                  vv
clus               REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  PPAP2B MUTATED                                           2
  PPAP2B WILD-TYPE                                        56
                  vv
clus               REGIONAL LYMPH NODE
  PPAP2B MUTATED                     5
  PPAP2B WILD-TYPE                 165
D112V4, multiclass
                                           clus
vv                                          PPAP2B MUTATED PPAP2B WILD-TYPE
  DISTANT METASTASIS                                     2               33
  PRIMARY TUMOR                                          0                4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE              2               56
  REGIONAL LYMPH NODE                                    5              165
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  PPAP2B MUTATED             0       0       0        1        0        2
  PPAP2B WILD-TYPE          10       6      22        9       24       15
                  vv
clus               STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  PPAP2B MUTATED           2         2         0         2          0
  PPAP2B WILD-TYPE         8        12         9        29         13
                  vv
clus               STAGE IIIB STAGE IIIC STAGE IV
  PPAP2B MUTATED            0          0        0
  PPAP2B WILD-TYPE         22         44       12
D112V5, multiclass
             clus
vv            PPAP2B MUTATED PPAP2B WILD-TYPE
  I OR II NOS              0               10
  STAGE 0                  0                6
  STAGE I                  0               22
  STAGE IA                 1                9
  STAGE IB                 0               24
  STAGE II                 2               15
  STAGE IIA                2                8
  STAGE IIB                2               12
  STAGE IIC                0                9
  STAGE III                2               29
  STAGE IIIA               0               13
  STAGE IIIB               0               22
  STAGE IIIC               0               44
  STAGE IV                 0               12
[1] 14  2
[1] 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
  PPAP2B MUTATED       1  1  2  3
  PPAP2B WILD-TYPE    50 57 51 52
D112V6, multiclass
       clus
vv      PPAP2B MUTATED PPAP2B WILD-TYPE
  T0+T1              1               50
  T2                 1               57
  T3                 2               51
  T4                 3               52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  PPAP2B MUTATED     7   0   2   0
  PPAP2B WILD-TYPE 131  48  30  33
D112V7, multiclass
    clus
vv   PPAP2B MUTATED PPAP2B WILD-TYPE
  N0              7              131
  N1              0               48
  N2              2               30
  N3              0               33
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                M0  M1 M1A M1B M1C
  PPAP2B MUTATED     9   0   0   0   0
  PPAP2B WILD-TYPE 231   4   2   2   5
D112V8, multiclass
     clus
vv    PPAP2B MUTATED PPAP2B WILD-TYPE
  M0               9              231
  M1               0                4
  M1A              0                2
  M1B              0                2
  M1C              0                5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D112V9, binary
                  cls
clus                0  1
  PPAP2B MUTATED    4  1
  PPAP2B WILD-TYPE 98 66
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PPAP2B MUTATED      4    1
  PPAP2B WILD-TYPE   98   66
     clus
vv    PPAP2B MUTATED PPAP2B WILD-TYPE
  NO               4               98
  YES              1               66
[1] 2 2
[1] FALSE
D112V10, binary
                  cls
clus                 0   1
  PPAP2B MUTATED     1   8
  PPAP2B WILD-TYPE  32 227
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PPAP2B MUTATED      1    8
  PPAP2B WILD-TYPE   32  227
     clus
vv    PPAP2B MUTATED PPAP2B WILD-TYPE
  NO               1               32
  YES              8              227
[1] 2 2
[1] FALSE
D112V11, continuous
D112V12, binary
                  cls
clus                 0   1
  PPAP2B MUTATED     2   7
  PPAP2B WILD-TYPE 101 158
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PPAP2B MUTATED      2    7
  PPAP2B WILD-TYPE  101  158
        clus
vv       PPAP2B MUTATED PPAP2B WILD-TYPE
  FEMALE              2              101
  MALE                7              158
[1] 2 2
[1] FALSE
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PPAP2B MUTATED       0                         0     9
  PPAP2B WILD-TYPE     3                         1   255
D112V13, multiclass
                           clus
vv                          PPAP2B MUTATED PPAP2B WILD-TYPE
  ASIAN                                  0                3
  BLACK OR AFRICAN AMERICAN              0                1
  WHITE                                  9              255
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D112V14, binary
                  cls
clus                 0   1
  PPAP2B MUTATED     0   8
  PPAP2B WILD-TYPE   3 253
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PPAP2B MUTATED      0    8
  PPAP2B WILD-TYPE    3  253
                        clus
vv                       PPAP2B MUTATED PPAP2B WILD-TYPE
  HISPANIC OR LATINO                  0                3
  NOT HISPANIC OR LATINO              8              253
[1] 2 2
[1] FALSE

Clustering(113) Variable = CD300E MUTATION ANALYSIS
D113V1, survival
                  sevent
clus2                0   1
  CD300E MUTATED     4   4
  CD300E WILD-TYPE 124 126
  CD300E MUTATED CD300E WILD-TYPE 
               8              250 
  CD300E MUTATED CD300E WILD-TYPE 
               4              126 
$`CD300E MUTATED`
TCGA-DA-A1HV TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A2MT TCGA-EE-A3AG TCGA-ER-A19M 
       48.79        30.84        29.65        23.05        15.95        28.60 
TCGA-FS-A1Z3 TCGA-FS-A1ZH 
       14.24        30.87 

$`CD300E WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.47         8.52       111.09        32.42        70.16       110.79 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       28.08        22.55        45.83        81.24        10.29        85.32 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
        8.38        21.14        88.50        68.22        69.90        11.41 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       30.87         7.50        36.16         6.31        92.42        56.19 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 
       64.44        45.11       114.67        15.25        46.98        46.32 
TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO 
       82.29        61.38        13.32        24.00         6.31         9.34 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H 
      103.59        26.37         5.39        80.22        42.71        15.09 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN 
       41.10        17.72         8.84        20.48        13.94        52.01 
TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 
       47.87         1.55         6.97        23.11         4.01         2.89 
TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 
        9.90        11.31        13.22        35.80        51.12        10.03 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 
       39.19        13.68         9.99        44.52        36.69        25.15 
TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 
        4.93        22.36         6.64        19.36         7.00        17.56 
TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN 
       14.83        13.15         0.20         0.00         0.00        13.22 
TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 
       11.57        10.55         6.31         8.12         1.12         1.35 
TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F 
       12.20         5.13         4.31        36.07         4.34         5.13 
TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D 
        9.21         1.18         7.99         9.90        37.97        11.15 
TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N 
       38.63         8.55         4.41         1.08        27.12         9.50 
TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W 
       12.03         8.09         8.84         9.99         2.43         8.68 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 
        8.09        11.31        49.22        23.90         9.67         8.94 
TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI 
       39.39        34.29        17.98        34.92        47.21        30.08 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP 
       19.43        16.01        35.54        28.31        33.83         5.42 
TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 
        1.15        13.02        34.98        36.33         8.84        98.27 
TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG 
        2.70         6.18        47.51         9.53        29.46        44.25 
TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM 
        7.96        14.56        63.42       111.78       111.91        56.02 
TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3AA 
       25.08        26.99        21.60        27.16         5.56       124.31 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AH 
      122.73        25.84         3.68        30.15        13.81        12.72 
TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA 
        3.22        22.92        21.60        21.60        16.14        22.22 
TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 
       27.35         0.46        13.94        33.60        31.40        18.61 
TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C 
       12.95        38.40         5.72        76.41        25.18         3.78 
TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J 
        3.52        11.90        11.11       114.15        34.88         4.21 
TCGA-ER-A19L TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W 
       13.45        42.84        34.68         9.57        36.07        17.72 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG 
       78.44        11.80         1.87         1.51        13.08        12.62 
TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN 
       11.74         9.04         6.58        22.49         1.71        18.41 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 
       85.74         4.90        64.47         3.45        11.01        23.80 
TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD 
       15.52         7.33         7.30         3.39        20.38         8.22 
TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM 
       19.53        11.08         7.17        12.92        12.89        47.38 
TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU 
       52.08         8.65         8.81        49.15        40.64         8.68 
TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 
       27.39         0.82         5.23        53.85         7.36        28.73 
TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 
       14.20        10.78         5.98         6.41         2.27         0.20 
TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
        0.99         0.13         0.16         0.43         9.90         7.23 
TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 
       12.85        24.85        31.33        84.72        10.13        16.24 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS 
       15.42        12.16        14.70         5.79 

  CD300E MUTATED CD300E WILD-TYPE 
           14.24             0.00 
  CD300E MUTATED CD300E WILD-TYPE 
           48.79           124.31 
  CD300E MUTATED CD300E WILD-TYPE 
          29.125           14.070 
[1] "14.2 - 48.8 (29.1)" "0.0 - 124.3 (14.1)"
[1] "hr=" "1.3"
D113V2, survival
                  sevent
clus2                0   1
  CD300E MUTATED     4   4
  CD300E WILD-TYPE 128 127
  CD300E MUTATED CD300E WILD-TYPE 
               8              255 
  CD300E MUTATED CD300E WILD-TYPE 
               4              127 
$`CD300E MUTATED`
TCGA-DA-A1HV TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A2MT TCGA-EE-A3AG TCGA-ER-A19M 
       48.89       101.95       103.56        41.59        23.47        61.05 
TCGA-FS-A1Z3 TCGA-FS-A1ZH 
       20.91        32.75 

$`CD300E WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.57        16.67       112.04       112.57        71.80       133.25 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       28.08        31.59        90.90        95.74        43.43       103.10 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
       65.49        23.77       115.53       168.00        69.90        11.87 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       48.76       113.52        42.08        12.10       171.58        56.19 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 
       66.08        45.11       130.72        58.06        46.98        46.32 
TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO 
      166.52        86.93        60.23        24.53        13.87         9.34 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H 
      103.59        39.75        21.47       161.85        43.69        40.14 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN 
      131.90        18.38        10.03        51.68        15.06       135.75 
TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 
      137.92       166.19         7.43       125.19       151.53        54.67 
TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA 
        3.65         6.41        11.34         3.25         9.90        25.18 
TCGA-D9-A6EC TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 
       66.25        36.03       117.21        20.38       194.83       176.55 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB 
       35.93       107.34        61.18        53.92        65.92        23.44 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q 
       68.09        28.60        10.49       215.44        15.68        13.87 
TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X 
       10.16        45.11        35.01         3.55        52.01        29.82 
TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 
       27.22         8.65        94.98        33.73        14.70        26.89 
TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H 
       68.15         4.96       109.64       151.27        78.87       168.26 
TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E 
       13.55        63.35        80.61        47.84        13.97        39.62 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P 
       72.07        32.19         2.60        44.35        18.61        56.42 
TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X 
       37.35        14.47        55.92        25.87       171.55        17.92 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB 
       46.82       102.90        24.43        39.29        58.75        47.54 
TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ 
       67.43       314.56       135.95       208.04        48.72        89.33 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR 
       54.74        79.66        75.48        90.97        13.91        14.30 
TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 
       55.59        44.88        94.82        21.67       129.27        28.83 
TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH 
       19.76        61.51        47.28       103.27       103.20        16.96 
TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN 
      204.66        96.23       144.76       203.05       167.90        47.54 
TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB 
      248.65        43.23       136.47        53.26       124.31       122.73 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AH TCGA-EE-A3J3 
       25.84         3.68        54.51        13.81       138.81       172.18 
TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JD 
      127.20        36.95        64.08        34.32        53.19        27.35 
TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 
       33.40       101.79       148.08        31.40        35.44        13.94 
TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D 
       50.76         9.17        77.75        98.40        48.89        12.59 
TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L 
       13.02        26.37       268.93       152.35         6.44       131.51 
TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 
       44.05       162.08        50.89        37.25       148.18        79.99 
TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH 
       43.82        23.34        20.15        16.37        31.27        32.05 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A 
      247.04        80.32        46.98        33.21        92.98       174.21 
TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z4 
        4.90       216.92        48.59       228.59       202.65        28.08 
TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE 
        7.79        27.72        48.85       357.37        53.52        40.27 
TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP 
       15.45         9.70        47.38        23.93       101.26        74.73 
TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW 
      133.55        11.41       148.80        53.16        26.56        49.48 
TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 
       27.09        27.02        77.82        66.67        28.73       174.84 
TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 
       12.43        26.73        49.45        77.88         0.20        22.92 
TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 
       47.54         0.16         2.40         9.90         7.23        14.04 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 
      120.46       117.93        84.72        10.13        64.44        62.79 
TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS 
       32.48        39.58         6.67 

  CD300E MUTATED CD300E WILD-TYPE 
           20.91             0.16 
  CD300E MUTATED CD300E WILD-TYPE 
          103.56           357.37 
  CD300E MUTATED CD300E WILD-TYPE 
           45.24            48.59 
[1] "20.9 - 103.6 (45.2)" "0.2 - 357.4 (48.6)" 
[1] "hr=" "1.2"
D113V3, continuous
                  vv
clus               DISTANT METASTASIS PRIMARY TUMOR
  CD300E MUTATED                    1             0
  CD300E WILD-TYPE                 34             4
                  vv
clus               REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  CD300E MUTATED                                           2
  CD300E WILD-TYPE                                        56
                  vv
clus               REGIONAL LYMPH NODE
  CD300E MUTATED                     5
  CD300E WILD-TYPE                 165
D113V4, multiclass
                                           clus
vv                                          CD300E MUTATED CD300E WILD-TYPE
  DISTANT METASTASIS                                     1               34
  PRIMARY TUMOR                                          0                4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE              2               56
  REGIONAL LYMPH NODE                                    5              165
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  CD300E MUTATED             0       0       1        0        2        1
  CD300E WILD-TYPE          10       6      21       10       22       16
                  vv
clus               STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  CD300E MUTATED           0         0         0         1          0
  CD300E WILD-TYPE        10        14         9        30         13
                  vv
clus               STAGE IIIB STAGE IIIC STAGE IV
  CD300E MUTATED            1          0        2
  CD300E WILD-TYPE         21         44       10
D113V5, multiclass
             clus
vv            CD300E MUTATED CD300E WILD-TYPE
  I OR II NOS              0               10
  STAGE 0                  0                6
  STAGE I                  1               21
  STAGE IA                 0               10
  STAGE IB                 2               22
  STAGE II                 1               16
  STAGE IIA                0               10
  STAGE IIB                0               14
  STAGE IIC                0                9
  STAGE III                1               30
  STAGE IIIA               0               13
  STAGE IIIB               1               21
  STAGE IIIC               0               44
  STAGE IV                 2               10
[1] 14  2
[1] 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
  CD300E MUTATED       2  3  2  0
  CD300E WILD-TYPE    49 55 51 55
D113V6, multiclass
       clus
vv      CD300E MUTATED CD300E WILD-TYPE
  T0+T1              2               49
  T2                 3               55
  T3                 2               51
  T4                 0               55
[1] 4 2
[1] TRUE
[1] "dimension 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
  CD300E MUTATED     5   0   3   0
  CD300E WILD-TYPE 133  48  29  33
D113V7, multiclass
    clus
vv   CD300E MUTATED CD300E WILD-TYPE
  N0              5              133
  N1              0               48
  N2              3               29
  N3              0               33
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                M0  M1 M1A M1B M1C
  CD300E MUTATED     6   1   0   0   1
  CD300E WILD-TYPE 234   3   2   2   4
D113V8, multiclass
     clus
vv    CD300E MUTATED CD300E WILD-TYPE
  M0               6              234
  M1               1                3
  M1A              0                2
  M1B              0                2
  M1C              1                4
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D113V9, binary
                  cls
clus                0  1
  CD300E MUTATED    4  1
  CD300E WILD-TYPE 98 66
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CD300E MUTATED      4    1
  CD300E WILD-TYPE   98   66
     clus
vv    CD300E MUTATED CD300E WILD-TYPE
  NO               4               98
  YES              1               66
[1] 2 2
[1] FALSE
D113V10, binary
                  cls
clus                 0   1
  CD300E MUTATED     3   5
  CD300E WILD-TYPE  30 230
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CD300E MUTATED      3    5
  CD300E WILD-TYPE   30  230
     clus
vv    CD300E MUTATED CD300E WILD-TYPE
  NO               3               30
  YES              5              230
[1] 2 2
[1] FALSE
D113V11, continuous
D113V12, binary
                  cls
clus                 0   1
  CD300E MUTATED     4   4
  CD300E WILD-TYPE  99 161
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CD300E MUTATED      4    4
  CD300E WILD-TYPE   99  161
        clus
vv       CD300E MUTATED CD300E WILD-TYPE
  FEMALE              4               99
  MALE                4              161
[1] 2 2
[1] FALSE
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CD300E MUTATED       0                         0     8
  CD300E WILD-TYPE     3                         1   256
D113V13, multiclass
                           clus
vv                          CD300E MUTATED CD300E WILD-TYPE
  ASIAN                                  0                3
  BLACK OR AFRICAN AMERICAN              0                1
  WHITE                                  8              256
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D113V14, binary
                  cls
clus                 0   1
  CD300E MUTATED     0   8
  CD300E WILD-TYPE   3 253
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CD300E MUTATED      0    8
  CD300E WILD-TYPE    3  253
                        clus
vv                       CD300E MUTATED CD300E WILD-TYPE
  HISPANIC OR LATINO                  0                3
  NOT HISPANIC OR LATINO              8              253
[1] 2 2
[1] FALSE

Clustering(114) Variable = ALDH5A1 MUTATION ANALYSIS
D114V1, survival
                   sevent
clus2                 0   1
  ALDH5A1 MUTATED     7   3
  ALDH5A1 WILD-TYPE 121 127
  ALDH5A1 MUTATED ALDH5A1 WILD-TYPE 
               10               248 
  ALDH5A1 MUTATED ALDH5A1 WILD-TYPE 
                3               127 
$`ALDH5A1 MUTATED`
TCGA-D3-A2JF TCGA-D3-A2JO TCGA-D3-A3C8 TCGA-D9-A3Z1 TCGA-EE-A181 TCGA-EE-A29E 
       30.87        64.44        46.32         4.01         1.12        38.63 
TCGA-EE-A2GI TCGA-EE-A2GU TCGA-EE-A2MJ TCGA-FW-A3R5 
       30.08        36.33        63.42         0.99 

$`ALDH5A1 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.47         8.52       111.09        32.42        70.16       110.79 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       28.08        22.55        45.83        81.24        10.29        85.32 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
        8.38        21.14        88.50        68.22        69.90        11.41 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JP 
        7.50        36.16         6.31        92.42        56.19        45.11 
TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE 
      114.67        15.25        46.98        82.29        61.38        13.32 
TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV 
       24.00         6.31         9.34       103.59        26.37         5.39 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N 
       80.22        42.71        15.09        41.10        17.72         8.84 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS 
       20.48        13.94        52.01        47.87         1.55         6.97 
TCGA-D3-A5GU TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1HV 
       23.11         2.89         9.90        11.31        13.22        48.79 
TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 
       35.80        51.12        10.03        39.19        13.68         9.99 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC 
       44.52        36.69        25.15         4.93        22.36         6.64 
TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R 
       19.36         7.00        17.56        14.83        13.15         0.20 
TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z 
        0.00         0.00        13.22        11.57        10.55         6.31 
TCGA-EE-A180 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B 
        8.12         1.35        12.20         5.13         4.31        36.07 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B 
        4.34         5.13         9.21         1.18         7.99         9.90 
TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M 
       37.97        11.15         8.55         4.41         1.08        27.12 
TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V 
        9.50        12.03         8.09         8.84         9.99         2.43 
TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 
        8.68         8.09        11.31        49.22        23.90         9.67 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH 
        8.94        39.39        34.29        17.98        34.92        47.21 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO 
       19.43        16.01        35.54        28.31        33.83        30.84 
TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2M5 TCGA-EE-A2M6 
        5.42         1.15        13.02        34.98         8.84        98.27 
TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG 
        2.70         6.18        47.51         9.53        29.46        44.25 
TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN 
        7.96        14.56       111.78       111.91        56.02        25.08 
TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU 
       26.99        21.60        29.65        27.16        23.05         5.56 
TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF 
      124.31       122.73        25.84         3.68        30.15        13.81 
TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 
       15.95        12.72         3.22        22.92        21.60        21.60 
TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI 
       16.14        22.22        27.35         0.46        13.94        33.60 
TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A 
       31.40        18.61        12.95        38.40         5.72        76.41 
TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G 
       25.18         3.78         3.52        11.90        11.11       114.15 
TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P 
       34.88         4.21        13.45        28.60        42.84        34.68 
TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
        9.57        36.07        17.72        78.44        11.80         1.87 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET 
        1.51        13.08        12.62        11.74         9.04         6.58 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW 
       22.49         1.71        18.41        85.74         4.90        64.47 
TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 
        3.45        11.01        23.80        14.24        15.52         7.33 
TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF 
        7.30         3.39        20.38         8.22        19.53        11.08 
TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP 
        7.17        30.87        12.92        12.89        47.38        52.08 
TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW 
        8.65         8.81        49.15        40.64         8.68        27.39 
TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 
        0.82         5.23        53.85         7.36        28.73        14.20 
TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU 
       10.78         5.98         6.41         2.27         0.20         0.13 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 
        0.16         0.43         9.90         7.23        12.85        24.85 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
       31.33        84.72        10.13        16.24        15.42        12.16 
TCGA-GN-A26D TCGA-QB-A6FS 
       14.70         5.79 

  ALDH5A1 MUTATED ALDH5A1 WILD-TYPE 
             0.99              0.00 
  ALDH5A1 MUTATED ALDH5A1 WILD-TYPE 
            64.44            124.31 
  ALDH5A1 MUTATED ALDH5A1 WILD-TYPE 
             33.6              14.4 
[1] "1.0 - 64.4 (33.6)"  "0.0 - 124.3 (14.4)"
[1] "hr=" "2.1"
D114V2, survival
                   sevent
clus2                 0   1
  ALDH5A1 MUTATED     7   3
  ALDH5A1 WILD-TYPE 125 128
  ALDH5A1 MUTATED ALDH5A1 WILD-TYPE 
               10               253 
  ALDH5A1 MUTATED ALDH5A1 WILD-TYPE 
                3               128 
$`ALDH5A1 MUTATED`
TCGA-D3-A2JF TCGA-D3-A2JO TCGA-D3-A3C8 TCGA-D9-A3Z1 TCGA-EE-A181 TCGA-EE-A29E 
       48.76        66.08        46.32        11.34        33.73        39.62 
TCGA-EE-A2GI TCGA-EE-A2GU TCGA-EE-A2MJ TCGA-FW-A3R5 
       48.72        94.82        96.23        22.92 

$`ALDH5A1 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.57        16.67       112.04       112.57        71.80       133.25 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       28.08        31.59        90.90        95.74        43.43       103.10 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
       65.49        23.77       115.53       168.00        69.90        11.87 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JP 
      113.52        42.08        12.10       171.58        56.19        45.11 
TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE 
      130.72        58.06        46.98       166.52        86.93        60.23 
TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV 
       24.53        13.87         9.34       103.59        39.75        21.47 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N 
      161.85        43.69        40.14       131.90        18.38        10.03 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS 
       51.68        15.06       135.75       137.92       166.19         7.43 
TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z3 
      125.19       151.53        54.67         3.65         6.41         3.25 
TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY 
        9.90        25.18        66.25        48.89        36.03       117.21 
TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 
       20.38       194.83       176.55        35.93       107.34        61.18 
TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 
       53.92        65.92        23.44        68.09        28.60        10.49 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH 
      215.44        15.68        13.87        10.16        45.11        35.01 
TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 
        3.55        52.01        29.82        27.22         8.65        94.98 
TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C 
       14.70        26.89        68.15         4.96       109.64       151.27 
TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C 
       78.87       168.26        13.55        63.35        80.61        47.84 
TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N 
       13.97        72.07        32.19         2.60        44.35        18.61 
TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W 
       56.42        37.35        14.47        55.92        25.87       171.55 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 
       17.92        46.82       102.90        24.43        39.29        58.75 
TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ 
       47.54        67.43       314.56       135.95       208.04        89.33 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP 
       54.74        79.66        75.48        90.97       101.95        13.91 
TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 
       14.30        55.59        44.88        21.67       129.27        28.83 
TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH 
       19.76        61.51        47.28       103.27       103.20        16.96 
TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP 
      204.66       144.76       203.05       167.90        47.54       248.65 
TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA 
       43.23       103.56       136.47        41.59        53.26       124.31 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG 
      122.73        25.84         3.68        54.51        13.81        23.47 
TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 
      138.81       172.18       127.20        36.95        64.08        34.32 
TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 
       53.19        27.35        33.40       101.79       148.08        31.40 
TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B 
       35.44        13.94        50.76         9.17        77.75        98.40 
TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H 
       48.89        12.59        13.02        26.37       268.93       152.35 
TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q 
        6.44       131.51        61.05        44.05       162.08        50.89 
TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE 
       37.25       148.18        79.99        43.82        23.34        20.15 
TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV 
       16.37        31.27        32.05       247.04        80.32        46.98 
TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX 
       33.21        92.98       174.21         4.90       216.92        48.59 
TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA 
      228.59       202.65        20.91        28.08         7.79        27.72 
TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG 
       48.85       357.37        53.52        40.27        15.45         9.70 
TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ 
       32.75        47.38        23.93       101.26        74.73       133.55 
TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY 
       11.41       148.80        53.16        26.56        49.48        27.09 
TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 
       27.02        77.82        66.67        28.73       174.84        12.43 
TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV 
       26.73        49.45        77.88         0.20        47.54         0.16 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 
        2.40         9.90         7.23        14.04       120.46       117.93 
TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D 
       84.72        10.13        64.44        62.79        32.48        39.58 
TCGA-QB-A6FS 
        6.67 

  ALDH5A1 MUTATED ALDH5A1 WILD-TYPE 
            11.34              0.16 
  ALDH5A1 MUTATED ALDH5A1 WILD-TYPE 
            96.23            357.37 
  ALDH5A1 MUTATED ALDH5A1 WILD-TYPE 
            47.52             48.59 
[1] "11.3 - 96.2 (47.5)" "0.2 - 357.4 (48.6)"
[1] "hr=" "1.3"
D114V3, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  ALDH5A1 MUTATED                    1             0
  ALDH5A1 WILD-TYPE                 34             4
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  ALDH5A1 MUTATED                                           2
  ALDH5A1 WILD-TYPE                                        56
                   vv
clus                REGIONAL LYMPH NODE
  ALDH5A1 MUTATED                     7
  ALDH5A1 WILD-TYPE                 163
D114V4, multiclass
                                           clus
vv                                          ALDH5A1 MUTATED ALDH5A1 WILD-TYPE
  DISTANT METASTASIS                                      1                34
  PRIMARY TUMOR                                           0                 4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE               2                56
  REGIONAL LYMPH NODE                                     7               163
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  ALDH5A1 MUTATED             0       0       0        3        0        1
  ALDH5A1 WILD-TYPE          10       6      22        7       24       16
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  ALDH5A1 MUTATED           0         0         0         2          0
  ALDH5A1 WILD-TYPE        10        14         9        29         13
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  ALDH5A1 MUTATED            1          3        0
  ALDH5A1 WILD-TYPE         21         41       12
D114V5, multiclass
             clus
vv            ALDH5A1 MUTATED ALDH5A1 WILD-TYPE
  I OR II NOS               0                10
  STAGE 0                   0                 6
  STAGE I                   0                22
  STAGE IA                  3                 7
  STAGE IB                  0                24
  STAGE II                  1                16
  STAGE IIA                 0                10
  STAGE IIB                 0                14
  STAGE IIC                 0                 9
  STAGE III                 2                29
  STAGE IIIA                0                13
  STAGE IIIB                1                21
  STAGE IIIC                3                41
  STAGE IV                  0                12
[1] 14  2
[1] 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
  ALDH5A1 MUTATED       3  1  2  1
  ALDH5A1 WILD-TYPE    48 57 51 54
D114V6, multiclass
       clus
vv      ALDH5A1 MUTATED ALDH5A1 WILD-TYPE
  T0+T1               3                48
  T2                  1                57
  T3                  2                51
  T4                  1                54
[1] 4 2
[1] TRUE
[1] "dimension 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
  ALDH5A1 MUTATED     5   1   1   3
  ALDH5A1 WILD-TYPE 133  47  31  30
D114V7, multiclass
    clus
vv   ALDH5A1 MUTATED ALDH5A1 WILD-TYPE
  N0               5               133
  N1               1                47
  N2               1                31
  N3               3                30
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1 M1A M1B M1C
  ALDH5A1 MUTATED    10   0   0   0   0
  ALDH5A1 WILD-TYPE 230   4   2   2   5
D114V8, multiclass
     clus
vv    ALDH5A1 MUTATED ALDH5A1 WILD-TYPE
  M0               10               230
  M1                0                 4
  M1A               0                 2
  M1B               0                 2
  M1C               0                 5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D114V9, binary
                   cls
clus                 0  1
  ALDH5A1 MUTATED    5  1
  ALDH5A1 WILD-TYPE 97 66
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ALDH5A1 MUTATED      5    1
  ALDH5A1 WILD-TYPE   97   66
     clus
vv    ALDH5A1 MUTATED ALDH5A1 WILD-TYPE
  NO                5                97
  YES               1                66
[1] 2 2
[1] FALSE
D114V10, binary
                   cls
clus                  0   1
  ALDH5A1 MUTATED     0  10
  ALDH5A1 WILD-TYPE  33 225
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ALDH5A1 MUTATED      0   10
  ALDH5A1 WILD-TYPE   33  225
     clus
vv    ALDH5A1 MUTATED ALDH5A1 WILD-TYPE
  NO                0                33
  YES              10               225
[1] 2 2
[1] FALSE
D114V11, continuous
D114V12, binary
                   cls
clus                  0   1
  ALDH5A1 MUTATED     4   6
  ALDH5A1 WILD-TYPE  99 159
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ALDH5A1 MUTATED      4    6
  ALDH5A1 WILD-TYPE   99  159
        clus
vv       ALDH5A1 MUTATED ALDH5A1 WILD-TYPE
  FEMALE               4                99
  MALE                 6               159
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ALDH5A1 MUTATED       0                         0    10
  ALDH5A1 WILD-TYPE     3                         1   254
D114V13, multiclass
                           clus
vv                          ALDH5A1 MUTATED ALDH5A1 WILD-TYPE
  ASIAN                                   0                 3
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  10               254
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D114V14, binary
                   cls
clus                  0   1
  ALDH5A1 MUTATED     0  10
  ALDH5A1 WILD-TYPE   3 251
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ALDH5A1 MUTATED      0   10
  ALDH5A1 WILD-TYPE    3  251
                        clus
vv                       ALDH5A1 MUTATED ALDH5A1 WILD-TYPE
  HISPANIC OR LATINO                   0                 3
  NOT HISPANIC OR LATINO              10               251
[1] 2 2
[1] FALSE

Clustering(115) Variable = SPRYD3 MUTATION ANALYSIS
D115V1, survival
                  sevent
clus2                0   1
  SPRYD3 MUTATED     4   3
  SPRYD3 WILD-TYPE 124 127
  SPRYD3 MUTATED SPRYD3 WILD-TYPE 
               7              251 
  SPRYD3 MUTATED SPRYD3 WILD-TYPE 
               3              127 
$`SPRYD3 MUTATED`
TCGA-D3-A3MU TCGA-D3-A5GU TCGA-EE-A20B TCGA-EE-A2MD TCGA-EE-A2MR TCGA-EE-A3J5 
       26.37        23.11        36.07         9.53        29.65        21.60 
TCGA-FS-A1ZK 
       12.89 

$`SPRYD3 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.47         8.52       111.09        32.42        70.16       110.79 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       28.08        22.55        45.83        81.24        10.29        85.32 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
        8.38        21.14        88.50        68.22        69.90        11.41 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       30.87         7.50        36.16         6.31        92.42        56.19 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 
       64.44        45.11       114.67        15.25        46.98        46.32 
TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO 
       82.29        61.38        13.32        24.00         6.31         9.34 
TCGA-D3-A3MR TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J 
      103.59         5.39        80.22        42.71        15.09        41.10 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO 
       17.72         8.84        20.48        13.94        52.01        47.87 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA 
        1.55         6.97         4.01         2.89         9.90        11.31 
TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 
       13.22        48.79        35.80        51.12        10.03        39.19 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA 
       13.68         9.99        44.52        36.69        25.15         4.93 
TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 
       22.36         6.64        19.36         7.00        17.56        14.83 
TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EE-A17X 
       13.15         0.20         0.00         0.00        13.22        11.57 
TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 
       10.55         6.31         8.12         1.12         1.35        12.20 
TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I 
        5.13         4.31         4.34         5.13         9.21         1.18 
TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G 
        7.99         9.90        37.97        11.15        38.63         8.55 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
        4.41         1.08        27.12         9.50        12.03         8.09 
TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 
        8.84         9.99         2.43         8.68         8.09        11.31 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC 
       49.22        23.90         9.67         8.94        39.39        34.29 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK 
       17.98        34.92        47.21        30.08        19.43        16.01 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR 
       35.54        28.31        33.83        30.84         5.42         1.15 
TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 
       13.02        34.98        36.33         8.84        98.27         2.70 
TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI 
        6.18        47.51        29.46        44.25         7.96        14.56 
TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP 
       63.42       111.78       111.91        56.02        25.08        26.99 
TCGA-EE-A2MQ TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB 
       21.60        27.16        23.05         5.56       124.31       122.73 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH 
       25.84         3.68        30.15        13.81        15.95        12.72 
TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JD 
        3.22        22.92        21.60        16.14        22.22        27.35 
TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 
        0.46        13.94        33.60        31.40        18.61        12.95 
TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D 
       38.40         5.72        76.41        25.18         3.78         3.52 
TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L 
       11.90        11.11       114.15        34.88         4.21        13.45 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W 
       28.60        42.84        34.68         9.57        36.07        17.72 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG 
       78.44        11.80         1.87         1.51        13.08        12.62 
TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN 
       11.74         9.04         6.58        22.49         1.71        18.41 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 
       85.74         4.90        64.47         3.45        11.01        23.80 
TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC 
       14.24        15.52         7.33         7.30         3.39        20.38 
TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ 
        8.22        19.53        11.08         7.17        30.87        12.92 
TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT 
       47.38        52.08         8.65         8.81        49.15        40.64 
TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 
        8.68        27.39         0.82         5.23        53.85         7.36 
TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD 
       28.73        14.20        10.78         5.98         6.41         2.27 
TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
        0.20         0.99         0.13         0.16         0.43         9.90 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 
        7.23        12.85        24.85        31.33        84.72        10.13 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS 
       16.24        15.42        12.16        14.70         5.79 

  SPRYD3 MUTATED SPRYD3 WILD-TYPE 
            9.53             0.00 
  SPRYD3 MUTATED SPRYD3 WILD-TYPE 
           36.07           124.31 
  SPRYD3 MUTATED SPRYD3 WILD-TYPE 
           23.11            14.56 
[1] "9.5 - 36.1 (23.1)"  "0.0 - 124.3 (14.6)"
[1] "hr=" "1.3"
D115V2, survival
                  sevent
clus2                0   1
  SPRYD3 MUTATED     4   3
  SPRYD3 WILD-TYPE 128 128
  SPRYD3 MUTATED SPRYD3 WILD-TYPE 
               7              256 
  SPRYD3 MUTATED SPRYD3 WILD-TYPE 
               3              128 
$`SPRYD3 MUTATED`
TCGA-D3-A3MU TCGA-D3-A5GU TCGA-EE-A20B TCGA-EE-A2MD TCGA-EE-A2MR TCGA-EE-A3J5 
       39.75       125.19       109.64        47.28       103.56        36.95 
TCGA-FS-A1ZK 
       23.93 

$`SPRYD3 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.57        16.67       112.04       112.57        71.80       133.25 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       28.08        31.59        90.90        95.74        43.43       103.10 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
       65.49        23.77       115.53       168.00        69.90        11.87 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       48.76       113.52        42.08        12.10       171.58        56.19 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 
       66.08        45.11       130.72        58.06        46.98        46.32 
TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO 
      166.52        86.93        60.23        24.53        13.87         9.34 
TCGA-D3-A3MR TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J 
      103.59        21.47       161.85        43.69        40.14       131.90 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO 
       18.38        10.03        51.68        15.06       135.75       137.92 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX 
      166.19         7.43       151.53        54.67         3.65         6.41 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1HV 
       11.34         3.25         9.90        25.18        66.25        48.89 
TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 
       36.03       117.21        20.38       194.83       176.55        35.93 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC 
      107.34        61.18        53.92        65.92        23.44        68.09 
TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R 
       28.60        10.49       215.44        15.68        13.87        10.16 
TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y 
       45.11        35.01         3.55        52.01        29.82        27.22 
TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 
        8.65        94.98        33.73        14.70        26.89        68.15 
TCGA-EE-A185 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A 
        4.96       151.27        78.87       168.26        13.55        63.35 
TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H 
       80.61        47.84        13.97        39.62        72.07        32.19 
TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R 
        2.60        44.35        18.61        56.42        37.35        14.47 
TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 
       55.92        25.87       171.55        17.92        46.82       102.90 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD 
       24.43        39.29        58.75        47.54        67.43       314.56 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
      135.95       208.04        48.72        89.33        54.74        79.66 
TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS 
       75.48        90.97       101.95        13.91        14.30        55.59 
TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 
       44.88        94.82        21.67       129.27        28.83        19.76 
TCGA-EE-A2MC TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ 
       61.51       103.27       103.20        16.96       204.66        96.23 
TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ 
      144.76       203.05       167.90        47.54       248.65        43.23 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC 
      136.47        41.59        53.26       124.31       122.73        25.84 
TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 
        3.68        54.51        13.81        23.47       138.81       172.18 
TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE 
      127.20        64.08        34.32        53.19        27.35        33.40 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 
      101.79       148.08        31.40        35.44        13.94        50.76 
TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E 
        9.17        77.75        98.40        48.89        12.59        13.02 
TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M 
       26.37       268.93       152.35         6.44       131.51        61.05 
TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 
       44.05       162.08        50.89        37.25       148.18        79.99 
TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH 
       43.82        23.34        20.15        16.37        31.27        32.05 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A 
      247.04        80.32        46.98        33.21        92.98       174.21 
TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
        4.90       216.92        48.59       228.59       202.65        20.91 
TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD 
       28.08         7.79        27.72        48.85       357.37        53.52 
TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZM 
       40.27        15.45         9.70        32.75        47.38       101.26 
TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU 
       74.73       133.55        11.41       148.80        53.16        26.56 
TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 
       49.48        27.09        27.02        77.82        66.67        28.73 
TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 
      174.84        12.43        26.73        49.45        77.88         0.20 
TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
       22.92        47.54         0.16         2.40         9.90         7.23 
TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 
       14.04       120.46       117.93        84.72        10.13        64.44 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS 
       62.79        32.48        39.58         6.67 

  SPRYD3 MUTATED SPRYD3 WILD-TYPE 
           23.93             0.16 
  SPRYD3 MUTATED SPRYD3 WILD-TYPE 
          125.19           357.37 
  SPRYD3 MUTATED SPRYD3 WILD-TYPE 
          47.280           48.655 
[1] "23.9 - 125.2 (47.3)" "0.2 - 357.4 (48.7)" 
[1] "hr=" "1.2"
D115V3, continuous
                  vv
clus               DISTANT METASTASIS PRIMARY TUMOR
  SPRYD3 MUTATED                    1             0
  SPRYD3 WILD-TYPE                 34             4
                  vv
clus               REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  SPRYD3 MUTATED                                           2
  SPRYD3 WILD-TYPE                                        56
                  vv
clus               REGIONAL LYMPH NODE
  SPRYD3 MUTATED                     4
  SPRYD3 WILD-TYPE                 166
D115V4, multiclass
                                           clus
vv                                          SPRYD3 MUTATED SPRYD3 WILD-TYPE
  DISTANT METASTASIS                                     1               34
  PRIMARY TUMOR                                          0                4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE              2               56
  REGIONAL LYMPH NODE                                    4              166
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  SPRYD3 MUTATED             0       0       1        0        1        3
  SPRYD3 WILD-TYPE          10       6      21       10       23       14
                  vv
clus               STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  SPRYD3 MUTATED           0         0         0         1          1
  SPRYD3 WILD-TYPE        10        14         9        30         12
                  vv
clus               STAGE IIIB STAGE IIIC STAGE IV
  SPRYD3 MUTATED            0          0        0
  SPRYD3 WILD-TYPE         22         44       12
D115V5, multiclass
             clus
vv            SPRYD3 MUTATED SPRYD3 WILD-TYPE
  I OR II NOS              0               10
  STAGE 0                  0                6
  STAGE I                  1               21
  STAGE IA                 0               10
  STAGE IB                 1               23
  STAGE II                 3               14
  STAGE IIA                0               10
  STAGE IIB                0               14
  STAGE IIC                0                9
  STAGE III                1               30
  STAGE IIIA               1               12
  STAGE IIIB               0               22
  STAGE IIIC               0               44
  STAGE IV                 0               12
[1] 14  2
[1] 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
  SPRYD3 MUTATED       1  1  3  2
  SPRYD3 WILD-TYPE    50 57 50 53
D115V6, multiclass
       clus
vv      SPRYD3 MUTATED SPRYD3 WILD-TYPE
  T0+T1              1               50
  T2                 1               57
  T3                 3               50
  T4                 2               53
[1] 4 2
[1] TRUE
[1] "dimension 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
  SPRYD3 MUTATED     5   1   1   0
  SPRYD3 WILD-TYPE 133  47  31  33
D115V7, multiclass
    clus
vv   SPRYD3 MUTATED SPRYD3 WILD-TYPE
  N0              5              133
  N1              1               47
  N2              1               31
  N3              0               33
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                M0  M1 M1A M1B M1C
  SPRYD3 MUTATED     7   0   0   0   0
  SPRYD3 WILD-TYPE 233   4   2   2   5
D115V8, multiclass
     clus
vv    SPRYD3 MUTATED SPRYD3 WILD-TYPE
  M0               7              233
  M1               0                4
  M1A              0                2
  M1B              0                2
  M1C              0                5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D115V9, binary
                  cls
clus                0  1
  SPRYD3 MUTATED    4  1
  SPRYD3 WILD-TYPE 98 66
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SPRYD3 MUTATED      4    1
  SPRYD3 WILD-TYPE   98   66
     clus
vv    SPRYD3 MUTATED SPRYD3 WILD-TYPE
  NO               4               98
  YES              1               66
[1] 2 2
[1] FALSE
D115V10, binary
                  cls
clus                 0   1
  SPRYD3 MUTATED     0   7
  SPRYD3 WILD-TYPE  33 228
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SPRYD3 MUTATED      0    7
  SPRYD3 WILD-TYPE   33  228
     clus
vv    SPRYD3 MUTATED SPRYD3 WILD-TYPE
  NO               0               33
  YES              7              228
[1] 2 2
[1] FALSE
D115V11, continuous
D115V12, binary
                  cls
clus                 0   1
  SPRYD3 MUTATED     1   6
  SPRYD3 WILD-TYPE 102 159
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SPRYD3 MUTATED      1    6
  SPRYD3 WILD-TYPE  102  159
        clus
vv       SPRYD3 MUTATED SPRYD3 WILD-TYPE
  FEMALE              1              102
  MALE                6              159
[1] 2 2
[1] FALSE
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SPRYD3 MUTATED       0                         0     7
  SPRYD3 WILD-TYPE     3                         1   257
D115V13, multiclass
                           clus
vv                          SPRYD3 MUTATED SPRYD3 WILD-TYPE
  ASIAN                                  0                3
  BLACK OR AFRICAN AMERICAN              0                1
  WHITE                                  7              257
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D115V14, binary
                  cls
clus                 0   1
  SPRYD3 MUTATED     0   7
  SPRYD3 WILD-TYPE   3 254
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SPRYD3 MUTATED      0    7
  SPRYD3 WILD-TYPE    3  254
                        clus
vv                       SPRYD3 MUTATED SPRYD3 WILD-TYPE
  HISPANIC OR LATINO                  0                3
  NOT HISPANIC OR LATINO              7              254
[1] 2 2
[1] FALSE

Clustering(116) Variable = MAP3K5 MUTATION ANALYSIS
D116V1, survival
                  sevent
clus2                0   1
  MAP3K5 MUTATED     7   9
  MAP3K5 WILD-TYPE 121 121
  MAP3K5 MUTATED MAP3K5 WILD-TYPE 
              16              242 
  MAP3K5 MUTATED MAP3K5 WILD-TYPE 
               9              121 
$`MAP3K5 MUTATED`
TCGA-D3-A1Q6 TCGA-D3-A2JF TCGA-D3-A51J TCGA-EE-A29E TCGA-EE-A2A2 TCGA-EE-A2MI 
       70.16        30.87        41.10        38.63        23.90        14.56 
TCGA-EE-A2MJ TCGA-EE-A2MR TCGA-EE-A3AA TCGA-EE-A3J5 TCGA-ER-A193 TCGA-ER-A19M 
       63.42        29.65       124.31        21.60        31.40        28.60 
TCGA-ER-A2NH TCGA-FS-A1Z3 TCGA-FS-A4F5 TCGA-GN-A266 
       11.74        14.24        28.73        10.13 

$`MAP3K5 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       16.47         8.52       111.09        32.42       110.79        28.08 
TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 
       22.55        45.83        81.24        10.29        85.32         8.38 
TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JG 
       21.14        88.50        68.22        69.90        11.41         7.50 
TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP 
       36.16         6.31        92.42        56.19        64.44        45.11 
TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC 
      114.67        15.25        46.98        46.32        82.29        61.38 
TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU 
       13.32        24.00         6.31         9.34       103.59        26.37 
TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51K TCGA-D3-A51N 
        5.39        80.22        42.71        15.09        17.72         8.84 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS 
       20.48        13.94        52.01        47.87         1.55         6.97 
TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC 
       23.11         4.01         2.89         9.90        11.31        13.22 
TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 
       48.79        35.80        51.12        10.03        39.19        13.68 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB 
        9.99        44.52        36.69        25.15         4.93        22.36 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q 
        6.64        19.36         7.00        17.56        14.83        13.15 
TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y 
        0.20         0.00         0.00        13.22        11.57        10.55 
TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 
        6.31         8.12         1.12         1.35        12.20         5.13 
TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I 
        4.31        36.07         4.34         5.13         9.21         1.18 
TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29H 
        7.99         9.90        37.97        11.15         8.55         4.41 
TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R 
        1.08        27.12         9.50        12.03         8.09         8.84 
TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 
        9.99         2.43         8.68         8.09        11.31        49.22 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE 
        9.67         8.94        39.39        34.29        17.98        34.92 
TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM 
       47.21        30.08        19.43        16.01        35.54        28.31 
TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT 
       33.83        30.84         5.42         1.15        13.02        34.98 
TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC 
       36.33         8.84        98.27         2.70         6.18        47.51 
TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MK TCGA-EE-A2ML 
        9.53        29.46        44.25         7.96       111.78       111.91 
TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MS TCGA-EE-A2MT 
       56.02        25.08        26.99        21.60        27.16        23.05 
TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF 
        5.56       122.73        25.84         3.68        30.15        13.81 
TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 
       15.95        12.72         3.22        22.92        21.60        16.14 
TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 
       22.22        27.35         0.46        13.94        33.60        18.61 
TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C 
       12.95        38.40         5.72        76.41        25.18         3.78 
TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J 
        3.52        11.90        11.11       114.15        34.88         4.21 
TCGA-ER-A19L TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W 
       13.45        42.84        34.68         9.57        36.07        17.72 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG 
       78.44        11.80         1.87         1.51        13.08        12.62 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A 
        9.04         6.58        22.49         1.71        18.41        85.74 
TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z4 
        4.90        64.47         3.45        11.01        23.80        15.52 
TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE 
        7.33         7.30         3.39        20.38         8.22        19.53 
TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM 
       11.08         7.17        30.87        12.92        12.89        47.38 
TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU 
       52.08         8.65         8.81        49.15        40.64         8.68 
TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 
       27.39         0.82         5.23        53.85         7.36        14.20 
TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 
       10.78         5.98         6.41         2.27         0.20         0.99 
TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 
        0.13         0.16         0.43         9.90         7.23        12.85 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
       24.85        31.33        84.72        16.24        15.42        12.16 
TCGA-GN-A26D TCGA-QB-A6FS 
       14.70         5.79 

  MAP3K5 MUTATED MAP3K5 WILD-TYPE 
           10.13             0.00 
  MAP3K5 MUTATED MAP3K5 WILD-TYPE 
          124.31           122.73 
  MAP3K5 MUTATED MAP3K5 WILD-TYPE 
          29.190           13.875 
[1] "10.1 - 124.3 (29.2)" "0.0 - 122.7 (13.9)" 
[1] "hr=" "1.3"
D116V2, survival
                  sevent
clus2                0   1
  MAP3K5 MUTATED     7   9
  MAP3K5 WILD-TYPE 125 122
  MAP3K5 MUTATED MAP3K5 WILD-TYPE 
              16              247 
  MAP3K5 MUTATED MAP3K5 WILD-TYPE 
               9              122 
$`MAP3K5 MUTATED`
TCGA-D3-A1Q6 TCGA-D3-A2JF TCGA-D3-A51J TCGA-EE-A29E TCGA-EE-A2A2 TCGA-EE-A2MI 
       71.80        48.76       131.90        39.62        24.43       204.66 
TCGA-EE-A2MJ TCGA-EE-A2MR TCGA-EE-A3AA TCGA-EE-A3J5 TCGA-ER-A193 TCGA-ER-A19M 
       96.23       103.56       124.31        36.95        31.40        61.05 
TCGA-ER-A2NH TCGA-FS-A1Z3 TCGA-FS-A4F5 TCGA-GN-A266 
       32.05        20.91        28.73        10.13 

$`MAP3K5 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       16.57        16.67       112.04       112.57       133.25        28.08 
TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 
       31.59        90.90        95.74        43.43       103.10        65.49 
TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JG 
       23.77       115.53       168.00        69.90        11.87       113.52 
TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP 
       42.08        12.10       171.58        56.19        66.08        45.11 
TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC 
      130.72        58.06        46.98        46.32       166.52        86.93 
TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU 
       60.23        24.53        13.87         9.34       103.59        39.75 
TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51K TCGA-D3-A51N 
       21.47       161.85        43.69        40.14        18.38        10.03 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS 
       51.68        15.06       135.75       137.92       166.19         7.43 
TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 
      125.19       151.53        54.67         3.65         6.41        11.34 
TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1HW 
        3.25         9.90        25.18        66.25        48.89        36.03 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 
      117.21        20.38       194.83       176.55        35.93       107.34 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
       61.18        53.92        65.92        23.44        68.09        28.60 
TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG 
       10.49       215.44        15.68        13.87        10.16        45.11 
TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z 
       35.01         3.55        52.01        29.82        27.22         8.65 
TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 
       94.98        33.73        14.70        26.89        68.15         4.96 
TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A 
      109.64       151.27        78.87       168.26        13.55        63.35 
TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L 
       80.61        47.84        13.97        72.07        32.19         2.60 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S 
       44.35        18.61        56.42        37.35        14.47        55.92 
TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A5 
       25.87       171.55        17.92        46.82       102.90        39.29 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH 
       58.75        47.54        67.43       314.56       135.95       208.04 
TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN 
       48.72        89.33        54.74        79.66        75.48        90.97 
TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU 
      101.95        13.91        14.30        55.59        44.88        94.82 
TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD 
       21.67       129.27        28.83        19.76        61.51        47.28 
TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM 
      103.27       103.20        16.96       144.76       203.05       167.90 
TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU 
       47.54       248.65        43.23       136.47        41.59        53.26 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG 
      122.73        25.84         3.68        54.51        13.81        23.47 
TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA 
      138.81       172.18       127.20        64.08        34.32        53.19 
TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 
       27.35        33.40       101.79       148.08        35.44        13.94 
TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D 
       50.76         9.17        77.75        98.40        48.89        12.59 
TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L 
       13.02        26.37       268.93       152.35         6.44       131.51 
TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 
       44.05       162.08        50.89        37.25       148.18        79.99 
TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES 
       43.82        23.34        20.15        16.37        31.27       247.04 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
       80.32        46.98        33.21        92.98       174.21         4.90 
TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1Z7 
      216.92        48.59       228.59       202.65        28.08         7.79 
TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF 
       27.72        48.85       357.37        53.52        40.27        15.45 
TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP 
        9.70        32.75        47.38        23.93       101.26        74.73 
TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW 
      133.55        11.41       148.80        53.16        26.56        49.48 
TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 
       27.09        27.02        77.82        66.67       174.84        12.43 
TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU 
       26.73        49.45        77.88         0.20        22.92        47.54 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 
        0.16         2.40         9.90         7.23        14.04       120.46 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D 
      117.93        84.72        64.44        62.79        32.48        39.58 
TCGA-QB-A6FS 
        6.67 

  MAP3K5 MUTATED MAP3K5 WILD-TYPE 
           10.13             0.16 
  MAP3K5 MUTATED MAP3K5 WILD-TYPE 
          204.66           357.37 
  MAP3K5 MUTATED MAP3K5 WILD-TYPE 
           44.19            48.59 
[1] "10.1 - 204.7 (44.2)" "0.2 - 357.4 (48.6)" 
[1] "hr=" "1.1"
D116V3, continuous
                  vv
clus               DISTANT METASTASIS PRIMARY TUMOR
  MAP3K5 MUTATED                    2             0
  MAP3K5 WILD-TYPE                 33             4
                  vv
clus               REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  MAP3K5 MUTATED                                           6
  MAP3K5 WILD-TYPE                                        52
                  vv
clus               REGIONAL LYMPH NODE
  MAP3K5 MUTATED                     9
  MAP3K5 WILD-TYPE                 161
D116V4, multiclass
                                           clus
vv                                          MAP3K5 MUTATED MAP3K5 WILD-TYPE
  DISTANT METASTASIS                                     2               33
  PRIMARY TUMOR                                          0                4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE              6               52
  REGIONAL LYMPH NODE                                    9              161
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  MAP3K5 MUTATED             0       1       1        1        2        0
  MAP3K5 WILD-TYPE          10       5      21        9       22       17
                  vv
clus               STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  MAP3K5 MUTATED           0         2         0         5          0
  MAP3K5 WILD-TYPE        10        12         9        26         13
                  vv
clus               STAGE IIIB STAGE IIIC STAGE IV
  MAP3K5 MUTATED            1          2        1
  MAP3K5 WILD-TYPE         21         42       11
D116V5, multiclass
             clus
vv            MAP3K5 MUTATED MAP3K5 WILD-TYPE
  I OR II NOS              0               10
  STAGE 0                  1                5
  STAGE I                  1               21
  STAGE IA                 1                9
  STAGE IB                 2               22
  STAGE II                 0               17
  STAGE IIA                0               10
  STAGE IIB                2               12
  STAGE IIC                0                9
  STAGE III                5               26
  STAGE IIIA               0               13
  STAGE IIIB               1               21
  STAGE IIIC               2               42
  STAGE IV                 1               11
[1] 14  2
[1] 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
  MAP3K5 MUTATED       3  3  2  6
  MAP3K5 WILD-TYPE    48 55 51 49
D116V6, multiclass
       clus
vv      MAP3K5 MUTATED MAP3K5 WILD-TYPE
  T0+T1              3               48
  T2                 3               55
  T3                 2               51
  T4                 6               49
[1] 4 2
[1] TRUE
[1] "dimension 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
  MAP3K5 MUTATED     9   6   0   1
  MAP3K5 WILD-TYPE 129  42  32  32
D116V7, multiclass
    clus
vv   MAP3K5 MUTATED MAP3K5 WILD-TYPE
  N0              9              129
  N1              6               42
  N2              0               32
  N3              1               32
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                M0  M1 M1A M1B M1C
  MAP3K5 MUTATED    15   1   0   0   0
  MAP3K5 WILD-TYPE 225   3   2   2   5
D116V8, multiclass
     clus
vv    MAP3K5 MUTATED MAP3K5 WILD-TYPE
  M0              15              225
  M1               1                3
  M1A              0                2
  M1B              0                2
  M1C              0                5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D116V9, binary
                  cls
clus                0  1
  MAP3K5 MUTATED    9  1
  MAP3K5 WILD-TYPE 93 66
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAP3K5 MUTATED      9    1
  MAP3K5 WILD-TYPE   93   66
     clus
vv    MAP3K5 MUTATED MAP3K5 WILD-TYPE
  NO               9               93
  YES              1               66
[1] 2 2
[1] FALSE
D116V10, binary
                  cls
clus                 0   1
  MAP3K5 MUTATED     4  13
  MAP3K5 WILD-TYPE  29 222
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAP3K5 MUTATED      4   13
  MAP3K5 WILD-TYPE   29  222
     clus
vv    MAP3K5 MUTATED MAP3K5 WILD-TYPE
  NO               4               29
  YES             13              222
[1] 2 2
[1] FALSE
D116V11, continuous
D116V12, binary
                  cls
clus                 0   1
  MAP3K5 MUTATED     2  15
  MAP3K5 WILD-TYPE 101 150
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAP3K5 MUTATED      2   15
  MAP3K5 WILD-TYPE  101  150
        clus
vv       MAP3K5 MUTATED MAP3K5 WILD-TYPE
  FEMALE              2              101
  MALE               15              150
[1] 2 2
[1] FALSE
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MAP3K5 MUTATED       0                         0    17
  MAP3K5 WILD-TYPE     3                         1   247
D116V13, multiclass
                           clus
vv                          MAP3K5 MUTATED MAP3K5 WILD-TYPE
  ASIAN                                  0                3
  BLACK OR AFRICAN AMERICAN              0                1
  WHITE                                 17              247
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D116V14, binary
                  cls
clus                 0   1
  MAP3K5 MUTATED     0  17
  MAP3K5 WILD-TYPE   3 244
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAP3K5 MUTATED      0   17
  MAP3K5 WILD-TYPE    3  244
                        clus
vv                       MAP3K5 MUTATED MAP3K5 WILD-TYPE
  HISPANIC OR LATINO                  0                3
  NOT HISPANIC OR LATINO             17              244
[1] 2 2
[1] FALSE

Clustering(117) Variable = CASP8 MUTATION ANALYSIS
D117V1, survival
                 sevent
clus2               0   1
  CASP8 MUTATED     4   2
  CASP8 WILD-TYPE 124 128
  CASP8 MUTATED CASP8 WILD-TYPE 
              6             252 
  CASP8 MUTATED CASP8 WILD-TYPE 
              2             128 
$`CASP8 MUTATED`
TCGA-D3-A2JC TCGA-EE-A29M TCGA-EE-A2M6 TCGA-EE-A3AG TCGA-EE-A3JI TCGA-FS-A1Z3 
       69.90        27.12        98.27        15.95        33.60        14.24 

$`CASP8 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.47         8.52       111.09        32.42        70.16       110.79 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       28.08        22.55        45.83        81.24        10.29        85.32 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JD TCGA-D3-A2JF 
        8.38        21.14        88.50        68.22        11.41        30.87 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO 
        7.50        36.16         6.31        92.42        56.19        64.44 
TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB 
       45.11       114.67        15.25        46.98        46.32        82.29 
TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR 
       61.38        13.32        24.00         6.31         9.34       103.59 
TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J 
       26.37         5.39        80.22        42.71        15.09        41.10 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO 
       17.72         8.84        20.48        13.94        52.01        47.87 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 
        1.55         6.97        23.11         4.01         2.89         9.90 
TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 
       11.31        13.22        48.79        35.80        51.12        10.03 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 
       39.19        13.68         9.99        44.52        36.69        25.15 
TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 
        4.93        22.36         6.64        19.36         7.00        17.56 
TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN 
       14.83        13.15         0.20         0.00         0.00        13.22 
TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 
       11.57        10.55         6.31         8.12         1.12         1.35 
TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F 
       12.20         5.13         4.31        36.07         4.34         5.13 
TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D 
        9.21         1.18         7.99         9.90        37.97        11.15 
TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P 
       38.63         8.55         4.41         1.08         9.50        12.03 
TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X 
        8.09         8.84         9.99         2.43         8.68         8.09 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB 
       11.31        49.22        23.90         9.67         8.94        39.39 
TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ 
       34.29        17.98        34.92        47.21        30.08        19.43 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP 
       16.01        35.54        28.31        33.83        30.84         5.42 
TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M7 
        1.15        13.02        34.98        36.33         8.84         2.70 
TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH 
        6.18        47.51         9.53        29.46        44.25         7.96 
TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN 
       14.56        63.42       111.78       111.91        56.02        25.08 
TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU 
       26.99        21.60        29.65        27.16        23.05         5.56 
TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF 
      124.31       122.73        25.84         3.68        30.15        13.81 
TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 
       12.72         3.22        22.92        21.60        21.60        16.14 
TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A195 
       22.22        27.35         0.46        13.94        31.40        18.61 
TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C 
       12.95        38.40         5.72        76.41        25.18         3.78 
TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J 
        3.52        11.90        11.11       114.15        34.88         4.21 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S 
       13.45        28.60        42.84        34.68         9.57        36.07 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF 
       17.72        78.44        11.80         1.87         1.51        13.08 
TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL 
       12.62        11.74         9.04         6.58        22.49         1.71 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY 
       18.41        85.74         4.90        64.47         3.45        11.01 
TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC 
       23.80        15.52         7.33         7.30         3.39        20.38 
TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ 
        8.22        19.53        11.08         7.17        30.87        12.92 
TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS 
       12.89        47.38        52.08         8.65         8.81        49.15 
TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 
       40.64         8.68        27.39         0.82         5.23        53.85 
TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC 
        7.36        28.73        14.20        10.78         5.98         6.41 
TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY 
        2.27         0.20         0.99         0.13         0.16         0.43 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        9.90         7.23        12.85        24.85        31.33        84.72 
TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS 
       10.13        16.24        15.42        12.16        14.70         5.79 

  CASP8 MUTATED CASP8 WILD-TYPE 
          14.24            0.00 
  CASP8 MUTATED CASP8 WILD-TYPE 
          98.27          124.31 
  CASP8 MUTATED CASP8 WILD-TYPE 
          30.36           14.38 
[1] "14.2 - 98.3 (30.4)" "0.0 - 124.3 (14.4)"
[1] "hr=" "2.4"
D117V2, survival
                 sevent
clus2               0   1
  CASP8 MUTATED     4   2
  CASP8 WILD-TYPE 128 129
  CASP8 MUTATED CASP8 WILD-TYPE 
              6             257 
  CASP8 MUTATED CASP8 WILD-TYPE 
              2             129 
$`CASP8 MUTATED`
TCGA-D3-A2JC TCGA-EE-A29M TCGA-EE-A2M6 TCGA-EE-A3AG TCGA-EE-A3JI TCGA-FS-A1Z3 
       69.90        44.35       129.27        23.47       148.08        20.91 

$`CASP8 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.57        16.67       112.04       112.57        71.80       133.25 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       28.08        31.59        90.90        95.74        43.43       103.10 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JD TCGA-D3-A2JF 
       65.49        23.77       115.53       168.00        11.87        48.76 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO 
      113.52        42.08        12.10       171.58        56.19        66.08 
TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB 
       45.11       130.72        58.06        46.98        46.32       166.52 
TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR 
       86.93        60.23        24.53        13.87         9.34       103.59 
TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J 
       39.75        21.47       161.85        43.69        40.14       131.90 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO 
       18.38        10.03        51.68        15.06       135.75       137.92 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW 
      166.19         7.43       125.19       151.53        54.67         3.65 
TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC 
        6.41        11.34         3.25         9.90        25.18        66.25 
TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 
       48.89        36.03       117.21        20.38       194.83       176.55 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB 
       35.93       107.34        61.18        53.92        65.92        23.44 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q 
       68.09        28.60        10.49       215.44        15.68        13.87 
TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X 
       10.16        45.11        35.01         3.55        52.01        29.82 
TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 
       27.22         8.65        94.98        33.73        14.70        26.89 
TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H 
       68.15         4.96       109.64       151.27        78.87       168.26 
TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E 
       13.55        63.35        80.61        47.84        13.97        39.62 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
       72.07        32.19         2.60        18.61        56.42        37.35 
TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 
       14.47        55.92        25.87       171.55        17.92        46.82 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC 
      102.90        24.43        39.29        58.75        47.54        67.43 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK 
      314.56       135.95       208.04        48.72        89.33        54.74 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR 
       79.66        75.48        90.97       101.95        13.91        14.30 
TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M7 TCGA-EE-A2M8 
       55.59        44.88        94.82        21.67        28.83        19.76 
TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI 
       61.51        47.28       103.27       103.20        16.96       204.66 
TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP 
       96.23       144.76       203.05       167.90        47.54       248.65 
TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA 
       43.23       103.56       136.47        41.59        53.26       124.31 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AH 
      122.73        25.84         3.68        54.51        13.81       138.81 
TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA 
      172.18       127.20        36.95        64.08        34.32        53.19 
TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 
       27.35        33.40       101.79        31.40        35.44        13.94 
TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D 
       50.76         9.17        77.75        98.40        48.89        12.59 
TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L 
       13.02        26.37       268.93       152.35         6.44       131.51 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W 
       61.05        44.05       162.08        50.89        37.25       148.18 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG 
       79.99        43.82        23.34        20.15        16.37        31.27 
TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN 
       32.05       247.04        80.32        46.98        33.21        92.98 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 
      174.21         4.90       216.92        48.59       228.59       202.65 
TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD 
       28.08         7.79        27.72        48.85       357.37        53.52 
TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK 
       40.27        15.45         9.70        32.75        47.38        23.93 
TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT 
      101.26        74.73       133.55        11.41       148.80        53.16 
TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 
       26.56        49.48        27.09        27.02        77.82        66.67 
TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD 
       28.73       174.84        12.43        26.73        49.45        77.88 
TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
        0.20        22.92        47.54         0.16         2.40         9.90 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 
        7.23        14.04       120.46       117.93        84.72        10.13 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS 
       64.44        62.79        32.48        39.58         6.67 

  CASP8 MUTATED CASP8 WILD-TYPE 
          20.91            0.16 
  CASP8 MUTATED CASP8 WILD-TYPE 
         148.08          357.37 
  CASP8 MUTATED CASP8 WILD-TYPE 
         57.125          48.590 
[1] "20.9 - 148.1 (57.1)" "0.2 - 357.4 (48.6)" 
[1] "hr=" "1.5"
D117V3, continuous
                 vv
clus              DISTANT METASTASIS PRIMARY TUMOR
  CASP8 MUTATED                    2             0
  CASP8 WILD-TYPE                 33             4
                 vv
clus              REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  CASP8 MUTATED                                           1                   5
  CASP8 WILD-TYPE                                        57                 165
D117V4, multiclass
                                           clus
vv                                          CASP8 MUTATED CASP8 WILD-TYPE
  DISTANT METASTASIS                                    2              33
  PRIMARY TUMOR                                         0               4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE             1              57
  REGIONAL LYMPH NODE                                   5             165
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  CASP8 MUTATED             2       0       2        0        1        0
  CASP8 WILD-TYPE           8       6      20       10       23       17
                 vv
clus              STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  CASP8 MUTATED           0         0         0         2          0          0
  CASP8 WILD-TYPE        10        14         9        29         13         22
                 vv
clus              STAGE IIIC STAGE IV
  CASP8 MUTATED            0        1
  CASP8 WILD-TYPE         44       11
D117V5, multiclass
             clus
vv            CASP8 MUTATED CASP8 WILD-TYPE
  I OR II NOS             2               8
  STAGE 0                 0               6
  STAGE I                 2              20
  STAGE IA                0              10
  STAGE IB                1              23
  STAGE II                0              17
  STAGE IIA               0              10
  STAGE IIB               0              14
  STAGE IIC               0               9
  STAGE III               2              29
  STAGE IIIA              0              13
  STAGE IIIB              0              22
  STAGE IIIC              0              44
  STAGE IV                1              11
[1] 14  2
[1] 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
  CASP8 MUTATED       3  3  0  0
  CASP8 WILD-TYPE    48 55 53 55
D117V6, multiclass
       clus
vv      CASP8 MUTATED CASP8 WILD-TYPE
  T0+T1             3              48
  T2                3              55
  T3                0              53
  T4                0              55
[1] 4 2
[1] TRUE
[1] "dimension 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
  CASP8 MUTATED     6   0   2   0
  CASP8 WILD-TYPE 132  48  30  33
D117V7, multiclass
    clus
vv   CASP8 MUTATED CASP8 WILD-TYPE
  N0             6             132
  N1             0              48
  N2             2              30
  N3             0              33
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               M0  M1 M1A M1B M1C
  CASP8 MUTATED     7   1   0   0   0
  CASP8 WILD-TYPE 233   3   2   2   5
D117V8, multiclass
     clus
vv    CASP8 MUTATED CASP8 WILD-TYPE
  M0              7             233
  M1              1               3
  M1A             0               2
  M1B             0               2
  M1C             0               5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D117V9, binary
                 cls
clus               0  1
  CASP8 MUTATED    3  0
  CASP8 WILD-TYPE 99 67
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CASP8 MUTATED      3    0
  CASP8 WILD-TYPE   99   67
     clus
vv    CASP8 MUTATED CASP8 WILD-TYPE
  NO              3              99
  YES             0              67
[1] 2 2
[1] FALSE
D117V10, binary
                 cls
clus                0   1
  CASP8 MUTATED     3   5
  CASP8 WILD-TYPE  30 230
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CASP8 MUTATED      3    5
  CASP8 WILD-TYPE   30  230
     clus
vv    CASP8 MUTATED CASP8 WILD-TYPE
  NO              3              30
  YES             5             230
[1] 2 2
[1] FALSE
D117V11, continuous
D117V12, binary
                 cls
clus                0   1
  CASP8 MUTATED     5   3
  CASP8 WILD-TYPE  98 162
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CASP8 MUTATED      5    3
  CASP8 WILD-TYPE   98  162
        clus
vv       CASP8 MUTATED CASP8 WILD-TYPE
  FEMALE             5              98
  MALE               3             162
[1] 2 2
[1] FALSE
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CASP8 MUTATED       0                         0     8
  CASP8 WILD-TYPE     3                         1   256
D117V13, multiclass
                           clus
vv                          CASP8 MUTATED CASP8 WILD-TYPE
  ASIAN                                 0               3
  BLACK OR AFRICAN AMERICAN             0               1
  WHITE                                 8             256
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D117V14, binary
                 cls
clus                0   1
  CASP8 MUTATED     0   8
  CASP8 WILD-TYPE   3 253
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CASP8 MUTATED      0    8
  CASP8 WILD-TYPE    3  253
                        clus
vv                       CASP8 MUTATED CASP8 WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO             8             253
[1] 2 2
[1] FALSE

Clustering(118) Variable = SNCAIP MUTATION ANALYSIS
D118V1, survival
                  sevent
clus2                0   1
  SNCAIP MUTATED    27  18
  SNCAIP WILD-TYPE 101 112
  SNCAIP MUTATED SNCAIP WILD-TYPE 
              45              213 
  SNCAIP MUTATED SNCAIP WILD-TYPE 
              18              112 
$`SNCAIP MUTATED`
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A2JA TCGA-D3-A2JO TCGA-D3-A51E 
       70.16       110.79        28.08        88.50        64.44        80.22 
TCGA-D3-A51T TCGA-D3-A5GO TCGA-D9-A3Z1 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-DA-A1HW 
       13.94        47.87         4.01         9.90        11.31        35.80 
TCGA-DA-A1I1 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A3F3 TCGA-EE-A182 TCGA-EE-A20C 
       39.19         9.99        44.52         7.00         1.35         4.34 
TCGA-EE-A20F TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29M TCGA-EE-A2A1 TCGA-EE-A2GB 
        5.13        11.15        38.63        27.12        49.22        39.39 
TCGA-EE-A2GC TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2MD 
       34.29        30.08        19.43        33.83        30.84         9.53 
TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A3AE TCGA-EE-A3AG TCGA-EE-A3JA TCGA-EE-A3JD 
       29.65        27.16        30.15        15.95        22.22        27.35 
TCGA-ER-A19E TCGA-ER-A19F TCGA-FS-A1Z3 TCGA-FS-A1ZS TCGA-FS-A1ZW TCGA-FS-A4F5 
       11.90        11.11        14.24        49.15        27.39        28.73 
TCGA-FS-A4FC TCGA-FW-A3R5 TCGA-GN-A266 
        6.41         0.99        10.13 

$`SNCAIP WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q9 TCGA-D3-A1QA 
       16.47         8.52       111.09        32.42        22.55        45.83 
TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JB 
       81.24        10.29        85.32         8.38        21.14        68.22 
TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK 
       69.90        11.41        30.87         7.50        36.16         6.31 
TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 
       92.42        56.19        45.11       114.67        15.25        46.98 
TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML 
       46.32        82.29        61.38        13.32        24.00         6.31 
TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51F TCGA-D3-A51H 
        9.34       103.59        26.37         5.39        42.71        15.09 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A5GN TCGA-D3-A5GR 
       41.10        17.72         8.84        20.48        52.01         1.55 
TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z3 TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1HY 
        6.97        23.11         2.89        13.22        48.79        51.12 
TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB 
       10.03        13.68        36.69        25.15         4.93        22.36 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R 
        6.64        19.36        17.56        14.83        13.15         0.20 
TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z 
        0.00         0.00        13.22        11.57        10.55         6.31 
TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B 
        8.12         1.12        12.20         5.13         4.31        36.07 
TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29G 
        9.21         1.18         7.99         9.90        37.97         8.55 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R 
        4.41         1.08         9.50        12.03         8.09         8.84 
TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A2 
        9.99         2.43         8.68         8.09        11.31        23.90 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GK 
        9.67         8.94        17.98        34.92        47.21        16.01 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT 
       35.54        28.31         5.42         1.15        13.02        34.98 
TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC 
       36.33         8.84        98.27         2.70         6.18        47.51 
TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK 
       29.46        44.25         7.96        14.56        63.42       111.78 
TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MT 
      111.91        56.02        25.08        26.99        21.60        23.05 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AF 
        5.56       124.31       122.73        25.84         3.68        13.81 
TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 
       12.72         3.22        22.92        21.60        21.60        16.14 
TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 
        0.46        13.94        33.60        31.40        18.61        12.95 
TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D 
       38.40         5.72        76.41        25.18         3.78         3.52 
TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N 
      114.15        34.88         4.21        13.45        28.60        42.84 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
       34.68         9.57        36.07        17.72        78.44        11.80 
TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES 
        1.87         1.51        13.08        12.62        11.74         9.04 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
        6.58        22.49         1.71        18.41        85.74         4.90 
TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1Z7 
       64.47         3.45        11.01        23.80        15.52         7.33 
TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF 
        7.30         3.39        20.38         8.22        19.53        11.08 
TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP 
        7.17        30.87        12.92        12.89        47.38        52.08 
TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZY TCGA-FS-A1ZZ 
        8.65         8.81        40.64         8.68         0.82         5.23 
TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FD 
       53.85         7.36        14.20        10.78         5.98         2.27 
TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
        0.20         0.13         0.16         0.43         9.90         7.23 
TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 
       12.85        24.85        31.33        84.72        16.24        15.42 
TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS 
       12.16        14.70         5.79 

  SNCAIP MUTATED SNCAIP WILD-TYPE 
            0.99             0.00 
  SNCAIP MUTATED SNCAIP WILD-TYPE 
          110.79           124.31 
  SNCAIP MUTATED SNCAIP WILD-TYPE 
           27.35            13.68 
[1] "1.0 - 110.8 (27.4)" "0.0 - 124.3 (13.7)"
[1] "hr=" "1.6"
D118V2, survival
                  sevent
clus2                0   1
  SNCAIP MUTATED    27  18
  SNCAIP WILD-TYPE 105 113
  SNCAIP MUTATED SNCAIP WILD-TYPE 
              45              218 
  SNCAIP MUTATED SNCAIP WILD-TYPE 
              18              113 
$`SNCAIP MUTATED`
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A2JA TCGA-D3-A2JO TCGA-D3-A51E 
       71.80       133.25        28.08       115.53        66.08       161.85 
TCGA-D3-A51T TCGA-D3-A5GO TCGA-D9-A3Z1 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-DA-A1HW 
       15.06       137.92        11.34         9.90        25.18        36.03 
TCGA-DA-A1I1 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A3F3 TCGA-EE-A182 TCGA-EE-A20C 
      194.83        35.93       107.34        10.49        14.70       151.27 
TCGA-EE-A20F TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29M TCGA-EE-A2A1 TCGA-EE-A2GB 
       78.87        13.97        39.62        44.35       102.90        47.54 
TCGA-EE-A2GC TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2MD 
       67.43        48.72        89.33        90.97       101.95        47.28 
TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A3AE TCGA-EE-A3AG TCGA-EE-A3JA TCGA-EE-A3JD 
      103.56       136.47        54.51        23.47        53.19        27.35 
TCGA-ER-A19E TCGA-ER-A19F TCGA-FS-A1Z3 TCGA-FS-A1ZS TCGA-FS-A1ZW TCGA-FS-A4F5 
       13.02        26.37        20.91       148.80        49.48        28.73 
TCGA-FS-A4FC TCGA-FW-A3R5 TCGA-GN-A266 
       49.45        22.92        10.13 

$`SNCAIP WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q9 TCGA-D3-A1QA 
       16.57        16.67       112.04       112.57        31.59        90.90 
TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JB 
       95.74        43.43       103.10        65.49        23.77       168.00 
TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK 
       69.90        11.87        48.76       113.52        42.08        12.10 
TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 
      171.58        56.19        45.11       130.72        58.06        46.98 
TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML 
       46.32       166.52        86.93        60.23        24.53        13.87 
TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51F TCGA-D3-A51H 
        9.34       103.59        39.75        21.47        43.69        40.14 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A5GN TCGA-D3-A5GR 
      131.90        18.38        10.03        51.68       135.75       166.19 
TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX 
        7.43       125.19       151.53        54.67         3.65         6.41 
TCGA-D9-A3Z3 TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I2 
        3.25        66.25        48.89       117.21        20.38       176.55 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
       61.18        53.92        65.92        23.44        68.09        28.60 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH 
      215.44        15.68        13.87        10.16        45.11        35.01 
TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 
        3.55        52.01        29.82        27.22         8.65        94.98 
TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20H 
       33.73        26.89        68.15         4.96       109.64       168.26 
TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29G TCGA-EE-A29H 
       13.55        63.35        80.61        47.84        72.07        32.19 
TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S 
        2.60        18.61        56.42        37.35        14.47        55.92 
TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A2 TCGA-EE-A2A5 
       25.87       171.55        17.92        46.82        24.43        39.29 
TCGA-EE-A2A6 TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GK TCGA-EE-A2GL 
       58.75       314.56       135.95       208.04        54.74        79.66 
TCGA-EE-A2GM TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU 
       75.48        13.91        14.30        55.59        44.88        94.82 
TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2ME 
       21.67       129.27        28.83        19.76        61.51       103.27 
TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML 
      103.20        16.96       204.66        96.23       144.76       203.05 
TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MT TCGA-EE-A2MU 
      167.90        47.54       248.65        43.23        41.59        53.26 
TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AH 
      124.31       122.73        25.84         3.68        13.81       138.81 
TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JE 
      172.18       127.20        36.95        64.08        34.32        33.40 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 
      101.79       148.08        31.40        35.44        13.94        50.76 
TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19G 
        9.17        77.75        98.40        48.89        12.59       268.93 
TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P 
      152.35         6.44       131.51        61.05        44.05       162.08 
TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
       50.89        37.25       148.18        79.99        43.82        23.34 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET 
       20.15        16.37        31.27        32.05       247.04        80.32 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW 
       46.98        33.21        92.98       174.21         4.90       216.92 
TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA 
       48.59       228.59       202.65        28.08         7.79        27.72 
TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG 
       48.85       357.37        53.52        40.27        15.45         9.70 
TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ 
       32.75        47.38        23.93       101.26        74.73       133.55 
TCGA-FS-A1ZR TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 
       11.41        53.16        26.56        27.09        27.02        77.82 
TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FD TCGA-FW-A3I3 
       66.67       174.84        12.43        26.73        77.88         0.20 
TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 
       47.54         0.16         2.40         9.90         7.23        14.04 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
      120.46       117.93        84.72        64.44        62.79        32.48 
TCGA-GN-A26D TCGA-QB-A6FS 
       39.58         6.67 

  SNCAIP MUTATED SNCAIP WILD-TYPE 
            9.90             0.16 
  SNCAIP MUTATED SNCAIP WILD-TYPE 
          194.83           357.37 
  SNCAIP MUTATED SNCAIP WILD-TYPE 
          48.720           48.215 
[1] "9.9 - 194.8 (48.7)" "0.2 - 357.4 (48.2)"
[1] "hr=" "1.2"
D118V3, continuous
                  vv
clus               DISTANT METASTASIS PRIMARY TUMOR
  SNCAIP MUTATED                    5             2
  SNCAIP WILD-TYPE                 30             2
                  vv
clus               REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  SNCAIP MUTATED                                          13
  SNCAIP WILD-TYPE                                        45
                  vv
clus               REGIONAL LYMPH NODE
  SNCAIP MUTATED                    26
  SNCAIP WILD-TYPE                 144
D118V4, multiclass
                                           clus
vv                                          SNCAIP MUTATED SNCAIP WILD-TYPE
  DISTANT METASTASIS                                     5               30
  PRIMARY TUMOR                                          2                2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE             13               45
  REGIONAL LYMPH NODE                                   26              144
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  SNCAIP MUTATED             1       2       2        3        6        5
  SNCAIP WILD-TYPE           9       4      20        7       18       12
                  vv
clus               STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  SNCAIP MUTATED           2         1         0         4          2
  SNCAIP WILD-TYPE         8        13         9        27         11
                  vv
clus               STAGE IIIB STAGE IIIC STAGE IV
  SNCAIP MUTATED            5          8        3
  SNCAIP WILD-TYPE         17         36        9
D118V5, multiclass
             clus
vv            SNCAIP MUTATED SNCAIP WILD-TYPE
  I OR II NOS              1                9
  STAGE 0                  2                4
  STAGE I                  2               20
  STAGE IA                 3                7
  STAGE IB                 6               18
  STAGE II                 5               12
  STAGE IIA                2                8
  STAGE IIB                1               13
  STAGE IIC                0                9
  STAGE III                4               27
  STAGE IIIA               2               11
  STAGE IIIB               5               17
  STAGE IIIC               8               36
  STAGE IV                 3                9
[1] 14  2
[1] 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
  SNCAIP MUTATED      11 13  9  5
  SNCAIP WILD-TYPE    40 45 44 50
D118V6, multiclass
       clus
vv      SNCAIP MUTATED SNCAIP WILD-TYPE
  T0+T1             11               40
  T2                13               45
  T3                 9               44
  T4                 5               50
[1] 4 2
[1] TRUE
[1] "dimension 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
  SNCAIP MUTATED    25  10   5   5
  SNCAIP WILD-TYPE 113  38  27  28
D118V7, multiclass
    clus
vv   SNCAIP MUTATED SNCAIP WILD-TYPE
  N0             25              113
  N1             10               38
  N2              5               27
  N3              5               28
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                M0  M1 M1A M1B M1C
  SNCAIP MUTATED    42   1   0   1   1
  SNCAIP WILD-TYPE 198   3   2   1   4
D118V8, multiclass
     clus
vv    SNCAIP MUTATED SNCAIP WILD-TYPE
  M0              42              198
  M1               1                3
  M1A              0                2
  M1B              1                1
  M1C              1                4
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D118V9, binary
                  cls
clus                0  1
  SNCAIP MUTATED   19 10
  SNCAIP WILD-TYPE 83 57
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SNCAIP MUTATED     19   10
  SNCAIP WILD-TYPE   83   57
     clus
vv    SNCAIP MUTATED SNCAIP WILD-TYPE
  NO              19               83
  YES             10               57
[1] 2 2
[1] FALSE
D118V10, binary
                  cls
clus                 0   1
  SNCAIP MUTATED     7  39
  SNCAIP WILD-TYPE  26 196
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SNCAIP MUTATED      7   39
  SNCAIP WILD-TYPE   26  196
     clus
vv    SNCAIP MUTATED SNCAIP WILD-TYPE
  NO               7               26
  YES             39              196
[1] 2 2
[1] FALSE
D118V11, continuous
D118V12, binary
                  cls
clus                 0   1
  SNCAIP MUTATED    15  31
  SNCAIP WILD-TYPE  88 134
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SNCAIP MUTATED     15   31
  SNCAIP WILD-TYPE   88  134
        clus
vv       SNCAIP MUTATED SNCAIP WILD-TYPE
  FEMALE             15               88
  MALE               31              134
[1] 2 2
[1] FALSE
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SNCAIP MUTATED       0                         0    46
  SNCAIP WILD-TYPE     3                         1   218
D118V13, multiclass
                           clus
vv                          SNCAIP MUTATED SNCAIP WILD-TYPE
  ASIAN                                  0                3
  BLACK OR AFRICAN AMERICAN              0                1
  WHITE                                 46              218
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D118V14, binary
                  cls
clus                 0   1
  SNCAIP MUTATED     0  46
  SNCAIP WILD-TYPE   3 215
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SNCAIP MUTATED      0   46
  SNCAIP WILD-TYPE    3  215
                        clus
vv                       SNCAIP MUTATED SNCAIP WILD-TYPE
  HISPANIC OR LATINO                  0                3
  NOT HISPANIC OR LATINO             46              215
[1] 2 2
[1] FALSE

Clustering(119) Variable = HLA-DRA MUTATION ANALYSIS
D119V1, survival
                   sevent
clus2                 0   1
  HLA-DRA MUTATED     7   4
  HLA-DRA WILD-TYPE 121 126
  HLA-DRA MUTATED HLA-DRA WILD-TYPE 
               11               247 
  HLA-DRA MUTATED HLA-DRA WILD-TYPE 
                4               126 
$`HLA-DRA MUTATED`
TCGA-D3-A1Q6 TCGA-D3-A2JO TCGA-D3-A3BZ TCGA-EE-A20C TCGA-EE-A29E TCGA-EE-A29R 
       70.16        64.44       114.67         4.34        38.63         8.84 
TCGA-EE-A2GO TCGA-EE-A2MI TCGA-EE-A2MR TCGA-FS-A4F5 TCGA-FW-A3R5 
       30.84        14.56        29.65        28.73         0.99 

$`HLA-DRA WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       16.47         8.52       111.09        32.42       110.79        28.08 
TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 
       22.55        45.83        81.24        10.29        85.32         8.38 
TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF 
       21.14        88.50        68.22        69.90        11.41        30.87 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JP 
        7.50        36.16         6.31        92.42        56.19        45.11 
TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE 
       15.25        46.98        46.32        82.29        61.38        13.32 
TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV 
       24.00         6.31         9.34       103.59        26.37         5.39 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N 
       80.22        42.71        15.09        41.10        17.72         8.84 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS 
       20.48        13.94        52.01        47.87         1.55         6.97 
TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC 
       23.11         4.01         2.89         9.90        11.31        13.22 
TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 
       48.79        35.80        51.12        10.03        39.19        13.68 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB 
        9.99        44.52        36.69        25.15         4.93        22.36 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q 
        6.64        19.36         7.00        17.56        14.83        13.15 
TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y 
        0.20         0.00         0.00        13.22        11.57        10.55 
TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 
        6.31         8.12         1.12         1.35        12.20         5.13 
TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A 
        4.31        36.07         5.13         9.21         1.18         7.99 
TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L 
        9.90        37.97        11.15         8.55         4.41         1.08 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29V 
       27.12         9.50        12.03         8.09         9.99         2.43 
TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 
        8.68         8.09        11.31        49.22        23.90         9.67 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH 
        8.94        39.39        34.29        17.98        34.92        47.21 
TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN 
       30.08        19.43        16.01        35.54        28.31        33.83 
TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 
        5.42         1.15        13.02        34.98        36.33         8.84 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME 
       98.27         2.70         6.18        47.51         9.53        29.46 
TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM 
       44.25         7.96        63.42       111.78       111.91        56.02 
TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU 
       25.08        26.99        21.60        27.16        23.05         5.56 
TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF 
      124.31       122.73        25.84         3.68        30.15        13.81 
TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 
       15.95        12.72         3.22        22.92        21.60        21.60 
TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI 
       16.14        22.22        27.35         0.46        13.94        33.60 
TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A 
       31.40        18.61        12.95        38.40         5.72        76.41 
TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G 
       25.18         3.78         3.52        11.90        11.11       114.15 
TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P 
       34.88         4.21        13.45        28.60        42.84        34.68 
TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
        9.57        36.07        17.72        78.44        11.80         1.87 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET 
        1.51        13.08        12.62        11.74         9.04         6.58 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW 
       22.49         1.71        18.41        85.74         4.90        64.47 
TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 
        3.45        11.01        23.80        14.24        15.52         7.33 
TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF 
        7.30         3.39        20.38         8.22        19.53        11.08 
TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP 
        7.17        30.87        12.92        12.89        47.38        52.08 
TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW 
        8.65         8.81        49.15        40.64         8.68        27.39 
TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 
        0.82         5.23        53.85         7.36        14.20        10.78 
TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV 
        5.98         6.41         2.27         0.20         0.13         0.16 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 
        0.43         9.90         7.23        12.85        24.85        31.33 
TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D 
       84.72        10.13        16.24        15.42        12.16        14.70 
TCGA-QB-A6FS 
        5.79 

  HLA-DRA MUTATED HLA-DRA WILD-TYPE 
             0.99              0.00 
  HLA-DRA MUTATED HLA-DRA WILD-TYPE 
           114.67            124.31 
  HLA-DRA MUTATED HLA-DRA WILD-TYPE 
            29.65             14.24 
[1] "1.0 - 114.7 (29.6)" "0.0 - 124.3 (14.2)"
[1] "hr=" "1.9"
D119V2, survival
                   sevent
clus2                 0   1
  HLA-DRA MUTATED     7   4
  HLA-DRA WILD-TYPE 125 127
  HLA-DRA MUTATED HLA-DRA WILD-TYPE 
               11               252 
  HLA-DRA MUTATED HLA-DRA WILD-TYPE 
                4               127 
$`HLA-DRA MUTATED`
TCGA-D3-A1Q6 TCGA-D3-A2JO TCGA-D3-A3BZ TCGA-EE-A20C TCGA-EE-A29E TCGA-EE-A29R 
       71.80        66.08       130.72       151.27        39.62        14.47 
TCGA-EE-A2GO TCGA-EE-A2MI TCGA-EE-A2MR TCGA-FS-A4F5 TCGA-FW-A3R5 
      101.95       204.66       103.56        28.73        22.92 

$`HLA-DRA WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       16.57        16.67       112.04       112.57       133.25        28.08 
TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 
       31.59        90.90        95.74        43.43       103.10        65.49 
TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF 
       23.77       115.53       168.00        69.90        11.87        48.76 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JP 
      113.52        42.08        12.10       171.58        56.19        45.11 
TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE 
       58.06        46.98        46.32       166.52        86.93        60.23 
TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV 
       24.53        13.87         9.34       103.59        39.75        21.47 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N 
      161.85        43.69        40.14       131.90        18.38        10.03 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS 
       51.68        15.06       135.75       137.92       166.19         7.43 
TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 
      125.19       151.53        54.67         3.65         6.41        11.34 
TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1HW 
        3.25         9.90        25.18        66.25        48.89        36.03 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 
      117.21        20.38       194.83       176.55        35.93       107.34 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
       61.18        53.92        65.92        23.44        68.09        28.60 
TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG 
       10.49       215.44        15.68        13.87        10.16        45.11 
TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z 
       35.01         3.55        52.01        29.82        27.22         8.65 
TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 
       94.98        33.73        14.70        26.89        68.15         4.96 
TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B 
      109.64        78.87       168.26        13.55        63.35        80.61 
TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M 
       47.84        13.97        72.07        32.19         2.60        44.35 
TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W 
       18.61        56.42        37.35        55.92        25.87       171.55 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 
       17.92        46.82       102.90        24.43        39.29        58.75 
TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI 
       47.54        67.43       314.56       135.95       208.04        48.72 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP 
       89.33        54.74        79.66        75.48        90.97        13.91 
TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 
       14.30        55.59        44.88        94.82        21.67       129.27 
TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG 
       28.83        19.76        61.51        47.28       103.27       103.20 
TCGA-EE-A2MH TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN 
       16.96        96.23       144.76       203.05       167.90        47.54 
TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA 
      248.65        43.23       136.47        41.59        53.26       124.31 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG 
      122.73        25.84         3.68        54.51        13.81        23.47 
TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 
      138.81       172.18       127.20        36.95        64.08        34.32 
TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 
       53.19        27.35        33.40       101.79       148.08        31.40 
TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B 
       35.44        13.94        50.76         9.17        77.75        98.40 
TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H 
       48.89        12.59        13.02        26.37       268.93       152.35 
TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q 
        6.44       131.51        61.05        44.05       162.08        50.89 
TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE 
       37.25       148.18        79.99        43.82        23.34        20.15 
TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV 
       16.37        31.27        32.05       247.04        80.32        46.98 
TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX 
       33.21        92.98       174.21         4.90       216.92        48.59 
TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA 
      228.59       202.65        20.91        28.08         7.79        27.72 
TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG 
       48.85       357.37        53.52        40.27        15.45         9.70 
TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ 
       32.75        47.38        23.93       101.26        74.73       133.55 
TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY 
       11.41       148.80        53.16        26.56        49.48        27.09 
TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB 
       27.02        77.82        66.67       174.84        12.43        26.73 
TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY 
       49.45        77.88         0.20        47.54         0.16         2.40 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        9.90         7.23        14.04       120.46       117.93        84.72 
TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS 
       10.13        64.44        62.79        32.48        39.58         6.67 

  HLA-DRA MUTATED HLA-DRA WILD-TYPE 
            14.47              0.16 
  HLA-DRA MUTATED HLA-DRA WILD-TYPE 
           204.66            357.37 
  HLA-DRA MUTATED HLA-DRA WILD-TYPE 
            71.80             47.69 
[1] "14.5 - 204.7 (71.8)" "0.2 - 357.4 (47.7)" 
[1] "hr=" "1.7"
D119V3, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  HLA-DRA MUTATED                    1             0
  HLA-DRA WILD-TYPE                 34             4
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  HLA-DRA MUTATED                                           4
  HLA-DRA WILD-TYPE                                        54
                   vv
clus                REGIONAL LYMPH NODE
  HLA-DRA MUTATED                     6
  HLA-DRA WILD-TYPE                 164
D119V4, multiclass
                                           clus
vv                                          HLA-DRA MUTATED HLA-DRA WILD-TYPE
  DISTANT METASTASIS                                      1                34
  PRIMARY TUMOR                                           0                 4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE               4                54
  REGIONAL LYMPH NODE                                     6               164
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  HLA-DRA MUTATED             0       1       1        0        1        1
  HLA-DRA WILD-TYPE          10       5      21       10       23       16
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  HLA-DRA MUTATED           0         2         0         2          0
  HLA-DRA WILD-TYPE        10        12         9        29         13
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  HLA-DRA MUTATED            1          2        0
  HLA-DRA WILD-TYPE         21         42       12
D119V5, multiclass
             clus
vv            HLA-DRA MUTATED HLA-DRA WILD-TYPE
  I OR II NOS               0                10
  STAGE 0                   1                 5
  STAGE I                   1                21
  STAGE IA                  0                10
  STAGE IB                  1                23
  STAGE II                  1                16
  STAGE IIA                 0                10
  STAGE IIB                 2                12
  STAGE IIC                 0                 9
  STAGE III                 2                29
  STAGE IIIA                0                13
  STAGE IIIB                1                21
  STAGE IIIC                2                42
  STAGE IV                  0                12
[1] 14  2
[1] 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-DRA MUTATED       0  2  3  3
  HLA-DRA WILD-TYPE    51 56 50 52
D119V6, multiclass
       clus
vv      HLA-DRA MUTATED HLA-DRA WILD-TYPE
  T0+T1               0                51
  T2                  2                56
  T3                  3                50
  T4                  3                52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  HLA-DRA MUTATED     6   3   1   1
  HLA-DRA WILD-TYPE 132  45  31  32
D119V7, multiclass
    clus
vv   HLA-DRA MUTATED HLA-DRA WILD-TYPE
  N0               6               132
  N1               3                45
  N2               1                31
  N3               1                32
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1 M1A M1B M1C
  HLA-DRA MUTATED    11   0   0   0   0
  HLA-DRA WILD-TYPE 229   4   2   2   5
D119V8, multiclass
     clus
vv    HLA-DRA MUTATED HLA-DRA WILD-TYPE
  M0               11               229
  M1                0                 4
  M1A               0                 2
  M1B               0                 2
  M1C               0                 5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D119V9, binary
                   cls
clus                 0  1
  HLA-DRA MUTATED    5  2
  HLA-DRA WILD-TYPE 97 65
[1] "tbl2"
                   cls
clus                [,1] [,2]
  HLA-DRA MUTATED      5    2
  HLA-DRA WILD-TYPE   97   65
     clus
vv    HLA-DRA MUTATED HLA-DRA WILD-TYPE
  NO                5                97
  YES               2                65
[1] 2 2
[1] FALSE
D119V10, binary
                   cls
clus                  0   1
  HLA-DRA MUTATED     0  11
  HLA-DRA WILD-TYPE  33 224
[1] "tbl2"
                   cls
clus                [,1] [,2]
  HLA-DRA MUTATED      0   11
  HLA-DRA WILD-TYPE   33  224
     clus
vv    HLA-DRA MUTATED HLA-DRA WILD-TYPE
  NO                0                33
  YES              11               224
[1] 2 2
[1] FALSE
D119V11, continuous
D119V12, binary
                   cls
clus                  0   1
  HLA-DRA MUTATED     4   7
  HLA-DRA WILD-TYPE  99 158
[1] "tbl2"
                   cls
clus                [,1] [,2]
  HLA-DRA MUTATED      4    7
  HLA-DRA WILD-TYPE   99  158
        clus
vv       HLA-DRA MUTATED HLA-DRA WILD-TYPE
  FEMALE               4                99
  MALE                 7               158
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  HLA-DRA MUTATED       0                         0    11
  HLA-DRA WILD-TYPE     3                         1   253
D119V13, multiclass
                           clus
vv                          HLA-DRA MUTATED HLA-DRA WILD-TYPE
  ASIAN                                   0                 3
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  11               253
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D119V14, binary
                   cls
clus                  0   1
  HLA-DRA MUTATED     1  10
  HLA-DRA WILD-TYPE   2 251
[1] "tbl2"
                   cls
clus                [,1] [,2]
  HLA-DRA MUTATED      1   10
  HLA-DRA WILD-TYPE    2  251
                        clus
vv                       HLA-DRA MUTATED HLA-DRA WILD-TYPE
  HISPANIC OR LATINO                   1                 2
  NOT HISPANIC OR LATINO              10               251
[1] 2 2
[1] FALSE

Clustering(120) Variable = ACTC1 MUTATION ANALYSIS
D120V1, survival
                 sevent
clus2               0   1
  ACTC1 MUTATED     9   6
  ACTC1 WILD-TYPE 119 124
  ACTC1 MUTATED ACTC1 WILD-TYPE 
             15             243 
  ACTC1 MUTATED ACTC1 WILD-TYPE 
              6             124 
$`ACTC1 MUTATED`
TCGA-D3-A2JL TCGA-DA-A1I0 TCGA-EE-A29B TCGA-EE-A29L TCGA-EE-A29S TCGA-EE-A29V 
       92.42        10.03         9.90         1.08         9.99         2.43 
TCGA-EE-A2MG TCGA-EE-A2ML TCGA-EE-A3J7 TCGA-FS-A1ZT TCGA-FS-A4F0 TCGA-FS-A4FD 
       44.25       111.91        21.60        40.64        53.85         2.27 
TCGA-FW-A3R5 TCGA-GN-A265 TCGA-GN-A266 
        0.99        84.72        10.13 

$`ACTC1 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.47         8.52       111.09        32.42        70.16       110.79 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       28.08        22.55        45.83        81.24        10.29        85.32 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
        8.38        21.14        88.50        68.22        69.90        11.41 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JN TCGA-D3-A2JO 
       30.87         7.50        36.16         6.31        56.19        64.44 
TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB 
       45.11       114.67        15.25        46.98        46.32        82.29 
TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR 
       61.38        13.32        24.00         6.31         9.34       103.59 
TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J 
       26.37         5.39        80.22        42.71        15.09        41.10 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO 
       17.72         8.84        20.48        13.94        52.01        47.87 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 
        1.55         6.97        23.11         4.01         2.89         9.90 
TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I1 
       11.31        13.22        48.79        35.80        51.12        39.19 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA 
       13.68         9.99        44.52        36.69        25.15         4.93 
TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 
       22.36         6.64        19.36         7.00        17.56        14.83 
TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EE-A17X 
       13.15         0.20         0.00         0.00        13.22        11.57 
TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 
       10.55         6.31         8.12         1.12         1.35        12.20 
TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H 
        5.13         4.31        36.07         4.34         5.13         9.21 
TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G 
        1.18         7.99        37.97        11.15        38.63         8.55 
TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R 
        4.41        27.12         9.50        12.03         8.09         8.84 
TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 
        8.68         8.09        11.31        49.22        23.90         9.67 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH 
        8.94        39.39        34.29        17.98        34.92        47.21 
TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN 
       30.08        19.43        16.01        35.54        28.31        33.83 
TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU 
       30.84         5.42         1.15        13.02        34.98        36.33 
TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD 
        8.84        98.27         2.70         6.18        47.51         9.53 
TCGA-EE-A2ME TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2MM 
       29.46         7.96        14.56        63.42       111.78        56.02 
TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT 
       25.08        26.99        21.60        29.65        27.16        23.05 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE 
        5.56       124.31       122.73        25.84         3.68        30.15 
TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 
       13.81        15.95        12.72         3.22        22.92        21.60 
TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI 
       16.14        22.22        27.35         0.46        13.94        33.60 
TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A 
       31.40        18.61        12.95        38.40         5.72        76.41 
TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G 
       25.18         3.78         3.52        11.90        11.11       114.15 
TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P 
       34.88         4.21        13.45        28.60        42.84        34.68 
TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
        9.57        36.07        17.72        78.44        11.80         1.87 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET 
        1.51        13.08        12.62        11.74         9.04         6.58 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW 
       22.49         1.71        18.41        85.74         4.90        64.47 
TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 
        3.45        11.01        23.80        14.24        15.52         7.33 
TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF 
        7.30         3.39        20.38         8.22        19.53        11.08 
TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP 
        7.17        30.87        12.92        12.89        47.38        52.08 
TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY 
        8.65         8.81        49.15         8.68        27.39         0.82 
TCGA-FS-A1ZZ TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB 
        5.23         7.36        28.73        14.20        10.78         5.98 
TCGA-FS-A4FC TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
        6.41         0.20         0.13         0.16         0.43         9.90 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A268 
        7.23        12.85        24.85        31.33        16.24        15.42 
TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS 
       12.16        14.70         5.79 

  ACTC1 MUTATED ACTC1 WILD-TYPE 
           0.99            0.00 
  ACTC1 MUTATED ACTC1 WILD-TYPE 
         111.91          124.31 
  ACTC1 MUTATED ACTC1 WILD-TYPE 
          10.13           14.83 
[1] "1.0 - 111.9 (10.1)" "0.0 - 124.3 (14.8)"
[1] "hr=" "1.4"
D120V2, survival
                 sevent
clus2               0   1
  ACTC1 MUTATED     9   6
  ACTC1 WILD-TYPE 123 125
  ACTC1 MUTATED ACTC1 WILD-TYPE 
             15             248 
  ACTC1 MUTATED ACTC1 WILD-TYPE 
              6             125 
$`ACTC1 MUTATED`
TCGA-D3-A2JL TCGA-DA-A1I0 TCGA-EE-A29B TCGA-EE-A29L TCGA-EE-A29S TCGA-EE-A29V 
      171.58        20.38        80.61         2.60        55.92        25.87 
TCGA-EE-A2MG TCGA-EE-A2ML TCGA-EE-A3J7 TCGA-FS-A1ZT TCGA-FS-A4F0 TCGA-FS-A4FD 
      103.20       203.05        64.08        53.16        77.82        77.88 
TCGA-FW-A3R5 TCGA-GN-A265 TCGA-GN-A266 
       22.92        84.72        10.13 

$`ACTC1 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.57        16.67       112.04       112.57        71.80       133.25 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       28.08        31.59        90.90        95.74        43.43       103.10 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
       65.49        23.77       115.53       168.00        69.90        11.87 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JN TCGA-D3-A2JO 
       48.76       113.52        42.08        12.10        56.19        66.08 
TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB 
       45.11       130.72        58.06        46.98        46.32       166.52 
TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR 
       86.93        60.23        24.53        13.87         9.34       103.59 
TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J 
       39.75        21.47       161.85        43.69        40.14       131.90 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO 
       18.38        10.03        51.68        15.06       135.75       137.92 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW 
      166.19         7.43       125.19       151.53        54.67         3.65 
TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC 
        6.41        11.34         3.25         9.90        25.18        66.25 
TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 
       48.89        36.03       117.21       194.83       176.55        35.93 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC 
      107.34        61.18        53.92        65.92        23.44        68.09 
TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R 
       28.60        10.49       215.44        15.68        13.87        10.16 
TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y 
       45.11        35.01         3.55        52.01        29.82        27.22 
TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 
        8.65        94.98        33.73        14.70        26.89        68.15 
TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I 
        4.96       109.64       151.27        78.87       168.26        13.55 
TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H 
       63.35        47.84        13.97        39.62        72.07        32.19 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29W 
       44.35        18.61        56.42        37.35        14.47       171.55 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 
       17.92        46.82       102.90        24.43        39.29        58.75 
TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI 
       47.54        67.43       314.56       135.95       208.04        48.72 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO 
       89.33        54.74        79.66        75.48        90.97       101.95 
TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 
       13.91        14.30        55.59        44.88        94.82        21.67 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME 
      129.27        28.83        19.76        61.51        47.28       103.27 
TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2MM TCGA-EE-A2MN 
       16.96       204.66        96.23       144.76       167.90        47.54 
TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU 
      248.65        43.23       103.56       136.47        41.59        53.26 
TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF 
      124.31       122.73        25.84         3.68        54.51        13.81 
TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J8 
       23.47       138.81       172.18       127.20        36.95        34.32 
TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 
       53.19        27.35        33.40       101.79       148.08        31.40 
TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B 
       35.44        13.94        50.76         9.17        77.75        98.40 
TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H 
       48.89        12.59        13.02        26.37       268.93       152.35 
TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q 
        6.44       131.51        61.05        44.05       162.08        50.89 
TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE 
       37.25       148.18        79.99        43.82        23.34        20.15 
TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV 
       16.37        31.27        32.05       247.04        80.32        46.98 
TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX 
       33.21        92.98       174.21         4.90       216.92        48.59 
TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA 
      228.59       202.65        20.91        28.08         7.79        27.72 
TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG 
       48.85       357.37        53.52        40.27        15.45         9.70 
TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ 
       32.75        47.38        23.93       101.26        74.73       133.55 
TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ 
       11.41       148.80        26.56        49.48        27.09        27.02 
TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC 
       66.67        28.73       174.84        12.43        26.73        49.45 
TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
        0.20        47.54         0.16         2.40         9.90         7.23 
TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
       14.04       120.46       117.93        64.44        62.79        32.48 
TCGA-GN-A26D TCGA-QB-A6FS 
       39.58         6.67 

  ACTC1 MUTATED ACTC1 WILD-TYPE 
           2.60            0.16 
  ACTC1 MUTATED ACTC1 WILD-TYPE 
         203.05          357.37 
  ACTC1 MUTATED ACTC1 WILD-TYPE 
          64.08           47.54 
[1] "2.6 - 203.1 (64.1)" "0.2 - 357.4 (47.5)"
[1] "hr=" "1.3"
D120V3, continuous
                 vv
clus              DISTANT METASTASIS PRIMARY TUMOR
  ACTC1 MUTATED                    3             0
  ACTC1 WILD-TYPE                 32             4
                 vv
clus              REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  ACTC1 MUTATED                                           4                   8
  ACTC1 WILD-TYPE                                        54                 162
D120V4, multiclass
                                           clus
vv                                          ACTC1 MUTATED ACTC1 WILD-TYPE
  DISTANT METASTASIS                                    3              32
  PRIMARY TUMOR                                         0               4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE             4              54
  REGIONAL LYMPH NODE                                   8             162
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  ACTC1 MUTATED             1       0       2        0        0        1
  ACTC1 WILD-TYPE           9       6      20       10       24       16
                 vv
clus              STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  ACTC1 MUTATED           1         2         0         2          0          0
  ACTC1 WILD-TYPE         9        12         9        29         13         22
                 vv
clus              STAGE IIIC STAGE IV
  ACTC1 MUTATED            3        1
  ACTC1 WILD-TYPE         41       11
D120V5, multiclass
             clus
vv            ACTC1 MUTATED ACTC1 WILD-TYPE
  I OR II NOS             1               9
  STAGE 0                 0               6
  STAGE I                 2              20
  STAGE IA                0              10
  STAGE IB                0              24
  STAGE II                1              16
  STAGE IIA               1               9
  STAGE IIB               2              12
  STAGE IIC               0               9
  STAGE III               2              29
  STAGE IIIA              0              13
  STAGE IIIB              0              22
  STAGE IIIC              3              41
  STAGE IV                1              11
[1] 14  2
[1] 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
  ACTC1 MUTATED       0  4  4  3
  ACTC1 WILD-TYPE    51 54 49 52
D120V6, multiclass
       clus
vv      ACTC1 MUTATED ACTC1 WILD-TYPE
  T0+T1             0              51
  T2                4              54
  T3                4              49
  T4                3              52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  ACTC1 MUTATED     7   2   1   3
  ACTC1 WILD-TYPE 131  46  31  30
D120V7, multiclass
    clus
vv   ACTC1 MUTATED ACTC1 WILD-TYPE
  N0             7             131
  N1             2              46
  N2             1              31
  N3             3              30
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               M0  M1 M1A M1B M1C
  ACTC1 MUTATED    12   0   1   0   0
  ACTC1 WILD-TYPE 228   4   1   2   5
D120V8, multiclass
     clus
vv    ACTC1 MUTATED ACTC1 WILD-TYPE
  M0             12             228
  M1              0               4
  M1A             1               1
  M1B             0               2
  M1C             0               5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D120V9, binary
                 cls
clus               0  1
  ACTC1 MUTATED    3  5
  ACTC1 WILD-TYPE 99 62
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ACTC1 MUTATED      3    5
  ACTC1 WILD-TYPE   99   62
     clus
vv    ACTC1 MUTATED ACTC1 WILD-TYPE
  NO              3              99
  YES             5              62
[1] 2 2
[1] FALSE
D120V10, binary
                 cls
clus                0   1
  ACTC1 MUTATED     2  13
  ACTC1 WILD-TYPE  31 222
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ACTC1 MUTATED      2   13
  ACTC1 WILD-TYPE   31  222
     clus
vv    ACTC1 MUTATED ACTC1 WILD-TYPE
  NO              2              31
  YES            13             222
[1] 2 2
[1] FALSE
D120V11, continuous
D120V12, binary
                 cls
clus                0   1
  ACTC1 MUTATED     2  13
  ACTC1 WILD-TYPE 101 152
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ACTC1 MUTATED      2   13
  ACTC1 WILD-TYPE  101  152
        clus
vv       ACTC1 MUTATED ACTC1 WILD-TYPE
  FEMALE             2             101
  MALE              13             152
[1] 2 2
[1] FALSE
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ACTC1 MUTATED       0                         0    15
  ACTC1 WILD-TYPE     3                         1   249
D120V13, multiclass
                           clus
vv                          ACTC1 MUTATED ACTC1 WILD-TYPE
  ASIAN                                 0               3
  BLACK OR AFRICAN AMERICAN             0               1
  WHITE                                15             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"
D120V14, binary
                 cls
clus                0   1
  ACTC1 MUTATED     0  15
  ACTC1 WILD-TYPE   3 246
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ACTC1 MUTATED      0   15
  ACTC1 WILD-TYPE    3  246
                        clus
vv                       ACTC1 MUTATED ACTC1 WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO            15             246
[1] 2 2
[1] FALSE

Clustering(121) Variable = ELOVL3 MUTATION ANALYSIS
D121V1, survival
                  sevent
clus2                0   1
  ELOVL3 MUTATED     2   3
  ELOVL3 WILD-TYPE 126 127
  ELOVL3 MUTATED ELOVL3 WILD-TYPE 
               5              253 
  ELOVL3 MUTATED ELOVL3 WILD-TYPE 
               3              127 
$`ELOVL3 MUTATED`
TCGA-EE-A182 TCGA-EE-A2MJ TCGA-FR-A3YN TCGA-FS-A1ZB TCGA-FS-A1ZW 
        1.35        63.42        18.41         3.39        27.39 

$`ELOVL3 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.47         8.52       111.09        32.42        70.16       110.79 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       28.08        22.55        45.83        81.24        10.29        85.32 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
        8.38        21.14        88.50        68.22        69.90        11.41 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       30.87         7.50        36.16         6.31        92.42        56.19 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 
       64.44        45.11       114.67        15.25        46.98        46.32 
TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO 
       82.29        61.38        13.32        24.00         6.31         9.34 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H 
      103.59        26.37         5.39        80.22        42.71        15.09 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN 
       41.10        17.72         8.84        20.48        13.94        52.01 
TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 
       47.87         1.55         6.97        23.11         4.01         2.89 
TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY 
        9.90        11.31        13.22        48.79        35.80        51.12 
TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 
       10.03        39.19        13.68         9.99        44.52        36.69 
TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 
       25.15         4.93        22.36         6.64        19.36         7.00 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH 
       17.56        14.83        13.15         0.20         0.00         0.00 
TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 
       13.22        11.57        10.55         6.31         8.12         1.12 
TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F 
       12.20         5.13         4.31        36.07         4.34         5.13 
TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D 
        9.21         1.18         7.99         9.90        37.97        11.15 
TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N 
       38.63         8.55         4.41         1.08        27.12         9.50 
TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W 
       12.03         8.09         8.84         9.99         2.43         8.68 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 
        8.09        11.31        49.22        23.90         9.67         8.94 
TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI 
       39.39        34.29        17.98        34.92        47.21        30.08 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO 
       19.43        16.01        35.54        28.31        33.83        30.84 
TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 
        5.42         1.15        13.02        34.98        36.33         8.84 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME 
       98.27         2.70         6.18        47.51         9.53        29.46 
TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM 
       44.25         7.96        14.56       111.78       111.91        56.02 
TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT 
       25.08        26.99        21.60        29.65        27.16        23.05 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE 
        5.56       124.31       122.73        25.84         3.68        30.15 
TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 
       13.81        15.95        12.72         3.22        22.92        21.60 
TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH 
       21.60        16.14        22.22        27.35         0.46        13.94 
TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 
       33.60        31.40        18.61        12.95        38.40         5.72 
TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F 
       76.41        25.18         3.78         3.52        11.90        11.11 
TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N 
      114.15        34.88         4.21        13.45        28.60        42.84 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
       34.68         9.57        36.07        17.72        78.44        11.80 
TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES 
        1.87         1.51        13.08        12.62        11.74         9.04 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW 
        6.58        22.49         1.71        85.74         4.90        64.47 
TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 
        3.45        11.01        23.80        14.24        15.52         7.33 
TCGA-FS-A1ZA TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG 
        7.30        20.38         8.22        19.53        11.08         7.17 
TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ 
       30.87        12.92        12.89        47.38        52.08         8.65 
TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZY TCGA-FS-A1ZZ 
        8.81        49.15        40.64         8.68         0.82         5.23 
TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB 
       53.85         7.36        28.73        14.20        10.78         5.98 
TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV 
        6.41         2.27         0.20         0.99         0.13         0.16 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 
        0.43         9.90         7.23        12.85        24.85        31.33 
TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D 
       84.72        10.13        16.24        15.42        12.16        14.70 
TCGA-QB-A6FS 
        5.79 

  ELOVL3 MUTATED ELOVL3 WILD-TYPE 
            1.35             0.00 
  ELOVL3 MUTATED ELOVL3 WILD-TYPE 
           63.42           124.31 
  ELOVL3 MUTATED ELOVL3 WILD-TYPE 
           18.41            14.70 
[1] "1.4 - 63.4 (18.4)"  "0.0 - 124.3 (14.7)"
[1] "hr=" "1.3"
D121V2, survival
                  sevent
clus2                0   1
  ELOVL3 MUTATED     2   3
  ELOVL3 WILD-TYPE 130 128
  ELOVL3 MUTATED ELOVL3 WILD-TYPE 
               5              258 
  ELOVL3 MUTATED ELOVL3 WILD-TYPE 
               3              128 
$`ELOVL3 MUTATED`
TCGA-EE-A182 TCGA-EE-A2MJ TCGA-FR-A3YN TCGA-FS-A1ZB TCGA-FS-A1ZW 
       14.70        96.23        92.98        48.85        49.48 

$`ELOVL3 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.57        16.67       112.04       112.57        71.80       133.25 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       28.08        31.59        90.90        95.74        43.43       103.10 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
       65.49        23.77       115.53       168.00        69.90        11.87 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       48.76       113.52        42.08        12.10       171.58        56.19 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 
       66.08        45.11       130.72        58.06        46.98        46.32 
TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO 
      166.52        86.93        60.23        24.53        13.87         9.34 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H 
      103.59        39.75        21.47       161.85        43.69        40.14 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN 
      131.90        18.38        10.03        51.68        15.06       135.75 
TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 
      137.92       166.19         7.43       125.19       151.53        54.67 
TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA 
        3.65         6.41        11.34         3.25         9.90        25.18 
TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 
       66.25        48.89        36.03       117.21        20.38       194.83 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA 
      176.55        35.93       107.34        61.18        53.92        65.92 
TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 
       23.44        68.09        28.60        10.49       215.44        15.68 
TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN 
       13.87        10.16        45.11        35.01         3.55        52.01 
TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A183 
       29.82        27.22         8.65        94.98        33.73        26.89 
TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H 
       68.15         4.96       109.64       151.27        78.87       168.26 
TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E 
       13.55        63.35        80.61        47.84        13.97        39.62 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P 
       72.07        32.19         2.60        44.35        18.61        56.42 
TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X 
       37.35        14.47        55.92        25.87       171.55        17.92 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB 
       46.82       102.90        24.43        39.29        58.75        47.54 
TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ 
       67.43       314.56       135.95       208.04        48.72        89.33 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP 
       54.74        79.66        75.48        90.97       101.95        13.91 
TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 
       14.30        55.59        44.88        94.82        21.67       129.27 
TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG 
       28.83        19.76        61.51        47.28       103.27       103.20 
TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN 
       16.96       204.66       144.76       203.05       167.90        47.54 
TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU 
      248.65        43.23       103.56       136.47        41.59        53.26 
TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF 
      124.31       122.73        25.84         3.68        54.51        13.81 
TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 
       23.47       138.81       172.18       127.20        36.95        64.08 
TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI 
       34.32        53.19        27.35        33.40       101.79       148.08 
TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A 
       31.40        35.44        13.94        50.76         9.17        77.75 
TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G 
       98.40        48.89        12.59        13.02        26.37       268.93 
TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P 
      152.35         6.44       131.51        61.05        44.05       162.08 
TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
       50.89        37.25       148.18        79.99        43.82        23.34 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET 
       20.15        16.37        31.27        32.05       247.04        80.32 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX 
       46.98        33.21       174.21         4.90       216.92        48.59 
TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA 
      228.59       202.65        20.91        28.08         7.79        27.72 
TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH 
      357.37        53.52        40.27        15.45         9.70        32.75 
TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR 
       47.38        23.93       101.26        74.73       133.55        11.41 
TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 
      148.80        53.16        26.56        27.09        27.02        77.82 
TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC 
       66.67        28.73       174.84        12.43        26.73        49.45 
TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY 
       77.88         0.20        22.92        47.54         0.16         2.40 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        9.90         7.23        14.04       120.46       117.93        84.72 
TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS 
       10.13        64.44        62.79        32.48        39.58         6.67 

  ELOVL3 MUTATED ELOVL3 WILD-TYPE 
           14.70             0.16 
  ELOVL3 MUTATED ELOVL3 WILD-TYPE 
           96.23           357.37 
  ELOVL3 MUTATED ELOVL3 WILD-TYPE 
           49.48            47.69 
[1] "14.7 - 96.2 (49.5)" "0.2 - 357.4 (47.7)"
[1] "hr=" "1.4"
D121V3, continuous
                  vv
clus               DISTANT METASTASIS PRIMARY TUMOR
  ELOVL3 MUTATED                    2             0
  ELOVL3 WILD-TYPE                 33             4
                  vv
clus               REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  ELOVL3 MUTATED                                           0
  ELOVL3 WILD-TYPE                                        58
                  vv
clus               REGIONAL LYMPH NODE
  ELOVL3 MUTATED                     3
  ELOVL3 WILD-TYPE                 167
D121V4, multiclass
                                           clus
vv                                          ELOVL3 MUTATED ELOVL3 WILD-TYPE
  DISTANT METASTASIS                                     2               33
  PRIMARY TUMOR                                          0                4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE              0               58
  REGIONAL LYMPH NODE                                    3              167
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  ELOVL3 MUTATED             0       0       0        0        1        1
  ELOVL3 WILD-TYPE          10       6      22       10       23       16
                  vv
clus               STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  ELOVL3 MUTATED           0         0         0         1          0
  ELOVL3 WILD-TYPE        10        14         9        30         13
                  vv
clus               STAGE IIIB STAGE IIIC STAGE IV
  ELOVL3 MUTATED            1          1        0
  ELOVL3 WILD-TYPE         21         43       12
D121V5, multiclass
             clus
vv            ELOVL3 MUTATED ELOVL3 WILD-TYPE
  I OR II NOS              0               10
  STAGE 0                  0                6
  STAGE I                  0               22
  STAGE IA                 0               10
  STAGE IB                 1               23
  STAGE II                 1               16
  STAGE IIA                0               10
  STAGE IIB                0               14
  STAGE IIC                0                9
  STAGE III                1               30
  STAGE IIIA               0               13
  STAGE IIIB               1               21
  STAGE IIIC               1               43
  STAGE IV                 0               12
[1] 14  2
[1] 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
  ELOVL3 MUTATED       0  2  1  2
  ELOVL3 WILD-TYPE    51 56 52 53
D121V6, multiclass
       clus
vv      ELOVL3 MUTATED ELOVL3 WILD-TYPE
  T0+T1              0               51
  T2                 2               56
  T3                 1               52
  T4                 2               53
[1] 4 2
[1] TRUE
[1] "dimension 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
  ELOVL3 MUTATED     3   2   0   0
  ELOVL3 WILD-TYPE 135  46  32  33
D121V7, multiclass
    clus
vv   ELOVL3 MUTATED ELOVL3 WILD-TYPE
  N0              3              135
  N1              2               46
  N2              0               32
  N3              0               33
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                M0  M1 M1A M1B M1C
  ELOVL3 MUTATED     5   0   0   0   0
  ELOVL3 WILD-TYPE 235   4   2   2   5
D121V8, multiclass
     clus
vv    ELOVL3 MUTATED ELOVL3 WILD-TYPE
  M0               5              235
  M1               0                4
  M1A              0                2
  M1B              0                2
  M1C              0                5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D121V9, binary
                  cls
clus                0  1
  ELOVL3 MUTATED    3  2
  ELOVL3 WILD-TYPE 99 65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ELOVL3 MUTATED      3    2
  ELOVL3 WILD-TYPE   99   65
     clus
vv    ELOVL3 MUTATED ELOVL3 WILD-TYPE
  NO               3               99
  YES              2               65
[1] 2 2
[1] FALSE
D121V10, binary
                  cls
clus                 0   1
  ELOVL3 MUTATED     0   5
  ELOVL3 WILD-TYPE  33 230
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ELOVL3 MUTATED      0    5
  ELOVL3 WILD-TYPE   33  230
     clus
vv    ELOVL3 MUTATED ELOVL3 WILD-TYPE
  NO               0               33
  YES              5              230
[1] 2 2
[1] FALSE
D121V11, continuous
D121V12, binary
                  cls
clus                 0   1
  ELOVL3 MUTATED     1   4
  ELOVL3 WILD-TYPE 102 161
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ELOVL3 MUTATED      1    4
  ELOVL3 WILD-TYPE  102  161
        clus
vv       ELOVL3 MUTATED ELOVL3 WILD-TYPE
  FEMALE              1              102
  MALE                4              161
[1] 2 2
[1] FALSE
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ELOVL3 MUTATED       0                         0     5
  ELOVL3 WILD-TYPE     3                         1   259
D121V13, multiclass
                           clus
vv                          ELOVL3 MUTATED ELOVL3 WILD-TYPE
  ASIAN                                  0                3
  BLACK OR AFRICAN AMERICAN              0                1
  WHITE                                  5              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"
D121V14, binary
                  cls
clus                 0   1
  ELOVL3 MUTATED     0   5
  ELOVL3 WILD-TYPE   3 256
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ELOVL3 MUTATED      0    5
  ELOVL3 WILD-TYPE    3  256
                        clus
vv                       ELOVL3 MUTATED ELOVL3 WILD-TYPE
  HISPANIC OR LATINO                  0                3
  NOT HISPANIC OR LATINO              5              256
[1] 2 2
[1] FALSE

Clustering(122) Variable = THSD7B MUTATION ANALYSIS
D122V1, survival
                  sevent
clus2               0  1
  THSD7B MUTATED   43 37
  THSD7B WILD-TYPE 85 93
  THSD7B MUTATED THSD7B WILD-TYPE 
              80              178 
  THSD7B MUTATED THSD7B WILD-TYPE 
              37               93 
$`THSD7B MUTATED`
TCGA-D3-A1Q4 TCGA-D3-A1Q6 TCGA-D3-A2J8 TCGA-D3-A2JF TCGA-D3-A2JO TCGA-D3-A3C7 
      111.09        70.16         8.38        30.87        64.44        46.98 
TCGA-D3-A3CB TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A5GU 
       82.29       103.59        26.37         5.39        80.22        23.11 
TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A3F8 
       13.22        48.79        44.52        36.69         4.93        14.83 
TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A185 TCGA-EE-A20C TCGA-EE-A20H TCGA-EE-A29A 
        1.12         1.35         4.31         4.34         9.21         7.99 
TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M 
       11.15        38.63         8.55         4.41         1.08        27.12 
TCGA-EE-A29N TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A2A1 TCGA-EE-A2GB TCGA-EE-A2GC 
        9.50         9.99         2.43        49.22        39.39        34.29 
TCGA-EE-A2GD TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GM TCGA-EE-A2GP TCGA-EE-A2GR 
       17.98        30.08        19.43        28.31         5.42         1.15 
TCGA-EE-A2M5 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2ML 
        8.84        47.51         9.53        14.56        63.42       111.91 
TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3AA 
       25.08        26.99        29.65        27.16         5.56       124.31 
TCGA-EE-A3AC TCGA-EE-A3AG TCGA-EE-A3J3 TCGA-EE-A3J5 TCGA-EE-A3JA TCGA-EE-A3JD 
       25.84        15.95         3.22        21.60        22.22        27.35 
TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19M TCGA-ER-A2NC 
       33.60        31.40        38.40        76.41        28.60        11.80 
TCGA-FR-A44A TCGA-FS-A1Z0 TCGA-FS-A1Z7 TCGA-FS-A1ZP TCGA-FS-A1ZT TCGA-FS-A1ZW 
       85.74        23.80         7.33        52.08        40.64        27.39 
TCGA-FS-A4F0 TCGA-FS-A4F5 TCGA-FS-A4FC TCGA-FW-A3R5 TCGA-FW-A3TV TCGA-GN-A266 
       53.85        28.73         6.41         0.99         0.16        10.13 
TCGA-GN-A268 TCGA-QB-A6FS 
       15.42         5.79 

$`THSD7B WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 
       16.47         8.52        32.42       110.79        28.08        22.55 
TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J9 TCGA-D3-A2JA 
       45.83        81.24        10.29        85.32        21.14        88.50 
TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK 
       68.22        69.90        11.41         7.50        36.16         6.31 
TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C8 
       92.42        56.19        45.11       114.67        15.25        46.32 
TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A51F 
       61.38        13.32        24.00         6.31         9.34        42.71 
TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T 
       15.09        41.10        17.72         8.84        20.48        13.94 
TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D9-A3Z1 TCGA-D9-A3Z3 
       52.01        47.87         1.55         6.97         4.01         2.89 
TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 
        9.90        11.31        35.80        51.12        10.03        39.19 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I8 TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
       13.68         9.99        25.15        22.36         6.64        19.36 
TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH 
        7.00        17.56        13.15         0.20         0.00         0.00 
TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A183 
       13.22        11.57        10.55         6.31         8.12        12.20 
TCGA-EE-A184 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29B TCGA-EE-A29C 
        5.13        36.07         5.13         1.18         9.90        37.97 
TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 
       12.03         8.09         8.84         8.68         8.09        11.31 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GK 
       23.90         9.67         8.94        34.92        47.21        16.01 
TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU 
       35.54        33.83        30.84        13.02        34.98        36.33 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH 
       98.27         2.70         6.18        29.46        44.25         7.96 
TCGA-EE-A2MK TCGA-EE-A2MM TCGA-EE-A2MQ TCGA-EE-A2MT TCGA-EE-A3AB TCGA-EE-A3AD 
      111.78        56.02        21.60        23.05       122.73         3.68 
TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AH TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 
       30.15        13.81        12.72        22.92        21.60        16.14 
TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19B 
        0.46        13.94        18.61        12.95         5.72        25.18 
TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H 
        3.78         3.52        11.90        11.11       114.15        34.88 
TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S 
        4.21        13.45        42.84        34.68         9.57        36.07 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG 
       17.72        78.44         1.87         1.51        13.08        12.62 
TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN 
       11.74         9.04         6.58        22.49         1.71        18.41 
TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1Z4 
        4.90        64.47         3.45        11.01        14.24        15.52 
TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF 
        7.30         3.39        20.38         8.22        19.53        11.08 
TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZQ 
        7.17        30.87        12.92        12.89        47.38         8.65 
TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZU TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F4 
        8.81        49.15         8.68         0.82         5.23         7.36 
TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU 
       14.20        10.78         5.98         2.27         0.20         0.13 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 
        0.43         9.90         7.23        12.85        24.85        31.33 
TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A26D 
       84.72        16.24        12.16        14.70 

  THSD7B MUTATED THSD7B WILD-TYPE 
            0.16             0.00 
  THSD7B MUTATED THSD7B WILD-TYPE 
          124.31           122.73 
  THSD7B MUTATED THSD7B WILD-TYPE 
           24.44            13.27 
[1] "0.2 - 124.3 (24.4)" "0.0 - 122.7 (13.3)"
[1] "hr=" "1.3"
D122V2, survival
                  sevent
clus2               0  1
  THSD7B MUTATED   45 37
  THSD7B WILD-TYPE 87 94
  THSD7B MUTATED THSD7B WILD-TYPE 
              82              181 
  THSD7B MUTATED THSD7B WILD-TYPE 
              37               94 
$`THSD7B MUTATED`
TCGA-D3-A1Q4 TCGA-D3-A1Q6 TCGA-D3-A2J8 TCGA-D3-A2JF TCGA-D3-A2JO TCGA-D3-A3C7 
      112.04        71.80        65.49        48.76        66.08        46.98 
TCGA-D3-A3CB TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A5GU 
      166.52       103.59        39.75        21.47       161.85       125.19 
TCGA-D9-A1JW TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA 
        3.65        66.25        48.89       107.34        61.18        65.92 
TCGA-DA-A3F8 TCGA-EB-A5UL TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A185 TCGA-EE-A20C 
       15.68         3.55        33.73        14.70         4.96       151.27 
TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H 
      168.26        63.35        13.97        39.62        72.07        32.19 
TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A2A1 
        2.60        44.35        18.61        55.92        25.87       102.90 
TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GM 
       47.54        67.43       314.56        48.72        89.33        75.48 
TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2M5 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2MI 
       13.91        14.30        21.67        61.51        47.28       204.66 
TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MR TCGA-EE-A2MS 
       96.23       203.05        47.54       248.65       103.56       136.47 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3AG TCGA-EE-A3J3 TCGA-EE-A3J5 
       53.26       124.31        25.84        23.47       172.18        36.95 
TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A198 TCGA-ER-A19A 
       53.19        27.35       148.08        31.40        50.76        77.75 
TCGA-ER-A19M TCGA-ER-A2NC TCGA-FR-A44A TCGA-FS-A1Z0 TCGA-FS-A1Z7 TCGA-FS-A1ZP 
       61.05        43.82       174.21       202.65         7.79        74.73 
TCGA-FS-A1ZT TCGA-FS-A1ZW TCGA-FS-A4F0 TCGA-FS-A4F5 TCGA-FS-A4FC TCGA-FW-A3R5 
       53.16        49.48        77.82        28.73        49.45        22.92 
TCGA-FW-A3TV TCGA-GN-A266 TCGA-GN-A268 TCGA-QB-A6FS 
        0.16        10.13        62.79         6.67 

$`THSD7B WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 
       16.57        16.67       112.57       133.25        28.08        31.59 
TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J9 TCGA-D3-A2JA 
       90.90        95.74        43.43       103.10        23.77       115.53 
TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK 
      168.00        69.90        11.87       113.52        42.08        12.10 
TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C8 
      171.58        56.19        45.11       130.72        58.06        46.32 
TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A51F 
       86.93        60.23        24.53        13.87         9.34        43.69 
TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T 
       40.14       131.90        18.38        10.03        51.68        15.06 
TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D9-A148 TCGA-D9-A149 
      135.75       137.92       166.19         7.43       151.53        54.67 
TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-DA-A1HW 
        6.41        11.34         3.25         9.90        25.18        36.03 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I8 
      117.21        20.38       194.83       176.55        35.93        53.92 
TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-EB-A44Q 
       23.44        68.09        28.60        10.49       215.44        13.87 
TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y 
       10.16        45.11        35.01        52.01        29.82        27.22 
TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A20B TCGA-EE-A20F 
        8.65        94.98        26.89        68.15       109.64        78.87 
TCGA-EE-A20I TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R 
       13.55        80.61        47.84        56.42        37.35        14.47 
TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 
      171.55        17.92        46.82        24.43        39.29        58.75 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GO 
      135.95       208.04        54.74        79.66        90.97       101.95 
TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 
       55.59        44.88        94.82       129.27        28.83        19.76 
TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MK TCGA-EE-A2MM TCGA-EE-A2MQ 
      103.27       103.20        16.96       144.76       167.90        43.23 
TCGA-EE-A2MT TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AH 
       41.59       122.73         3.68        54.51        13.81       138.81 
TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A195 
      127.20        64.08        34.32        33.40       101.79        35.44 
TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E 
       13.94         9.17        98.40        48.89        12.59        13.02 
TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19N 
       26.37       268.93       152.35         6.44       131.51        44.05 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2ND 
      162.08        50.89        37.25       148.18        79.99        23.34 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET 
       20.15        16.37        31.27        32.05       247.04        80.32 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX 
       46.98        33.21        92.98         4.90       216.92        48.59 
TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC 
      228.59        20.91        28.08        27.72        48.85       357.37 
TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ 
       53.52        40.27        15.45         9.70        32.75        47.38 
TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZU 
       23.93       101.26       133.55        11.41       148.80        26.56 
TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB 
       27.09        27.02        66.67       174.84        12.43        26.73 
TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
       77.88         0.20        47.54         2.40         9.90         7.23 
TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A26A 
       14.04       120.46       117.93        84.72        64.44        32.48 
TCGA-GN-A26D 
       39.58 

  THSD7B MUTATED THSD7B WILD-TYPE 
            0.16             0.20 
  THSD7B MUTATED THSD7B WILD-TYPE 
          314.56           357.37 
  THSD7B MUTATED THSD7B WILD-TYPE 
          53.175           45.110 
[1] "0.2 - 314.6 (53.2)" "0.2 - 357.4 (45.1)"
[1] "hr=" "1.3"
D122V3, continuous
                  vv
clus               DISTANT METASTASIS PRIMARY TUMOR
  THSD7B MUTATED                   12             1
  THSD7B WILD-TYPE                 23             3
                  vv
clus               REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  THSD7B MUTATED                                          21
  THSD7B WILD-TYPE                                        37
                  vv
clus               REGIONAL LYMPH NODE
  THSD7B MUTATED                    49
  THSD7B WILD-TYPE                 121
D122V4, multiclass
                                           clus
vv                                          THSD7B MUTATED THSD7B WILD-TYPE
  DISTANT METASTASIS                                    12               23
  PRIMARY TUMOR                                          1                3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE             21               37
  REGIONAL LYMPH NODE                                   49              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               I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  THSD7B MUTATED             4       1       7        6        9        7
  THSD7B WILD-TYPE           6       5      15        4       15       10
                  vv
clus               STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  THSD7B MUTATED           2         6         1        13          4
  THSD7B WILD-TYPE         8         8         8        18          9
                  vv
clus               STAGE IIIB STAGE IIIC STAGE IV
  THSD7B MUTATED            9          9        2
  THSD7B WILD-TYPE         13         35       10
D122V5, multiclass
             clus
vv            THSD7B MUTATED THSD7B WILD-TYPE
  I OR II NOS              4                6
  STAGE 0                  1                5
  STAGE I                  7               15
  STAGE IA                 6                4
  STAGE IB                 9               15
  STAGE II                 7               10
  STAGE IIA                2                8
  STAGE IIB                6                8
  STAGE IIC                1                8
  STAGE III               13               18
  STAGE IIIA               4                9
  STAGE IIIB               9               13
  STAGE IIIC               9               35
  STAGE IV                 2               10
[1] 14  2
[1] 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
  THSD7B MUTATED      18 25 16 15
  THSD7B WILD-TYPE    33 33 37 40
D122V6, multiclass
       clus
vv      THSD7B MUTATED THSD7B WILD-TYPE
  T0+T1             18               33
  T2                25               33
  T3                16               37
  T4                15               40
[1] 4 2
[1] TRUE
[1] "dimension 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
  THSD7B MUTATED   46 19 12  4
  THSD7B WILD-TYPE 92 29 20 29
D122V7, multiclass
    clus
vv   THSD7B MUTATED THSD7B WILD-TYPE
  N0             46               92
  N1             19               29
  N2             12               20
  N3              4               29
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                M0  M1 M1A M1B M1C
  THSD7B MUTATED    80   1   0   0   1
  THSD7B WILD-TYPE 160   3   2   2   4
D122V8, multiclass
     clus
vv    THSD7B MUTATED THSD7B WILD-TYPE
  M0              80              160
  M1               1                3
  M1A              0                2
  M1B              0                2
  M1C              1                4
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D122V9, binary
                  cls
clus                0  1
  THSD7B MUTATED   38 17
  THSD7B WILD-TYPE 64 50
[1] "tbl2"
                  cls
clus               [,1] [,2]
  THSD7B MUTATED     38   17
  THSD7B WILD-TYPE   64   50
     clus
vv    THSD7B MUTATED THSD7B WILD-TYPE
  NO              38               64
  YES             17               50
[1] 2 2
[1] FALSE
D122V10, binary
                  cls
clus                 0   1
  THSD7B MUTATED    11  72
  THSD7B WILD-TYPE  22 163
[1] "tbl2"
                  cls
clus               [,1] [,2]
  THSD7B MUTATED     11   72
  THSD7B WILD-TYPE   22  163
     clus
vv    THSD7B MUTATED THSD7B WILD-TYPE
  NO              11               22
  YES             72              163
[1] 2 2
[1] FALSE
D122V11, continuous
D122V12, binary
                  cls
clus                 0   1
  THSD7B MUTATED    25  58
  THSD7B WILD-TYPE  78 107
[1] "tbl2"
                  cls
clus               [,1] [,2]
  THSD7B MUTATED     25   58
  THSD7B WILD-TYPE   78  107
        clus
vv       THSD7B MUTATED THSD7B WILD-TYPE
  FEMALE             25               78
  MALE               58              107
[1] 2 2
[1] FALSE
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  THSD7B MUTATED       0                         0    83
  THSD7B WILD-TYPE     3                         1   181
D122V13, multiclass
                           clus
vv                          THSD7B MUTATED THSD7B WILD-TYPE
  ASIAN                                  0                3
  BLACK OR AFRICAN AMERICAN              0                1
  WHITE                                 83              181
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D122V14, binary
                  cls
clus                 0   1
  THSD7B MUTATED     0  82
  THSD7B WILD-TYPE   3 179
[1] "tbl2"
                  cls
clus               [,1] [,2]
  THSD7B MUTATED      0   82
  THSD7B WILD-TYPE    3  179
                        clus
vv                       THSD7B MUTATED THSD7B WILD-TYPE
  HISPANIC OR LATINO                  0                3
  NOT HISPANIC OR LATINO             82              179
[1] 2 2
[1] FALSE

Clustering(123) Variable = SLC27A5 MUTATION ANALYSIS
D123V1, survival
                   sevent
clus2                 0   1
  SLC27A5 MUTATED     5   3
  SLC27A5 WILD-TYPE 123 127
  SLC27A5 MUTATED SLC27A5 WILD-TYPE 
                8               250 
  SLC27A5 MUTATED SLC27A5 WILD-TYPE 
                3               127 
$`SLC27A5 MUTATED`
TCGA-D3-A3C7 TCGA-D3-A51T TCGA-EE-A17X TCGA-EE-A2MD TCGA-EE-A3AC TCGA-EE-A3AG 
       46.98        13.94        11.57         9.53        25.84        15.95 
TCGA-EE-A3JI TCGA-FS-A4FC 
       33.60         6.41 

$`SLC27A5 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.47         8.52       111.09        32.42        70.16       110.79 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       28.08        22.55        45.83        81.24        10.29        85.32 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
        8.38        21.14        88.50        68.22        69.90        11.41 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       30.87         7.50        36.16         6.31        92.42        56.19 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C8 TCGA-D3-A3CB 
       64.44        45.11       114.67        15.25        46.32        82.29 
TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR 
       61.38        13.32        24.00         6.31         9.34       103.59 
TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J 
       26.37         5.39        80.22        42.71        15.09        41.10 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR 
       17.72         8.84        20.48        52.01        47.87         1.55 
TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA 
        6.97        23.11         4.01         2.89         9.90        11.31 
TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 
       13.22        48.79        35.80        51.12        10.03        39.19 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA 
       13.68         9.99        44.52        36.69        25.15         4.93 
TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 
       22.36         6.64        19.36         7.00        17.56        14.83 
TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EE-A17Y 
       13.15         0.20         0.00         0.00        13.22        10.55 
TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 
        6.31         8.12         1.12         1.35        12.20         5.13 
TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I 
        4.31        36.07         4.34         5.13         9.21         1.18 
TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G 
        7.99         9.90        37.97        11.15        38.63         8.55 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
        4.41         1.08        27.12         9.50        12.03         8.09 
TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 
        8.84         9.99         2.43         8.68         8.09        11.31 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC 
       49.22        23.90         9.67         8.94        39.39        34.29 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK 
       17.98        34.92        47.21        30.08        19.43        16.01 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR 
       35.54        28.31        33.83        30.84         5.42         1.15 
TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 
       13.02        34.98        36.33         8.84        98.27         2.70 
TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI 
        6.18        47.51        29.46        44.25         7.96        14.56 
TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP 
       63.42       111.78       111.91        56.02        25.08        26.99 
TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA 
       21.60        29.65        27.16        23.05         5.56       124.31 
TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AH TCGA-EE-A3J3 
      122.73         3.68        30.15        13.81        12.72         3.22 
TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JD 
       22.92        21.60        21.60        16.14        22.22        27.35 
TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 
        0.46        13.94        31.40        18.61        12.95        38.40 
TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E 
        5.72        76.41        25.18         3.78         3.52        11.90 
TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M 
       11.11       114.15        34.88         4.21        13.45        28.60 
TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 
       42.84        34.68         9.57        36.07        17.72        78.44 
TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH 
       11.80         1.87         1.51        13.08        12.62        11.74 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A 
        9.04         6.58        22.49         1.71        18.41        85.74 
TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
        4.90        64.47         3.45        11.01        23.80        14.24 
TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD 
       15.52         7.33         7.30         3.39        20.38         8.22 
TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK 
       19.53        11.08         7.17        30.87        12.92        12.89 
TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT 
       47.38        52.08         8.65         8.81        49.15        40.64 
TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 
        8.68        27.39         0.82         5.23        53.85         7.36 
TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FD TCGA-FW-A3I3 
       28.73        14.20        10.78         5.98         2.27         0.20 
TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
        0.99         0.13         0.16         0.43         9.90         7.23 
TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 
       12.85        24.85        31.33        84.72        10.13        16.24 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS 
       15.42        12.16        14.70         5.79 

  SLC27A5 MUTATED SLC27A5 WILD-TYPE 
             6.41              0.00 
  SLC27A5 MUTATED SLC27A5 WILD-TYPE 
            46.98            124.31 
  SLC27A5 MUTATED SLC27A5 WILD-TYPE 
           14.945            14.765 
[1] "6.4 - 47.0 (14.9)"  "0.0 - 124.3 (14.8)"
[1] "hr=" "1.3"
D123V2, survival
                   sevent
clus2                 0   1
  SLC27A5 MUTATED     5   3
  SLC27A5 WILD-TYPE 127 128
  SLC27A5 MUTATED SLC27A5 WILD-TYPE 
                8               255 
  SLC27A5 MUTATED SLC27A5 WILD-TYPE 
                3               128 
$`SLC27A5 MUTATED`
TCGA-D3-A3C7 TCGA-D3-A51T TCGA-EE-A17X TCGA-EE-A2MD TCGA-EE-A3AC TCGA-EE-A3AG 
       46.98        15.06        29.82        47.28        25.84        23.47 
TCGA-EE-A3JI TCGA-FS-A4FC 
      148.08        49.45 

$`SLC27A5 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.57        16.67       112.04       112.57        71.80       133.25 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       28.08        31.59        90.90        95.74        43.43       103.10 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
       65.49        23.77       115.53       168.00        69.90        11.87 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       48.76       113.52        42.08        12.10       171.58        56.19 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C8 TCGA-D3-A3CB 
       66.08        45.11       130.72        58.06        46.32       166.52 
TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR 
       86.93        60.23        24.53        13.87         9.34       103.59 
TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J 
       39.75        21.47       161.85        43.69        40.14       131.90 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR 
       18.38        10.03        51.68       135.75       137.92       166.19 
TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX 
        7.43       125.19       151.53        54.67         3.65         6.41 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1HV 
       11.34         3.25         9.90        25.18        66.25        48.89 
TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 
       36.03       117.21        20.38       194.83       176.55        35.93 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC 
      107.34        61.18        53.92        65.92        23.44        68.09 
TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R 
       28.60        10.49       215.44        15.68        13.87        10.16 
TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17Y TCGA-EE-A17Z 
       45.11        35.01         3.55        52.01        27.22         8.65 
TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 
       94.98        33.73        14.70        26.89        68.15         4.96 
TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A 
      109.64       151.27        78.87       168.26        13.55        63.35 
TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H 
       80.61        47.84        13.97        39.62        72.07        32.19 
TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R 
        2.60        44.35        18.61        56.42        37.35        14.47 
TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 
       55.92        25.87       171.55        17.92        46.82       102.90 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD 
       24.43        39.29        58.75        47.54        67.43       314.56 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
      135.95       208.04        48.72        89.33        54.74        79.66 
TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS 
       75.48        90.97       101.95        13.91        14.30        55.59 
TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 
       44.88        94.82        21.67       129.27        28.83        19.76 
TCGA-EE-A2MC TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ 
       61.51       103.27       103.20        16.96       204.66        96.23 
TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ 
      144.76       203.05       167.90        47.54       248.65        43.23 
TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB 
      103.56       136.47        41.59        53.26       124.31       122.73 
TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 
        3.68        54.51        13.81       138.81       172.18       127.20 
TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE 
       36.95        64.08        34.32        53.19        27.35        33.40 
TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 
      101.79        31.40        35.44        13.94        50.76         9.17 
TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F 
       77.75        98.40        48.89        12.59        13.02        26.37 
TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N 
      268.93       152.35         6.44       131.51        61.05        44.05 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
      162.08        50.89        37.25       148.18        79.99        43.82 
TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES 
       23.34        20.15        16.37        31.27        32.05       247.04 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
       80.32        46.98        33.21        92.98       174.21         4.90 
TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 
      216.92        48.59       228.59       202.65        20.91        28.08 
TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE 
        7.79        27.72        48.85       357.37        53.52        40.27 
TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM 
       15.45         9.70        32.75        47.38        23.93       101.26 
TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU 
       74.73       133.55        11.41       148.80        53.16        26.56 
TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 
       49.48        27.09        27.02        77.82        66.67        28.73 
TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 
      174.84        12.43        26.73        77.88         0.20        22.92 
TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 
       47.54         0.16         2.40         9.90         7.23        14.04 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 
      120.46       117.93        84.72        10.13        64.44        62.79 
TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS 
       32.48        39.58         6.67 

  SLC27A5 MUTATED SLC27A5 WILD-TYPE 
            15.06              0.16 
  SLC27A5 MUTATED SLC27A5 WILD-TYPE 
           148.08            357.37 
  SLC27A5 MUTATED SLC27A5 WILD-TYPE 
            38.40             48.76 
[1] "15.1 - 148.1 (38.4)" "0.2 - 357.4 (48.8)" 
[1] "hr=" "1.1"
D123V3, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  SLC27A5 MUTATED                    0             0
  SLC27A5 WILD-TYPE                 35             4
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  SLC27A5 MUTATED                                           2
  SLC27A5 WILD-TYPE                                        56
                   vv
clus                REGIONAL LYMPH NODE
  SLC27A5 MUTATED                     6
  SLC27A5 WILD-TYPE                 164
D123V4, multiclass
                                           clus
vv                                          SLC27A5 MUTATED SLC27A5 WILD-TYPE
  DISTANT METASTASIS                                      0                35
  PRIMARY TUMOR                                           0                 4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE               2                56
  REGIONAL LYMPH NODE                                     6               164
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  SLC27A5 MUTATED             0       0       1        1        0        1
  SLC27A5 WILD-TYPE          10       6      21        9       24       16
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  SLC27A5 MUTATED           1         0         0         3          0
  SLC27A5 WILD-TYPE         9        14         9        28         13
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  SLC27A5 MUTATED            0          1        0
  SLC27A5 WILD-TYPE         22         43       12
D123V5, multiclass
             clus
vv            SLC27A5 MUTATED SLC27A5 WILD-TYPE
  I OR II NOS               0                10
  STAGE 0                   0                 6
  STAGE I                   1                21
  STAGE IA                  1                 9
  STAGE IB                  0                24
  STAGE II                  1                16
  STAGE IIA                 1                 9
  STAGE IIB                 0                14
  STAGE IIC                 0                 9
  STAGE III                 3                28
  STAGE IIIA                0                13
  STAGE IIIB                0                22
  STAGE IIIC                1                43
  STAGE IV                  0                12
[1] 14  2
[1] 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
  SLC27A5 MUTATED       4  1  2  1
  SLC27A5 WILD-TYPE    47 57 51 54
D123V6, multiclass
       clus
vv      SLC27A5 MUTATED SLC27A5 WILD-TYPE
  T0+T1               4                47
  T2                  1                57
  T3                  2                51
  T4                  1                54
[1] 4 2
[1] TRUE
[1] "dimension 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
  SLC27A5 MUTATED     4   2   2   0
  SLC27A5 WILD-TYPE 134  46  30  33
D123V7, multiclass
    clus
vv   SLC27A5 MUTATED SLC27A5 WILD-TYPE
  N0               4               134
  N1               2                46
  N2               2                30
  N3               0                33
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1 M1A M1B M1C
  SLC27A5 MUTATED     8   0   0   0   0
  SLC27A5 WILD-TYPE 232   4   2   2   5
D123V8, multiclass
     clus
vv    SLC27A5 MUTATED SLC27A5 WILD-TYPE
  M0                8               232
  M1                0                 4
  M1A               0                 2
  M1B               0                 2
  M1C               0                 5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D123V9, binary
                   cls
clus                 0  1
  SLC27A5 MUTATED    3  2
  SLC27A5 WILD-TYPE 99 65
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC27A5 MUTATED      3    2
  SLC27A5 WILD-TYPE   99   65
     clus
vv    SLC27A5 MUTATED SLC27A5 WILD-TYPE
  NO                3                99
  YES               2                65
[1] 2 2
[1] FALSE
D123V10, binary
                   cls
clus                  0   1
  SLC27A5 MUTATED     3   5
  SLC27A5 WILD-TYPE  30 230
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC27A5 MUTATED      3    5
  SLC27A5 WILD-TYPE   30  230
     clus
vv    SLC27A5 MUTATED SLC27A5 WILD-TYPE
  NO                3                30
  YES               5               230
[1] 2 2
[1] FALSE
D123V11, continuous
D123V12, binary
                   cls
clus                  0   1
  SLC27A5 MUTATED     3   5
  SLC27A5 WILD-TYPE 100 160
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC27A5 MUTATED      3    5
  SLC27A5 WILD-TYPE  100  160
        clus
vv       SLC27A5 MUTATED SLC27A5 WILD-TYPE
  FEMALE               3               100
  MALE                 5               160
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SLC27A5 MUTATED       0                         0     8
  SLC27A5 WILD-TYPE     3                         1   256
D123V13, multiclass
                           clus
vv                          SLC27A5 MUTATED SLC27A5 WILD-TYPE
  ASIAN                                   0                 3
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                   8               256
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D123V14, binary
                   cls
clus                  0   1
  SLC27A5 MUTATED     0   7
  SLC27A5 WILD-TYPE   3 254
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC27A5 MUTATED      0    7
  SLC27A5 WILD-TYPE    3  254
                        clus
vv                       SLC27A5 MUTATED SLC27A5 WILD-TYPE
  HISPANIC OR LATINO                   0                 3
  NOT HISPANIC OR LATINO               7               254
[1] 2 2
[1] FALSE

Clustering(124) Variable = PDE4DIP MUTATION ANALYSIS
D124V1, survival
                   sevent
clus2                 0   1
  PDE4DIP MUTATED    23  18
  PDE4DIP WILD-TYPE 105 112
  PDE4DIP MUTATED PDE4DIP WILD-TYPE 
               41               217 
  PDE4DIP MUTATED PDE4DIP WILD-TYPE 
               18               112 
$`PDE4DIP MUTATED`
TCGA-D3-A1Q3 TCGA-D3-A2J6 TCGA-D3-A2JC TCGA-D3-A3CE TCGA-D3-A3MU TCGA-D3-A51T 
        8.52        10.29        69.90        13.32        26.37        13.94 
TCGA-D9-A3Z1 TCGA-D9-A6EC TCGA-DA-A1HW TCGA-DA-A1I5 TCGA-DA-A3F5 TCGA-EE-A181 
        4.01        13.22        35.80        44.52        17.56         1.12 
TCGA-EE-A182 TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29S 
        1.35        37.97        38.63         1.08        27.12         9.99 
TCGA-EE-A29V TCGA-EE-A2GB TCGA-EE-A2GO TCGA-EE-A2GR TCGA-EE-A2MC TCGA-EE-A2MD 
        2.43        39.39        30.84         1.15        47.51         9.53 
TCGA-EE-A2MJ TCGA-EE-A2MR TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD 
       63.42        29.65       124.31       122.73        25.84         3.68 
TCGA-EE-A3AE TCGA-EE-A3AH TCGA-ER-A19H TCGA-FS-A1ZA TCGA-FS-A1ZW TCGA-FS-A4F0 
       30.15        12.72        34.88         7.30        27.39        53.85 
TCGA-FS-A4F5 TCGA-FW-A3R5 TCGA-GN-A262 TCGA-GN-A265 TCGA-GN-A266 
       28.73         0.99        24.85        84.72        10.13 

$`PDE4DIP WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       16.47       111.09        32.42        70.16       110.79        28.08 
TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 
       22.55        45.83        81.24        85.32         8.38        21.14 
TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH 
       88.50        68.22        11.41        30.87         7.50        36.16 
TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ 
        6.31        92.42        56.19        64.44        45.11       114.67 
TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CF 
       15.25        46.98        46.32        82.29        61.38        24.00 
TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F 
        6.31         9.34       103.59         5.39        80.22        42.71 
TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A5GN 
       15.09        41.10        17.72         8.84        20.48        52.01 
TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z3 TCGA-D9-A6E9 
       47.87         1.55         6.97        23.11         2.89         9.90 
TCGA-D9-A6EA TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 
       11.31        48.79        51.12        10.03        39.19        13.68 
TCGA-DA-A1I4 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC 
        9.99        36.69        25.15         4.93        22.36         6.64 
TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG 
       19.36         7.00        14.83        13.15         0.20         0.00 
TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 
        0.00        13.22        11.57        10.55         6.31         8.12 
TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F 
       12.20         5.13         4.31        36.07         4.34         5.13 
TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29D TCGA-EE-A29G 
        9.21         1.18         7.99         9.90        11.15         8.55 
TCGA-EE-A29H TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29W 
        4.41         9.50        12.03         8.09         8.84         8.68 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 
        8.09        11.31        49.22        23.90         9.67         8.94 
TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ 
       34.29        17.98        34.92        47.21        30.08        19.43 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GS 
       16.01        35.54        28.31        33.83         5.42        13.02 
TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 
       34.98        36.33         8.84        98.27         2.70         6.18 
TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2ML 
       29.46        44.25         7.96        14.56       111.78       111.91 
TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MS TCGA-EE-A2MT 
       56.02        25.08        26.99        21.60        27.16        23.05 
TCGA-EE-A2MU TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 
        5.56        13.81        15.95         3.22        22.92        21.60 
TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH 
       21.60        16.14        22.22        27.35         0.46        13.94 
TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 
       33.60        31.40        18.61        12.95        38.40         5.72 
TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F 
       76.41        25.18         3.78         3.52        11.90        11.11 
TCGA-ER-A19G TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P 
      114.15         4.21        13.45        28.60        42.84        34.68 
TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
        9.57        36.07        17.72        78.44        11.80         1.87 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET 
        1.51        13.08        12.62        11.74         9.04         6.58 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW 
       22.49         1.71        18.41        85.74         4.90        64.47 
TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 
        3.45        11.01        23.80        14.24        15.52         7.33 
TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG 
        3.39        20.38         8.22        19.53        11.08         7.17 
TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ 
       30.87        12.92        12.89        47.38        52.08         8.65 
TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZY TCGA-FS-A1ZZ 
        8.81        49.15        40.64         8.68         0.82         5.23 
TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD 
        7.36        14.20        10.78         5.98         6.41         2.27 
TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
        0.20         0.13         0.16         0.43         9.90         7.23 
TCGA-GF-A6C8 TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D 
       12.85        31.33        16.24        15.42        12.16        14.70 
TCGA-QB-A6FS 
        5.79 

  PDE4DIP MUTATED PDE4DIP WILD-TYPE 
             0.99              0.00 
  PDE4DIP MUTATED PDE4DIP WILD-TYPE 
           124.31            114.67 
  PDE4DIP MUTATED PDE4DIP WILD-TYPE 
            25.84             14.24 
[1] "1.0 - 124.3 (25.8)" "0.0 - 114.7 (14.2)"
[1] "hr=" "1.3"
D124V2, survival
                   sevent
clus2                 0   1
  PDE4DIP MUTATED    23  18
  PDE4DIP WILD-TYPE 109 113
  PDE4DIP MUTATED PDE4DIP WILD-TYPE 
               41               222 
  PDE4DIP MUTATED PDE4DIP WILD-TYPE 
               18               113 
$`PDE4DIP MUTATED`
TCGA-D3-A1Q3 TCGA-D3-A2J6 TCGA-D3-A2JC TCGA-D3-A3CE TCGA-D3-A3MU TCGA-D3-A51T 
       16.67        43.43        69.90        60.23        39.75        15.06 
TCGA-D9-A3Z1 TCGA-D9-A6EC TCGA-DA-A1HW TCGA-DA-A1I5 TCGA-DA-A3F5 TCGA-EE-A181 
       11.34        66.25        36.03       107.34       215.44        33.73 
TCGA-EE-A182 TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29S 
       14.70        47.84        39.62         2.60        44.35        55.92 
TCGA-EE-A29V TCGA-EE-A2GB TCGA-EE-A2GO TCGA-EE-A2GR TCGA-EE-A2MC TCGA-EE-A2MD 
       25.87        47.54       101.95        14.30        61.51        47.28 
TCGA-EE-A2MJ TCGA-EE-A2MR TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD 
       96.23       103.56       124.31       122.73        25.84         3.68 
TCGA-EE-A3AE TCGA-EE-A3AH TCGA-ER-A19H TCGA-FS-A1ZA TCGA-FS-A1ZW TCGA-FS-A4F0 
       54.51       138.81       152.35        27.72        49.48        77.82 
TCGA-FS-A4F5 TCGA-FW-A3R5 TCGA-GN-A262 TCGA-GN-A265 TCGA-GN-A266 
       28.73        22.92       120.46        84.72        10.13 

$`PDE4DIP WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       16.57       112.04       112.57        71.80       133.25        28.08 
TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 
       31.59        90.90        95.74       103.10        65.49        23.77 
TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH 
      115.53       168.00        11.87        48.76       113.52        42.08 
TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ 
       12.10       171.58        56.19        66.08        45.11       130.72 
TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CF 
       58.06        46.98        46.32       166.52        86.93        24.53 
TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F 
       13.87         9.34       103.59        21.47       161.85        43.69 
TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A5GN 
       40.14       131.90        18.38        10.03        51.68       135.75 
TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 
      137.92       166.19         7.43       125.19       151.53        54.67 
TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-DA-A1HV 
        3.65         6.41         3.25         9.90        25.18        48.89 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I7 
      117.21        20.38       194.83       176.55        35.93        61.18 
TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 
       53.92        65.92        23.44        68.09        28.60        10.49 
TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL 
       15.68        13.87        10.16        45.11        35.01         3.55 
TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A183 
       52.01        29.82        27.22         8.65        94.98        26.89 
TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H 
       68.15         4.96       109.64       151.27        78.87       168.26 
TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29H 
       13.55        63.35        80.61        13.97        72.07        32.19 
TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29W TCGA-EE-A29X 
       18.61        56.42        37.35        14.47       171.55        17.92 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GC 
       46.82       102.90        24.43        39.29        58.75        67.43 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK 
      314.56       135.95       208.04        48.72        89.33        54.74 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GS TCGA-EE-A2GT 
       79.66        75.48        90.97        13.91        55.59        44.88 
TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2ME 
       94.82        21.67       129.27        28.83        19.76       103.27 
TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM 
      103.20        16.96       204.66       144.76       203.05       167.90 
TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU 
       47.54       248.65        43.23       136.47        41.59        53.26 
TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 
       13.81        23.47       172.18       127.20        36.95        64.08 
TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI 
       34.32        53.19        27.35        33.40       101.79       148.08 
TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A 
       31.40        35.44        13.94        50.76         9.17        77.75 
TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G 
       98.40        48.89        12.59        13.02        26.37       268.93 
TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q 
        6.44       131.51        61.05        44.05       162.08        50.89 
TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE 
       37.25       148.18        79.99        43.82        23.34        20.15 
TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV 
       16.37        31.27        32.05       247.04        80.32        46.98 
TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX 
       33.21        92.98       174.21         4.90       216.92        48.59 
TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZB 
      228.59       202.65        20.91        28.08         7.79        48.85 
TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH 
      357.37        53.52        40.27        15.45         9.70        32.75 
TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR 
       47.38        23.93       101.26        74.73       133.55        11.41 
TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F4 
      148.80        53.16        26.56        27.09        27.02        66.67 
TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 
      174.84        12.43        26.73        49.45        77.88         0.20 
TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 
       47.54         0.16         2.40         9.90         7.23        14.04 
TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS 
      117.93        64.44        62.79        32.48        39.58         6.67 

  PDE4DIP MUTATED PDE4DIP WILD-TYPE 
             2.60              0.16 
  PDE4DIP MUTATED PDE4DIP WILD-TYPE 
           215.44            357.37 
  PDE4DIP MUTATED PDE4DIP WILD-TYPE 
            47.54             48.74 
[1] "2.6 - 215.4 (47.5)" "0.2 - 357.4 (48.7)"
[1] "hr=" "1"  
D124V3, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  PDE4DIP MUTATED                    5             1
  PDE4DIP WILD-TYPE                 30             3
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  PDE4DIP MUTATED                                           7
  PDE4DIP WILD-TYPE                                        51
                   vv
clus                REGIONAL LYMPH NODE
  PDE4DIP MUTATED                    29
  PDE4DIP WILD-TYPE                 141
D124V4, multiclass
                                           clus
vv                                          PDE4DIP MUTATED PDE4DIP WILD-TYPE
  DISTANT METASTASIS                                      5                30
  PRIMARY TUMOR                                           1                 3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE               7                51
  REGIONAL LYMPH NODE                                    29               141
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  PDE4DIP MUTATED             1       0       2        1        3        5
  PDE4DIP WILD-TYPE           9       6      20        9       21       12
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  PDE4DIP MUTATED           1         2         1         8          2
  PDE4DIP WILD-TYPE         9        12         8        23         11
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  PDE4DIP MUTATED            5          6        1
  PDE4DIP WILD-TYPE         17         38       11
D124V5, multiclass
             clus
vv            PDE4DIP MUTATED PDE4DIP WILD-TYPE
  I OR II NOS               1                 9
  STAGE 0                   0                 6
  STAGE I                   2                20
  STAGE IA                  1                 9
  STAGE IB                  3                21
  STAGE II                  5                12
  STAGE IIA                 1                 9
  STAGE IIB                 2                12
  STAGE IIC                 1                 8
  STAGE III                 8                23
  STAGE IIIA                2                11
  STAGE IIIB                5                17
  STAGE IIIC                6                38
  STAGE IV                  1                11
[1] 14  2
[1] 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
  PDE4DIP MUTATED      10  9 10  8
  PDE4DIP WILD-TYPE    41 49 43 47
D124V6, multiclass
       clus
vv      PDE4DIP MUTATED PDE4DIP WILD-TYPE
  T0+T1              10                41
  T2                  9                49
  T3                 10                43
  T4                  8                47
[1] 4 2
[1] TRUE
[1] "dimension 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
  PDE4DIP MUTATED    19  11   6   3
  PDE4DIP WILD-TYPE 119  37  26  30
D124V7, multiclass
    clus
vv   PDE4DIP MUTATED PDE4DIP WILD-TYPE
  N0              19               119
  N1              11                37
  N2               6                26
  N3               3                30
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1 M1A M1B M1C
  PDE4DIP MUTATED    38   0   0   0   1
  PDE4DIP WILD-TYPE 202   4   2   2   4
D124V8, multiclass
     clus
vv    PDE4DIP MUTATED PDE4DIP WILD-TYPE
  M0               38               202
  M1                0                 4
  M1A               0                 2
  M1B               0                 2
  M1C               1                 4
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D124V9, binary
                   cls
clus                 0  1
  PDE4DIP MUTATED   16 10
  PDE4DIP WILD-TYPE 86 57
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PDE4DIP MUTATED     16   10
  PDE4DIP WILD-TYPE   86   57
     clus
vv    PDE4DIP MUTATED PDE4DIP WILD-TYPE
  NO               16                86
  YES              10                57
[1] 2 2
[1] FALSE
D124V10, binary
                   cls
clus                  0   1
  PDE4DIP MUTATED     8  34
  PDE4DIP WILD-TYPE  25 201
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PDE4DIP MUTATED      8   34
  PDE4DIP WILD-TYPE   25  201
     clus
vv    PDE4DIP MUTATED PDE4DIP WILD-TYPE
  NO                8                25
  YES              34               201
[1] 2 2
[1] FALSE
D124V11, continuous
D124V12, binary
                   cls
clus                  0   1
  PDE4DIP MUTATED    16  26
  PDE4DIP WILD-TYPE  87 139
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PDE4DIP MUTATED     16   26
  PDE4DIP WILD-TYPE   87  139
        clus
vv       PDE4DIP MUTATED PDE4DIP WILD-TYPE
  FEMALE              16                87
  MALE                26               139
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PDE4DIP MUTATED       0                         0    42
  PDE4DIP WILD-TYPE     3                         1   222
D124V13, multiclass
                           clus
vv                          PDE4DIP MUTATED PDE4DIP WILD-TYPE
  ASIAN                                   0                 3
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  42               222
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D124V14, binary
                   cls
clus                  0   1
  PDE4DIP MUTATED     0  42
  PDE4DIP WILD-TYPE   3 219
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PDE4DIP MUTATED      0   42
  PDE4DIP WILD-TYPE    3  219
                        clus
vv                       PDE4DIP MUTATED PDE4DIP WILD-TYPE
  HISPANIC OR LATINO                   0                 3
  NOT HISPANIC OR LATINO              42               219
[1] 2 2
[1] FALSE

Clustering(125) Variable = KANK3 MUTATION ANALYSIS
D125V1, survival
                 sevent
clus2               0   1
  KANK3 MUTATED     5   2
  KANK3 WILD-TYPE 123 128
  KANK3 MUTATED KANK3 WILD-TYPE 
              7             251 
  KANK3 MUTATED KANK3 WILD-TYPE 
              2             128 
$`KANK3 MUTATED`
TCGA-DA-A1I4 TCGA-EE-A2A2 TCGA-EE-A2GM TCGA-EE-A2MD TCGA-EE-A2MR TCGA-EE-A3JI 
        9.99        23.90        28.31         9.53        29.65        33.60 
TCGA-FW-A3R5 
        0.99 

$`KANK3 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.47         8.52       111.09        32.42        70.16       110.79 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       28.08        22.55        45.83        81.24        10.29        85.32 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
        8.38        21.14        88.50        68.22        69.90        11.41 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       30.87         7.50        36.16         6.31        92.42        56.19 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 
       64.44        45.11       114.67        15.25        46.98        46.32 
TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO 
       82.29        61.38        13.32        24.00         6.31         9.34 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H 
      103.59        26.37         5.39        80.22        42.71        15.09 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN 
       41.10        17.72         8.84        20.48        13.94        52.01 
TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 
       47.87         1.55         6.97        23.11         4.01         2.89 
TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY 
        9.90        11.31        13.22        48.79        35.80        51.12 
TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 
       10.03        39.19        13.68        44.52        36.69        25.15 
TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 
        4.93        22.36         6.64        19.36         7.00        17.56 
TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN 
       14.83        13.15         0.20         0.00         0.00        13.22 
TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 
       11.57        10.55         6.31         8.12         1.12         1.35 
TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F 
       12.20         5.13         4.31        36.07         4.34         5.13 
TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D 
        9.21         1.18         7.99         9.90        37.97        11.15 
TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N 
       38.63         8.55         4.41         1.08        27.12         9.50 
TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W 
       12.03         8.09         8.84         9.99         2.43         8.68 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB 
        8.09        11.31        49.22         9.67         8.94        39.39 
TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ 
       34.29        17.98        34.92        47.21        30.08        19.43 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR 
       16.01        35.54        33.83        30.84         5.42         1.15 
TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 
       13.02        34.98        36.33         8.84        98.27         2.70 
TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI 
        6.18        47.51        29.46        44.25         7.96        14.56 
TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP 
       63.42       111.78       111.91        56.02        25.08        26.99 
TCGA-EE-A2MQ TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB 
       21.60        27.16        23.05         5.56       124.31       122.73 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH 
       25.84         3.68        30.15        13.81        15.95        12.72 
TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA 
        3.22        22.92        21.60        21.60        16.14        22.22 
TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 
       27.35         0.46        13.94        31.40        18.61        12.95 
TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D 
       38.40         5.72        76.41        25.18         3.78         3.52 
TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L 
       11.90        11.11       114.15        34.88         4.21        13.45 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W 
       28.60        42.84        34.68         9.57        36.07        17.72 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG 
       78.44        11.80         1.87         1.51        13.08        12.62 
TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN 
       11.74         9.04         6.58        22.49         1.71        18.41 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 
       85.74         4.90        64.47         3.45        11.01        23.80 
TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC 
       14.24        15.52         7.33         7.30         3.39        20.38 
TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ 
        8.22        19.53        11.08         7.17        30.87        12.92 
TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS 
       12.89        47.38        52.08         8.65         8.81        49.15 
TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 
       40.64         8.68        27.39         0.82         5.23        53.85 
TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC 
        7.36        28.73        14.20        10.78         5.98         6.41 
TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
        2.27         0.20         0.13         0.16         0.43         9.90 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 
        7.23        12.85        24.85        31.33        84.72        10.13 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS 
       16.24        15.42        12.16        14.70         5.79 

  KANK3 MUTATED KANK3 WILD-TYPE 
           0.99            0.00 
  KANK3 MUTATED KANK3 WILD-TYPE 
          33.60          124.31 
  KANK3 MUTATED KANK3 WILD-TYPE 
           23.9            14.7 
[1] "1.0 - 33.6 (23.9)"  "0.0 - 124.3 (14.7)"
[1] "hr=" "1.7"
D125V2, survival
                 sevent
clus2               0   1
  KANK3 MUTATED     5   2
  KANK3 WILD-TYPE 127 129
  KANK3 MUTATED KANK3 WILD-TYPE 
              7             256 
  KANK3 MUTATED KANK3 WILD-TYPE 
              2             129 
$`KANK3 MUTATED`
TCGA-DA-A1I4 TCGA-EE-A2A2 TCGA-EE-A2GM TCGA-EE-A2MD TCGA-EE-A2MR TCGA-EE-A3JI 
       35.93        24.43        75.48        47.28       103.56       148.08 
TCGA-FW-A3R5 
       22.92 

$`KANK3 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.57        16.67       112.04       112.57        71.80       133.25 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       28.08        31.59        90.90        95.74        43.43       103.10 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
       65.49        23.77       115.53       168.00        69.90        11.87 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       48.76       113.52        42.08        12.10       171.58        56.19 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 
       66.08        45.11       130.72        58.06        46.98        46.32 
TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO 
      166.52        86.93        60.23        24.53        13.87         9.34 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H 
      103.59        39.75        21.47       161.85        43.69        40.14 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN 
      131.90        18.38        10.03        51.68        15.06       135.75 
TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 
      137.92       166.19         7.43       125.19       151.53        54.67 
TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA 
        3.65         6.41        11.34         3.25         9.90        25.18 
TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 
       66.25        48.89        36.03       117.21        20.38       194.83 
TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB 
      176.55       107.34        61.18        53.92        65.92        23.44 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q 
       68.09        28.60        10.49       215.44        15.68        13.87 
TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X 
       10.16        45.11        35.01         3.55        52.01        29.82 
TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 
       27.22         8.65        94.98        33.73        14.70        26.89 
TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H 
       68.15         4.96       109.64       151.27        78.87       168.26 
TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E 
       13.55        63.35        80.61        47.84        13.97        39.62 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P 
       72.07        32.19         2.60        44.35        18.61        56.42 
TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X 
       37.35        14.47        55.92        25.87       171.55        17.92 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC 
       46.82       102.90        39.29        58.75        47.54        67.43 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK 
      314.56       135.95       208.04        48.72        89.33        54.74 
TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS 
       79.66        90.97       101.95        13.91        14.30        55.59 
TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 
       44.88        94.82        21.67       129.27        28.83        19.76 
TCGA-EE-A2MC TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ 
       61.51       103.27       103.20        16.96       204.66        96.23 
TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ 
      144.76       203.05       167.90        47.54       248.65        43.23 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC 
      136.47        41.59        53.26       124.31       122.73        25.84 
TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 
        3.68        54.51        13.81        23.47       138.81       172.18 
TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JD 
      127.20        36.95        64.08        34.32        53.19        27.35 
TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 
       33.40       101.79        31.40        35.44        13.94        50.76 
TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E 
        9.17        77.75        98.40        48.89        12.59        13.02 
TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M 
       26.37       268.93       152.35         6.44       131.51        61.05 
TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 
       44.05       162.08        50.89        37.25       148.18        79.99 
TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH 
       43.82        23.34        20.15        16.37        31.27        32.05 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A 
      247.04        80.32        46.98        33.21        92.98       174.21 
TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
        4.90       216.92        48.59       228.59       202.65        20.91 
TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD 
       28.08         7.79        27.72        48.85       357.37        53.52 
TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK 
       40.27        15.45         9.70        32.75        47.38        23.93 
TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT 
      101.26        74.73       133.55        11.41       148.80        53.16 
TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 
       26.56        49.48        27.09        27.02        77.82        66.67 
TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD 
       28.73       174.84        12.43        26.73        49.45        77.88 
TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
        0.20        47.54         0.16         2.40         9.90         7.23 
TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 
       14.04       120.46       117.93        84.72        10.13        64.44 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS 
       62.79        32.48        39.58         6.67 

  KANK3 MUTATED KANK3 WILD-TYPE 
          22.92            0.16 
  KANK3 MUTATED KANK3 WILD-TYPE 
         148.08          357.37 
  KANK3 MUTATED KANK3 WILD-TYPE 
         47.280          48.655 
[1] "22.9 - 148.1 (47.3)" "0.2 - 357.4 (48.7)" 
[1] "hr=" "1.6"
D125V3, continuous
                 vv
clus              DISTANT METASTASIS PRIMARY TUMOR
  KANK3 MUTATED                    0             0
  KANK3 WILD-TYPE                 35             4
                 vv
clus              REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  KANK3 MUTATED                                           2                   5
  KANK3 WILD-TYPE                                        56                 165
D125V4, multiclass
                                           clus
vv                                          KANK3 MUTATED KANK3 WILD-TYPE
  DISTANT METASTASIS                                    0              35
  PRIMARY TUMOR                                         0               4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE             2              56
  REGIONAL LYMPH NODE                                   5             165
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  KANK3 MUTATED             0       0       2        0        0        1
  KANK3 WILD-TYPE          10       6      20       10       24       16
                 vv
clus              STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  KANK3 MUTATED           0         0         1         1          0          0
  KANK3 WILD-TYPE        10        14         8        30         13         22
                 vv
clus              STAGE IIIC STAGE IV
  KANK3 MUTATED            2        0
  KANK3 WILD-TYPE         42       12
D125V5, multiclass
             clus
vv            KANK3 MUTATED KANK3 WILD-TYPE
  I OR II NOS             0              10
  STAGE 0                 0               6
  STAGE I                 2              20
  STAGE IA                0              10
  STAGE IB                0              24
  STAGE II                1              16
  STAGE IIA               0              10
  STAGE IIB               0              14
  STAGE IIC               1               8
  STAGE III               1              30
  STAGE IIIA              0              13
  STAGE IIIB              0              22
  STAGE IIIC              2              42
  STAGE IV                0              12
[1] 14  2
[1] 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
  KANK3 MUTATED       0  2  2  2
  KANK3 WILD-TYPE    51 56 51 53
D125V6, multiclass
       clus
vv      KANK3 MUTATED KANK3 WILD-TYPE
  T0+T1             0              51
  T2                2              56
  T3                2              51
  T4                2              53
[1] 4 2
[1] TRUE
[1] "dimension 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
  KANK3 MUTATED     4   1   2   0
  KANK3 WILD-TYPE 134  47  30  33
D125V7, multiclass
    clus
vv   KANK3 MUTATED KANK3 WILD-TYPE
  N0             4             134
  N1             1              47
  N2             2              30
  N3             0              33
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               M0  M1 M1A M1B M1C
  KANK3 MUTATED     7   0   0   0   0
  KANK3 WILD-TYPE 233   4   2   2   5
D125V8, multiclass
     clus
vv    KANK3 MUTATED KANK3 WILD-TYPE
  M0              7             233
  M1              0               4
  M1A             0               2
  M1B             0               2
  M1C             0               5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D125V9, binary
                 cls
clus                0   1
  KANK3 MUTATED     2   4
  KANK3 WILD-TYPE 100  63
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KANK3 MUTATED      2    4
  KANK3 WILD-TYPE  100   63
     clus
vv    KANK3 MUTATED KANK3 WILD-TYPE
  NO              2             100
  YES             4              63
[1] 2 2
[1] FALSE
D125V10, binary
                 cls
clus                0   1
  KANK3 MUTATED     0   7
  KANK3 WILD-TYPE  33 228
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KANK3 MUTATED      0    7
  KANK3 WILD-TYPE   33  228
     clus
vv    KANK3 MUTATED KANK3 WILD-TYPE
  NO              0              33
  YES             7             228
[1] 2 2
[1] FALSE
D125V11, continuous
D125V12, binary
                 cls
clus                0   1
  KANK3 MUTATED     1   6
  KANK3 WILD-TYPE 102 159
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KANK3 MUTATED      1    6
  KANK3 WILD-TYPE  102  159
        clus
vv       KANK3 MUTATED KANK3 WILD-TYPE
  FEMALE             1             102
  MALE               6             159
[1] 2 2
[1] FALSE
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  KANK3 MUTATED       0                         0     7
  KANK3 WILD-TYPE     3                         1   257
D125V13, multiclass
                           clus
vv                          KANK3 MUTATED KANK3 WILD-TYPE
  ASIAN                                 0               3
  BLACK OR AFRICAN AMERICAN             0               1
  WHITE                                 7             257
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D125V14, binary
                 cls
clus                0   1
  KANK3 MUTATED     0   7
  KANK3 WILD-TYPE   3 254
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KANK3 MUTATED      0    7
  KANK3 WILD-TYPE    3  254
                        clus
vv                       KANK3 MUTATED KANK3 WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO             7             254
[1] 2 2
[1] FALSE

Clustering(126) Variable = RUNX1T1 MUTATION ANALYSIS
D126V1, survival
                   sevent
clus2                 0   1
  RUNX1T1 MUTATED    15  18
  RUNX1T1 WILD-TYPE 113 112
  RUNX1T1 MUTATED RUNX1T1 WILD-TYPE 
               33               225 
  RUNX1T1 MUTATED RUNX1T1 WILD-TYPE 
               18               112 
$`RUNX1T1 MUTATED`
TCGA-D3-A2JF TCGA-D3-A51T TCGA-D3-A5GS TCGA-D9-A3Z1 TCGA-D9-A6EA TCGA-D9-A6EC 
       30.87        13.94         6.97         4.01        11.31        13.22 
TCGA-EB-A5UN TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A20C TCGA-EE-A29C TCGA-EE-A29D 
       13.22         8.12         1.12         4.34        37.97        11.15 
TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29Q TCGA-EE-A2A0 TCGA-EE-A2GC TCGA-EE-A2GI 
       38.63         8.55         8.09        11.31        34.29        30.08 
TCGA-EE-A2GO TCGA-EE-A2M5 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2MJ TCGA-EE-A2MR 
       30.84         8.84        47.51         9.53        63.42        29.65 
TCGA-EE-A3AA TCGA-EE-A3AG TCGA-EE-A3J5 TCGA-ER-A193 TCGA-ER-A2NE TCGA-FS-A1ZA 
      124.31        15.95        21.60        31.40         1.51         7.30 
TCGA-FS-A1ZR TCGA-FS-A1ZW TCGA-FW-A3R5 
        8.81        27.39         0.99 

$`RUNX1T1 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.47         8.52       111.09        32.42        70.16       110.79 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       28.08        22.55        45.83        81.24        10.29        85.32 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
        8.38        21.14        88.50        68.22        69.90        11.41 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO 
        7.50        36.16         6.31        92.42        56.19        64.44 
TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB 
       45.11       114.67        15.25        46.98        46.32        82.29 
TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR 
       61.38        13.32        24.00         6.31         9.34       103.59 
TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J 
       26.37         5.39        80.22        42.71        15.09        41.10 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR 
       17.72         8.84        20.48        52.01        47.87         1.55 
TCGA-D3-A5GU TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY 
       23.11         2.89         9.90        48.79        35.80        51.12 
TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 
       10.03        39.19        13.68         9.99        44.52        36.69 
TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 
       25.15         4.93        22.36         6.64        19.36         7.00 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH 
       17.56        14.83        13.15         0.20         0.00         0.00 
TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 
       11.57        10.55         6.31         1.35        12.20         5.13 
TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A 
        4.31        36.07         5.13         9.21         1.18         7.99 
TCGA-EE-A29B TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P 
        9.90         4.41         1.08        27.12         9.50        12.03 
TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A1 
        8.84         9.99         2.43         8.68         8.09        49.22 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE 
       23.90         9.67         8.94        39.39        17.98        34.92 
TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN 
       47.21        19.43        16.01        35.54        28.31        33.83 
TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M6 
        5.42         1.15        13.02        34.98        36.33        98.27 
TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI 
        2.70         6.18        29.46        44.25         7.96        14.56 
TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ 
      111.78       111.91        56.02        25.08        26.99        21.60 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD 
       27.16        23.05         5.56       122.73        25.84         3.68 
TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 
       30.15        13.81        12.72         3.22        22.92        21.60 
TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI 
       16.14        22.22        27.35         0.46        13.94        33.60 
TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B 
       18.61        12.95        38.40         5.72        76.41        25.18 
TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H 
        3.78         3.52        11.90        11.11       114.15        34.88 
TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q 
        4.21        13.45        28.60        42.84        34.68         9.57 
TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NF 
       36.07        17.72        78.44        11.80         1.87        13.08 
TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL 
       12.62        11.74         9.04         6.58        22.49         1.71 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY 
       18.41        85.74         4.90        64.47         3.45        11.01 
TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZB TCGA-FS-A1ZC 
       23.80        14.24        15.52         7.33         3.39        20.38 
TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ 
        8.22        19.53        11.08         7.17        30.87        12.92 
TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZT 
       12.89        47.38        52.08         8.65        49.15        40.64 
TCGA-FS-A1ZU TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 
        8.68         0.82         5.23        53.85         7.36        28.73 
TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 
       14.20        10.78         5.98         6.41         2.27         0.20 
TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 
        0.13         0.16         0.43         9.90         7.23        12.85 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 
       24.85        31.33        84.72        10.13        16.24        15.42 
TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS 
       12.16        14.70         5.79 

  RUNX1T1 MUTATED RUNX1T1 WILD-TYPE 
             0.99              0.00 
  RUNX1T1 MUTATED RUNX1T1 WILD-TYPE 
           124.31            122.73 
  RUNX1T1 MUTATED RUNX1T1 WILD-TYPE 
            13.22             15.25 
[1] "1.0 - 124.3 (13.2)" "0.0 - 122.7 (15.2)"
[1] "hr=" "1.2"
D126V2, survival
                   sevent
clus2                 0   1
  RUNX1T1 MUTATED    15  18
  RUNX1T1 WILD-TYPE 117 113
  RUNX1T1 MUTATED RUNX1T1 WILD-TYPE 
               33               230 
  RUNX1T1 MUTATED RUNX1T1 WILD-TYPE 
               18               113 
$`RUNX1T1 MUTATED`
TCGA-D3-A2JF TCGA-D3-A51T TCGA-D3-A5GS TCGA-D9-A3Z1 TCGA-D9-A6EA TCGA-D9-A6EC 
       48.76        15.06         7.43        11.34        25.18        66.25 
TCGA-EB-A5UN TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A20C TCGA-EE-A29C TCGA-EE-A29D 
       52.01        94.98        33.73       151.27        47.84        13.97 
TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29Q TCGA-EE-A2A0 TCGA-EE-A2GC TCGA-EE-A2GI 
       39.62        72.07        37.35        46.82        67.43        48.72 
TCGA-EE-A2GO TCGA-EE-A2M5 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2MJ TCGA-EE-A2MR 
      101.95        21.67        61.51        47.28        96.23       103.56 
TCGA-EE-A3AA TCGA-EE-A3AG TCGA-EE-A3J5 TCGA-ER-A193 TCGA-ER-A2NE TCGA-FS-A1ZA 
      124.31        23.47        36.95        31.40        20.15        27.72 
TCGA-FS-A1ZR TCGA-FS-A1ZW TCGA-FW-A3R5 
       11.41        49.48        22.92 

$`RUNX1T1 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.57        16.67       112.04       112.57        71.80       133.25 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       28.08        31.59        90.90        95.74        43.43       103.10 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
       65.49        23.77       115.53       168.00        69.90        11.87 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO 
      113.52        42.08        12.10       171.58        56.19        66.08 
TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB 
       45.11       130.72        58.06        46.98        46.32       166.52 
TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR 
       86.93        60.23        24.53        13.87         9.34       103.59 
TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J 
       39.75        21.47       161.85        43.69        40.14       131.90 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR 
       18.38        10.03        51.68       135.75       137.92       166.19 
TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z3 
      125.19       151.53        54.67         3.65         6.41         3.25 
TCGA-D9-A6E9 TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 
        9.90        48.89        36.03       117.21        20.38       194.83 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA 
      176.55        35.93       107.34        61.18        53.92        65.92 
TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 
       23.44        68.09        28.60        10.49       215.44        15.68 
TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EE-A17X 
       13.87        10.16        45.11        35.01         3.55        29.82 
TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 
       27.22         8.65        14.70        26.89        68.15         4.96 
TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B 
      109.64        78.87       168.26        13.55        63.35        80.61 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29R 
       32.19         2.60        44.35        18.61        56.42        14.47 
TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A1 TCGA-EE-A2A2 
       55.92        25.87       171.55        17.92       102.90        24.43 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH 
       39.29        58.75        47.54       314.56       135.95       208.04 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP 
       89.33        54.74        79.66        75.48        90.97        13.91 
TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 
       14.30        55.59        44.88        94.82       129.27        28.83 
TCGA-EE-A2M8 TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MK 
       19.76       103.27       103.20        16.96       204.66       144.76 
TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MS 
      203.05       167.90        47.54       248.65        43.23       136.47 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE 
       41.59        53.26       122.73        25.84         3.68        54.51 
TCGA-EE-A3AF TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 
       13.81       138.81       172.18       127.20        64.08        34.32 
TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 
       53.19        27.35        33.40       101.79       148.08        35.44 
TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C 
       13.94        50.76         9.17        77.75        98.40        48.89 
TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J 
       12.59        13.02        26.37       268.93       152.35         6.44 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S 
      131.51        61.05        44.05       162.08        50.89        37.25 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NF TCGA-ER-A2NG 
      148.18        79.99        43.82        23.34        16.37        31.27 
TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN 
       32.05       247.04        80.32        46.98        33.21        92.98 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 
      174.21         4.90       216.92        48.59       228.59       202.65 
TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD 
       20.91        28.08         7.79        48.85       357.37        53.52 
TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK 
       40.27        15.45         9.70        32.75        47.38        23.93 
TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU 
      101.26        74.73       133.55       148.80        53.16        26.56 
TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 
       27.09        27.02        77.82        66.67        28.73       174.84 
TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU 
       12.43        26.73        49.45        77.88         0.20        47.54 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 
        0.16         2.40         9.90         7.23        14.04       120.46 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
      117.93        84.72        10.13        64.44        62.79        32.48 
TCGA-GN-A26D TCGA-QB-A6FS 
       39.58         6.67 

  RUNX1T1 MUTATED RUNX1T1 WILD-TYPE 
             7.43              0.16 
  RUNX1T1 MUTATED RUNX1T1 WILD-TYPE 
           151.27            357.37 
  RUNX1T1 MUTATED RUNX1T1 WILD-TYPE 
            46.82             48.89 
[1] "7.4 - 151.3 (46.8)" "0.2 - 357.4 (48.9)"
[1] "hr=" "1.5"
D126V3, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  RUNX1T1 MUTATED                    6             2
  RUNX1T1 WILD-TYPE                 29             2
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  RUNX1T1 MUTATED                                           6
  RUNX1T1 WILD-TYPE                                        52
                   vv
clus                REGIONAL LYMPH NODE
  RUNX1T1 MUTATED                    19
  RUNX1T1 WILD-TYPE                 151
D126V4, multiclass
                                           clus
vv                                          RUNX1T1 MUTATED RUNX1T1 WILD-TYPE
  DISTANT METASTASIS                                      6                29
  PRIMARY TUMOR                                           2                 2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE               6                52
  REGIONAL LYMPH NODE                                    19               151
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  RUNX1T1 MUTATED             0       2       3        2        1        4
  RUNX1T1 WILD-TYPE          10       4      19        8       23       13
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  RUNX1T1 MUTATED           1         3         1         6          2
  RUNX1T1 WILD-TYPE         9        11         8        25         11
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  RUNX1T1 MUTATED            3          4        1
  RUNX1T1 WILD-TYPE         19         40       11
D126V5, multiclass
             clus
vv            RUNX1T1 MUTATED RUNX1T1 WILD-TYPE
  I OR II NOS               0                10
  STAGE 0                   2                 4
  STAGE I                   3                19
  STAGE IA                  2                 8
  STAGE IB                  1                23
  STAGE II                  4                13
  STAGE IIA                 1                 9
  STAGE IIB                 3                11
  STAGE IIC                 1                 8
  STAGE III                 6                25
  STAGE IIIA                2                11
  STAGE IIIB                3                19
  STAGE IIIC                4                40
  STAGE IV                  1                11
[1] 14  2
[1] 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
  RUNX1T1 MUTATED       5  7 10  8
  RUNX1T1 WILD-TYPE    46 51 43 47
D126V6, multiclass
       clus
vv      RUNX1T1 MUTATED RUNX1T1 WILD-TYPE
  T0+T1               5                46
  T2                  7                51
  T3                 10                43
  T4                  8                47
[1] 4 2
[1] TRUE
[1] "dimension 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
  RUNX1T1 MUTATED    18   8   4   2
  RUNX1T1 WILD-TYPE 120  40  28  31
D126V7, multiclass
    clus
vv   RUNX1T1 MUTATED RUNX1T1 WILD-TYPE
  N0              18               120
  N1               8                40
  N2               4                28
  N3               2                31
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1 M1A M1B M1C
  RUNX1T1 MUTATED    32   0   0   0   1
  RUNX1T1 WILD-TYPE 208   4   2   2   4
D126V8, multiclass
     clus
vv    RUNX1T1 MUTATED RUNX1T1 WILD-TYPE
  M0               32               208
  M1                0                 4
  M1A               0                 2
  M1B               0                 2
  M1C               1                 4
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D126V9, binary
                   cls
clus                 0  1
  RUNX1T1 MUTATED   17  8
  RUNX1T1 WILD-TYPE 85 59
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RUNX1T1 MUTATED     17    8
  RUNX1T1 WILD-TYPE   85   59
     clus
vv    RUNX1T1 MUTATED RUNX1T1 WILD-TYPE
  NO               17                85
  YES               8                59
[1] 2 2
[1] FALSE
D126V10, binary
                   cls
clus                  0   1
  RUNX1T1 MUTATED     2  31
  RUNX1T1 WILD-TYPE  31 204
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RUNX1T1 MUTATED      2   31
  RUNX1T1 WILD-TYPE   31  204
     clus
vv    RUNX1T1 MUTATED RUNX1T1 WILD-TYPE
  NO                2                31
  YES              31               204
[1] 2 2
[1] FALSE
D126V11, continuous
D126V12, binary
                   cls
clus                  0   1
  RUNX1T1 MUTATED     7  26
  RUNX1T1 WILD-TYPE  96 139
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RUNX1T1 MUTATED      7   26
  RUNX1T1 WILD-TYPE   96  139
        clus
vv       RUNX1T1 MUTATED RUNX1T1 WILD-TYPE
  FEMALE               7                96
  MALE                26               139
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RUNX1T1 MUTATED       0                         0    33
  RUNX1T1 WILD-TYPE     3                         1   231
D126V13, multiclass
                           clus
vv                          RUNX1T1 MUTATED RUNX1T1 WILD-TYPE
  ASIAN                                   0                 3
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  33               231
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D126V14, binary
                   cls
clus                  0   1
  RUNX1T1 MUTATED     0  33
  RUNX1T1 WILD-TYPE   3 228
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RUNX1T1 MUTATED      0   33
  RUNX1T1 WILD-TYPE    3  228
                        clus
vv                       RUNX1T1 MUTATED RUNX1T1 WILD-TYPE
  HISPANIC OR LATINO                   0                 3
  NOT HISPANIC OR LATINO              33               228
[1] 2 2
[1] FALSE

Clustering(127) Variable = WDR12 MUTATION ANALYSIS
D127V1, survival
                 sevent
clus2               0   1
  WDR12 MUTATED     3   7
  WDR12 WILD-TYPE 125 123
  WDR12 MUTATED WDR12 WILD-TYPE 
             10             248 
  WDR12 MUTATED WDR12 WILD-TYPE 
              7             123 
$`WDR12 MUTATED`
TCGA-D3-A1Q3 TCGA-D3-A1Q6 TCGA-D3-A2J6 TCGA-D3-A2J8 TCGA-D3-A2JC TCGA-EE-A29L 
        8.52        70.16        10.29         8.38        69.90         1.08 
TCGA-EE-A2MI TCGA-EE-A3AB TCGA-ER-A19F TCGA-GN-A262 
       14.56       122.73        11.11        24.85 

$`WDR12 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 
       16.47       111.09        32.42       110.79        28.08        22.55 
TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J7 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB 
       45.83        81.24        85.32        21.14        88.50        68.22 
TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL 
       11.41        30.87         7.50        36.16         6.31        92.42 
TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 
       56.19        64.44        45.11       114.67        15.25        46.98 
TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML 
       46.32        82.29        61.38        13.32        24.00         6.31 
TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F 
        9.34       103.59        26.37         5.39        80.22        42.71 
TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T 
       15.09        41.10        17.72         8.84        20.48        13.94 
TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 
       52.01        47.87         1.55         6.97        23.11         4.01 
TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1HW 
        2.89         9.90        11.31        13.22        48.79        35.80 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 
       51.12        10.03        39.19        13.68         9.99        44.52 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
       36.69        25.15         4.93        22.36         6.64        19.36 
TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG 
        7.00        17.56        14.83        13.15         0.20         0.00 
TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 
        0.00        13.22        11.57        10.55         6.31         8.12 
TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B 
        1.12         1.35        12.20         5.13         4.31        36.07 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B 
        4.34         5.13         9.21         1.18         7.99         9.90 
TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M 
       37.97        11.15        38.63         8.55         4.41        27.12 
TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V 
        9.50        12.03         8.09         8.84         9.99         2.43 
TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 
        8.68         8.09        11.31        49.22        23.90         9.67 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH 
        8.94        39.39        34.29        17.98        34.92        47.21 
TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN 
       30.08        19.43        16.01        35.54        28.31        33.83 
TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU 
       30.84         5.42         1.15        13.02        34.98        36.33 
TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD 
        8.84        98.27         2.70         6.18        47.51         9.53 
TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML 
       29.46        44.25         7.96        63.42       111.78       111.91 
TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS 
       56.02        25.08        26.99        21.60        29.65        27.16 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE 
       23.05         5.56       124.31        25.84         3.68        30.15 
TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 
       13.81        15.95        12.72         3.22        22.92        21.60 
TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH 
       21.60        16.14        22.22        27.35         0.46        13.94 
TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 
       33.60        31.40        18.61        12.95        38.40         5.72 
TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19G 
       76.41        25.18         3.78         3.52        11.90       114.15 
TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P 
       34.88         4.21        13.45        28.60        42.84        34.68 
TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
        9.57        36.07        17.72        78.44        11.80         1.87 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET 
        1.51        13.08        12.62        11.74         9.04         6.58 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW 
       22.49         1.71        18.41        85.74         4.90        64.47 
TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 
        3.45        11.01        23.80        14.24        15.52         7.33 
TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF 
        7.30         3.39        20.38         8.22        19.53        11.08 
TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP 
        7.17        30.87        12.92        12.89        47.38        52.08 
TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW 
        8.65         8.81        49.15        40.64         8.68        27.39 
TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 
        0.82         5.23        53.85         7.36        28.73        14.20 
TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 
       10.78         5.98         6.41         2.27         0.20         0.99 
TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 
        0.13         0.16         0.43         9.90         7.23        12.85 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
       31.33        84.72        10.13        16.24        15.42        12.16 
TCGA-GN-A26D TCGA-QB-A6FS 
       14.70         5.79 

  WDR12 MUTATED WDR12 WILD-TYPE 
           1.08            0.00 
  WDR12 MUTATED WDR12 WILD-TYPE 
         122.73          124.31 
  WDR12 MUTATED WDR12 WILD-TYPE 
         12.835          14.960 
[1] "1.1 - 122.7 (12.8)" "0.0 - 124.3 (15.0)"
[1] "hr=" "1.2"
D127V2, survival
                 sevent
clus2               0   1
  WDR12 MUTATED     4   7
  WDR12 WILD-TYPE 128 124
  WDR12 MUTATED WDR12 WILD-TYPE 
             11             252 
  WDR12 MUTATED WDR12 WILD-TYPE 
              7             124 
$`WDR12 MUTATED`
TCGA-D3-A1Q3 TCGA-D3-A1Q6 TCGA-D3-A2J6 TCGA-D3-A2J8 TCGA-D3-A2JC TCGA-D9-A148 
       16.67        71.80        43.43        65.49        69.90       151.53 
TCGA-EE-A29L TCGA-EE-A2MI TCGA-EE-A3AB TCGA-ER-A19F TCGA-GN-A262 
        2.60       204.66       122.73        26.37       120.46 

$`WDR12 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 
       16.57       112.04       112.57       133.25        28.08        31.59 
TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J7 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB 
       90.90        95.74       103.10        23.77       115.53       168.00 
TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL 
       11.87        48.76       113.52        42.08        12.10       171.58 
TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 
       56.19        66.08        45.11       130.72        58.06        46.98 
TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML 
       46.32       166.52        86.93        60.23        24.53        13.87 
TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F 
        9.34       103.59        39.75        21.47       161.85        43.69 
TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T 
       40.14       131.90        18.38        10.03        51.68        15.06 
TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A149 
      135.75       137.92       166.19         7.43       125.19        54.67 
TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA 
        3.65         6.41        11.34         3.25         9.90        25.18 
TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 
       66.25        48.89        36.03       117.21        20.38       194.83 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA 
      176.55        35.93       107.34        61.18        53.92        65.92 
TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 
       23.44        68.09        28.60        10.49       215.44        15.68 
TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN 
       13.87        10.16        45.11        35.01         3.55        52.01 
TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 
       29.82        27.22         8.65        94.98        33.73        14.70 
TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F 
       26.89        68.15         4.96       109.64       151.27        78.87 
TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D 
      168.26        13.55        63.35        80.61        47.84        13.97 
TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P 
       39.62        72.07        32.19        44.35        18.61        56.42 
TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X 
       37.35        14.47        55.92        25.87       171.55        17.92 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB 
       46.82       102.90        24.43        39.29        58.75        47.54 
TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ 
       67.43       314.56       135.95       208.04        48.72        89.33 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP 
       54.74        79.66        75.48        90.97       101.95        13.91 
TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 
       14.30        55.59        44.88        94.82        21.67       129.27 
TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG 
       28.83        19.76        61.51        47.28       103.27       103.20 
TCGA-EE-A2MH TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN 
       16.96        96.23       144.76       203.05       167.90        47.54 
TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU 
      248.65        43.23       103.56       136.47        41.59        53.26 
TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG 
      124.31        25.84         3.68        54.51        13.81        23.47 
TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 
      138.81       172.18       127.20        36.95        64.08        34.32 
TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 
       53.19        27.35        33.40       101.79       148.08        31.40 
TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B 
       35.44        13.94        50.76         9.17        77.75        98.40 
TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J 
       48.89        12.59        13.02       268.93       152.35         6.44 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S 
      131.51        61.05        44.05       162.08        50.89        37.25 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF 
      148.18        79.99        43.82        23.34        20.15        16.37 
TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL 
       31.27        32.05       247.04        80.32        46.98        33.21 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY 
       92.98       174.21         4.90       216.92        48.59       228.59 
TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB 
      202.65        20.91        28.08         7.79        27.72        48.85 
TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH 
      357.37        53.52        40.27        15.45         9.70        32.75 
TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR 
       47.38        23.93       101.26        74.73       133.55        11.41 
TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ 
      148.80        53.16        26.56        49.48        27.09        27.02 
TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB 
       77.82        66.67        28.73       174.84        12.43        26.73 
TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV 
       49.45        77.88         0.20        22.92        47.54         0.16 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A264 TCGA-GN-A265 
        2.40         9.90         7.23        14.04       117.93        84.72 
TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS 
       10.13        64.44        62.79        32.48        39.58         6.67 

  WDR12 MUTATED WDR12 WILD-TYPE 
           2.60            0.16 
  WDR12 MUTATED WDR12 WILD-TYPE 
         204.66          357.37 
  WDR12 MUTATED WDR12 WILD-TYPE 
          69.90           47.69 
[1] "2.6 - 204.7 (69.9)" "0.2 - 357.4 (47.7)"
[1] "hr=" "1.1"
D127V3, continuous
                 vv
clus              DISTANT METASTASIS PRIMARY TUMOR
  WDR12 MUTATED                    0             0
  WDR12 WILD-TYPE                 35             4
                 vv
clus              REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  WDR12 MUTATED                                           2                   9
  WDR12 WILD-TYPE                                        56                 161
D127V4, multiclass
                                           clus
vv                                          WDR12 MUTATED WDR12 WILD-TYPE
  DISTANT METASTASIS                                    0              35
  PRIMARY TUMOR                                         0               4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE             2              56
  REGIONAL LYMPH NODE                                   9             161
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  WDR12 MUTATED             0       0       0        0        1        0
  WDR12 WILD-TYPE          10       6      22       10       23       17
                 vv
clus              STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  WDR12 MUTATED           0         2         1         3          0          0
  WDR12 WILD-TYPE        10        12         8        28         13         22
                 vv
clus              STAGE IIIC STAGE IV
  WDR12 MUTATED            1        0
  WDR12 WILD-TYPE         43       12
D127V5, multiclass
             clus
vv            WDR12 MUTATED WDR12 WILD-TYPE
  I OR II NOS             0              10
  STAGE 0                 0               6
  STAGE I                 0              22
  STAGE IA                0              10
  STAGE IB                1              23
  STAGE II                0              17
  STAGE IIA               0              10
  STAGE IIB               2              12
  STAGE IIC               1               8
  STAGE III               3              28
  STAGE IIIA              0              13
  STAGE IIIB              0              22
  STAGE IIIC              1              43
  STAGE IV                0              12
[1] 14  2
[1] 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
  WDR12 MUTATED       2  1  1  4
  WDR12 WILD-TYPE    49 57 52 51
D127V6, multiclass
       clus
vv      WDR12 MUTATED WDR12 WILD-TYPE
  T0+T1             2              49
  T2                1              57
  T3                1              52
  T4                4              51
[1] 4 2
[1] TRUE
[1] "dimension 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
  WDR12 MUTATED     5   1   2   2
  WDR12 WILD-TYPE 133  47  30  31
D127V7, multiclass
    clus
vv   WDR12 MUTATED WDR12 WILD-TYPE
  N0             5             133
  N1             1              47
  N2             2              30
  N3             2              31
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               M0  M1 M1A M1B M1C
  WDR12 MUTATED     9   0   0   1   0
  WDR12 WILD-TYPE 231   4   2   1   5
D127V8, multiclass
     clus
vv    WDR12 MUTATED WDR12 WILD-TYPE
  M0              9             231
  M1              0               4
  M1A             0               2
  M1B             1               1
  M1C             0               5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D127V9, binary
                 cls
clus                0   1
  WDR12 MUTATED     2   3
  WDR12 WILD-TYPE 100  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WDR12 MUTATED      2    3
  WDR12 WILD-TYPE  100   64
     clus
vv    WDR12 MUTATED WDR12 WILD-TYPE
  NO              2             100
  YES             3              64
[1] 2 2
[1] FALSE
D127V10, binary
                 cls
clus                0   1
  WDR12 MUTATED     2   9
  WDR12 WILD-TYPE  31 226
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WDR12 MUTATED      2    9
  WDR12 WILD-TYPE   31  226
     clus
vv    WDR12 MUTATED WDR12 WILD-TYPE
  NO              2              31
  YES             9             226
[1] 2 2
[1] FALSE
D127V11, continuous
D127V12, binary
                 cls
clus                0   1
  WDR12 MUTATED     2   9
  WDR12 WILD-TYPE 101 156
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WDR12 MUTATED      2    9
  WDR12 WILD-TYPE  101  156
        clus
vv       WDR12 MUTATED WDR12 WILD-TYPE
  FEMALE             2             101
  MALE               9             156
[1] 2 2
[1] FALSE
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  WDR12 MUTATED       0                         0    11
  WDR12 WILD-TYPE     3                         1   253
D127V13, multiclass
                           clus
vv                          WDR12 MUTATED WDR12 WILD-TYPE
  ASIAN                                 0               3
  BLACK OR AFRICAN AMERICAN             0               1
  WHITE                                11             253
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D127V14, binary
                 cls
clus                0   1
  WDR12 MUTATED     0  11
  WDR12 WILD-TYPE   3 250
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WDR12 MUTATED      0   11
  WDR12 WILD-TYPE    3  250
                        clus
vv                       WDR12 MUTATED WDR12 WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO            11             250
[1] 2 2
[1] FALSE

Clustering(128) Variable = POTEG MUTATION ANALYSIS
D128V1, survival
                 sevent
clus2               0   1
  POTEG MUTATED    14  15
  POTEG WILD-TYPE 114 115
  POTEG MUTATED POTEG WILD-TYPE 
             29             229 
  POTEG MUTATED POTEG WILD-TYPE 
             15             115 
$`POTEG MUTATED`
TCGA-D3-A2JF TCGA-D9-A6E9 TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1HY TCGA-EE-A182 
       30.87         9.90        13.22        48.79        51.12         1.35 
TCGA-EE-A20C TCGA-EE-A20H TCGA-EE-A29D TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29S 
        4.34         9.21        11.15         1.08        27.12         9.99 
TCGA-EE-A29V TCGA-EE-A2A5 TCGA-EE-A2GI TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A3AB 
        2.43         9.67        30.08        14.56        63.42       122.73 
TCGA-EE-A3AH TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-ER-A19D TCGA-ER-A19J TCGA-FS-A1ZP 
       12.72        22.92        21.60         3.52         4.21        52.08 
TCGA-FS-A1ZT TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4FC TCGA-FW-A3R5 
       40.64         5.23        53.85         6.41         0.99 

$`POTEG WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.47         8.52       111.09        32.42        70.16       110.79 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       28.08        22.55        45.83        81.24        10.29        85.32 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
        8.38        21.14        88.50        68.22        69.90        11.41 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO 
        7.50        36.16         6.31        92.42        56.19        64.44 
TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB 
       45.11       114.67        15.25        46.98        46.32        82.29 
TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR 
       61.38        13.32        24.00         6.31         9.34       103.59 
TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J 
       26.37         5.39        80.22        42.71        15.09        41.10 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO 
       17.72         8.84        20.48        13.94        52.01        47.87 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6EA 
        1.55         6.97        23.11         4.01         2.89        11.31 
TCGA-DA-A1HW TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 
       35.80        10.03        39.19        13.68         9.99        44.52 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
       36.69        25.15         4.93        22.36         6.64        19.36 
TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG 
        7.00        17.56        14.83        13.15         0.20         0.00 
TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 
        0.00        13.22        11.57        10.55         6.31         8.12 
TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20F 
        1.12        12.20         5.13         4.31        36.07         5.13 
TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G 
        1.18         7.99         9.90        37.97        38.63         8.55 
TCGA-EE-A29H TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29W 
        4.41         9.50        12.03         8.09         8.84         8.68 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB 
        8.09        11.31        49.22        23.90         8.94        39.39 
TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK 
       34.29        17.98        34.92        47.21        19.43        16.01 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR 
       35.54        28.31        33.83        30.84         5.42         1.15 
TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 
       13.02        34.98        36.33         8.84        98.27         2.70 
TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH 
        6.18        47.51         9.53        29.46        44.25         7.96 
TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ 
      111.78       111.91        56.02        25.08        26.99        21.60 
TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AC 
       29.65        27.16        23.05         5.56       124.31        25.84 
TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3J3 TCGA-EE-A3J5 
        3.68        30.15        13.81        15.95         3.22        21.60 
TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI 
       16.14        22.22        27.35         0.46        13.94        33.60 
TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A 
       31.40        18.61        12.95        38.40         5.72        76.41 
TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H 
       25.18         3.78        11.90        11.11       114.15        34.88 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S 
       13.45        28.60        42.84        34.68         9.57        36.07 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF 
       17.72        78.44        11.80         1.87         1.51        13.08 
TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL 
       12.62        11.74         9.04         6.58        22.49         1.71 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY 
       18.41        85.74         4.90        64.47         3.45        11.01 
TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB 
       23.80        14.24        15.52         7.33         7.30         3.39 
TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH 
       20.38         8.22        19.53        11.08         7.17        30.87 
TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS 
       12.92        12.89        47.38         8.65         8.81        49.15 
TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 
        8.68        27.39         0.82         7.36        28.73        14.20 
TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV 
       10.78         5.98         2.27         0.20         0.13         0.16 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 
        0.43         9.90         7.23        12.85        24.85        31.33 
TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D 
       84.72        10.13        16.24        15.42        12.16        14.70 
TCGA-QB-A6FS 
        5.79 

  POTEG MUTATED POTEG WILD-TYPE 
           0.99            0.00 
  POTEG MUTATED POTEG WILD-TYPE 
         122.73          124.31 
  POTEG MUTATED POTEG WILD-TYPE 
          12.72           15.25 
[1] "1.0 - 122.7 (12.7)" "0.0 - 124.3 (15.2)"
[1] "hr=" "1.1"
D128V2, survival
                 sevent
clus2               0   1
  POTEG MUTATED    14  15
  POTEG WILD-TYPE 118 116
  POTEG MUTATED POTEG WILD-TYPE 
             29             234 
  POTEG MUTATED POTEG WILD-TYPE 
             15             116 
$`POTEG MUTATED`
TCGA-D3-A2JF TCGA-D9-A6E9 TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1HY TCGA-EE-A182 
       48.76         9.90        66.25        48.89       117.21        14.70 
TCGA-EE-A20C TCGA-EE-A20H TCGA-EE-A29D TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29S 
      151.27       168.26        13.97         2.60        44.35        55.92 
TCGA-EE-A29V TCGA-EE-A2A5 TCGA-EE-A2GI TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A3AB 
       25.87        39.29        48.72       204.66        96.23       122.73 
TCGA-EE-A3AH TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-ER-A19D TCGA-ER-A19J TCGA-FS-A1ZP 
      138.81       127.20        64.08        12.59         6.44        74.73 
TCGA-FS-A1ZT TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4FC TCGA-FW-A3R5 
       53.16        27.02        77.82        49.45        22.92 

$`POTEG WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.57        16.67       112.04       112.57        71.80       133.25 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       28.08        31.59        90.90        95.74        43.43       103.10 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
       65.49        23.77       115.53       168.00        69.90        11.87 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO 
      113.52        42.08        12.10       171.58        56.19        66.08 
TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB 
       45.11       130.72        58.06        46.98        46.32       166.52 
TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR 
       86.93        60.23        24.53        13.87         9.34       103.59 
TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J 
       39.75        21.47       161.85        43.69        40.14       131.90 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO 
       18.38        10.03        51.68        15.06       135.75       137.92 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW 
      166.19         7.43       125.19       151.53        54.67         3.65 
TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6EA TCGA-DA-A1HW TCGA-DA-A1I0 
        6.41        11.34         3.25        25.18        36.03        20.38 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 
      194.83       176.55        35.93       107.34        61.18        53.92 
TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 
       65.92        23.44        68.09        28.60        10.49       215.44 
TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL 
       15.68        13.87        10.16        45.11        35.01         3.55 
TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 
       52.01        29.82        27.22         8.65        94.98        33.73 
TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20I 
       26.89        68.15         4.96       109.64        78.87        13.55 
TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H 
       63.35        80.61        47.84        39.62        72.07        32.19 
TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29W TCGA-EE-A29X 
       18.61        56.42        37.35        14.47       171.55        17.92 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC 
       46.82       102.90        24.43        58.75        47.54        67.43 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
      314.56       135.95       208.04        89.33        54.74        79.66 
TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS 
       75.48        90.97       101.95        13.91        14.30        55.59 
TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 
       44.88        94.82        21.67       129.27        28.83        19.76 
TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MK 
       61.51        47.28       103.27       103.20        16.96       144.76 
TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR 
      203.05       167.90        47.54       248.65        43.23       103.56 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3AD 
      136.47        41.59        53.26       124.31        25.84         3.68 
TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3J3 TCGA-EE-A3J5 TCGA-EE-A3J8 
       54.51        13.81        23.47       172.18        36.95        34.32 
TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 
       53.19        27.35        33.40       101.79       148.08        31.40 
TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B 
       35.44        13.94        50.76         9.17        77.75        98.40 
TCGA-ER-A19C TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19L 
       48.89        13.02        26.37       268.93       152.35       131.51 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W 
       61.05        44.05       162.08        50.89        37.25       148.18 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG 
       79.99        43.82        23.34        20.15        16.37        31.27 
TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN 
       32.05       247.04        80.32        46.98        33.21        92.98 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 
      174.21         4.90       216.92        48.59       228.59       202.65 
TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC 
       20.91        28.08         7.79        27.72        48.85       357.37 
TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ 
       53.52        40.27        15.45         9.70        32.75        47.38 
TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZU 
       23.93       101.26       133.55        11.41       148.80        26.56 
TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 
       49.48        27.09        66.67        28.73       174.84        12.43 
TCGA-FS-A4FB TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY 
       26.73        77.88         0.20        47.54         0.16         2.40 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        9.90         7.23        14.04       120.46       117.93        84.72 
TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS 
       10.13        64.44        62.79        32.48        39.58         6.67 

  POTEG MUTATED POTEG WILD-TYPE 
           2.60            0.16 
  POTEG MUTATED POTEG WILD-TYPE 
         204.66          357.37 
  POTEG MUTATED POTEG WILD-TYPE 
          49.45           47.54 
[1] "2.6 - 204.7 (49.5)" "0.2 - 357.4 (47.5)"
[1] "hr=" "1.1"
D128V3, continuous
                 vv
clus              DISTANT METASTASIS PRIMARY TUMOR
  POTEG MUTATED                    7             2
  POTEG WILD-TYPE                 28             2
                 vv
clus              REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  POTEG MUTATED                                           6                  14
  POTEG WILD-TYPE                                        52                 156
D128V4, multiclass
                                           clus
vv                                          POTEG MUTATED POTEG WILD-TYPE
  DISTANT METASTASIS                                    7              28
  PRIMARY TUMOR                                         2               2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE             6              52
  REGIONAL LYMPH NODE                                  14             156
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  POTEG MUTATED             0       1       2        2        3        3
  POTEG WILD-TYPE          10       5      20        8       21       14
                 vv
clus              STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  POTEG MUTATED           2         3         0         4          2          1
  POTEG WILD-TYPE         8        11         9        27         11         21
                 vv
clus              STAGE IIIC STAGE IV
  POTEG MUTATED            5        1
  POTEG WILD-TYPE         39       11
D128V5, multiclass
             clus
vv            POTEG MUTATED POTEG WILD-TYPE
  I OR II NOS             0              10
  STAGE 0                 1               5
  STAGE I                 2              20
  STAGE IA                2               8
  STAGE IB                3              21
  STAGE II                3              14
  STAGE IIA               2               8
  STAGE IIB               3              11
  STAGE IIC               0               9
  STAGE III               4              27
  STAGE IIIA              2              11
  STAGE IIIB              1              21
  STAGE IIIC              5              39
  STAGE IV                1              11
[1] 14  2
[1] 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
  POTEG MUTATED       4  7 10  5
  POTEG WILD-TYPE    47 51 43 50
D128V6, multiclass
       clus
vv      POTEG MUTATED POTEG WILD-TYPE
  T0+T1             4              47
  T2                7              51
  T3               10              43
  T4                5              50
[1] 4 2
[1] TRUE
[1] "dimension 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
  POTEG MUTATED    17   6   3   3
  POTEG WILD-TYPE 121  42  29  30
D128V7, multiclass
    clus
vv   POTEG MUTATED POTEG WILD-TYPE
  N0            17             121
  N1             6              42
  N2             3              29
  N3             3              30
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               M0  M1 M1A M1B M1C
  POTEG MUTATED    28   1   0   0   0
  POTEG WILD-TYPE 212   3   2   2   5
D128V8, multiclass
     clus
vv    POTEG MUTATED POTEG WILD-TYPE
  M0             28             212
  M1              1               3
  M1A             0               2
  M1B             0               2
  M1C             0               5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D128V9, binary
                 cls
clus               0  1
  POTEG MUTATED   12  8
  POTEG WILD-TYPE 90 59
[1] "tbl2"
                 cls
clus              [,1] [,2]
  POTEG MUTATED     12    8
  POTEG WILD-TYPE   90   59
     clus
vv    POTEG MUTATED POTEG WILD-TYPE
  NO             12              90
  YES             8              59
[1] 2 2
[1] FALSE
D128V10, binary
                 cls
clus                0   1
  POTEG MUTATED     3  26
  POTEG WILD-TYPE  30 209
[1] "tbl2"
                 cls
clus              [,1] [,2]
  POTEG MUTATED      3   26
  POTEG WILD-TYPE   30  209
     clus
vv    POTEG MUTATED POTEG WILD-TYPE
  NO              3              30
  YES            26             209
[1] 2 2
[1] FALSE
D128V11, continuous
D128V12, binary
                 cls
clus                0   1
  POTEG MUTATED     9  20
  POTEG WILD-TYPE  94 145
[1] "tbl2"
                 cls
clus              [,1] [,2]
  POTEG MUTATED      9   20
  POTEG WILD-TYPE   94  145
        clus
vv       POTEG MUTATED POTEG WILD-TYPE
  FEMALE             9              94
  MALE              20             145
[1] 2 2
[1] FALSE
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  POTEG MUTATED       0                         0    29
  POTEG WILD-TYPE     3                         1   235
D128V13, multiclass
                           clus
vv                          POTEG MUTATED POTEG WILD-TYPE
  ASIAN                                 0               3
  BLACK OR AFRICAN AMERICAN             0               1
  WHITE                                29             235
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D128V14, binary
                 cls
clus                0   1
  POTEG MUTATED     1  28
  POTEG WILD-TYPE   2 233
[1] "tbl2"
                 cls
clus              [,1] [,2]
  POTEG MUTATED      1   28
  POTEG WILD-TYPE    2  233
                        clus
vv                       POTEG MUTATED POTEG WILD-TYPE
  HISPANIC OR LATINO                 1               2
  NOT HISPANIC OR LATINO            28             233
[1] 2 2
[1] FALSE

Clustering(129) Variable = ITPR2 MUTATION ANALYSIS
D129V1, survival
                 sevent
clus2               0   1
  ITPR2 MUTATED     9   6
  ITPR2 WILD-TYPE 119 124
  ITPR2 MUTATED ITPR2 WILD-TYPE 
             15             243 
  ITPR2 MUTATED ITPR2 WILD-TYPE 
              6             124 
$`ITPR2 MUTATED`
TCGA-D3-A3C7 TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A3F8 TCGA-EE-A20C TCGA-EE-A29D 
       46.98        13.22        48.79        14.83         4.34        11.15 
TCGA-EE-A2A1 TCGA-EE-A2MD TCGA-EE-A2ML TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3JD 
       49.22         9.53       111.91        21.60        21.60        27.35 
TCGA-FS-A4F9 TCGA-FW-A3R5 TCGA-GF-A4EO 
       10.78         0.99         7.23 

$`ITPR2 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.47         8.52       111.09        32.42        70.16       110.79 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       28.08        22.55        45.83        81.24        10.29        85.32 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
        8.38        21.14        88.50        68.22        69.90        11.41 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       30.87         7.50        36.16         6.31        92.42        56.19 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C8 TCGA-D3-A3CB 
       64.44        45.11       114.67        15.25        46.32        82.29 
TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR 
       61.38        13.32        24.00         6.31         9.34       103.59 
TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J 
       26.37         5.39        80.22        42.71        15.09        41.10 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO 
       17.72         8.84        20.48        13.94        52.01        47.87 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 
        1.55         6.97        23.11         4.01         2.89         9.90 
TCGA-D9-A6EA TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 
       11.31        35.80        51.12        10.03        39.19        13.68 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB 
        9.99        44.52        36.69        25.15         4.93        22.36 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-EB-A44Q TCGA-EB-A44R 
        6.64        19.36         7.00        17.56        13.15         0.20 
TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z 
        0.00         0.00        13.22        11.57        10.55         6.31 
TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 
        8.12         1.12         1.35        12.20         5.13         4.31 
TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B 
       36.07         5.13         9.21         1.18         7.99         9.90 
TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M 
       37.97        38.63         8.55         4.41         1.08        27.12 
TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V 
        9.50        12.03         8.09         8.84         9.99         2.43 
TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 
        8.68         8.09        11.31        23.90         9.67         8.94 
TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI 
       39.39        34.29        17.98        34.92        47.21        30.08 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO 
       19.43        16.01        35.54        28.31        33.83        30.84 
TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 
        5.42         1.15        13.02        34.98        36.33         8.84 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2ME TCGA-EE-A2MG 
       98.27         2.70         6.18        47.51        29.46        44.25 
TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2MM TCGA-EE-A2MN 
        7.96        14.56        63.42       111.78        56.02        25.08 
TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU 
       26.99        21.60        29.65        27.16        23.05         5.56 
TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF 
      124.31       122.73        25.84         3.68        30.15        13.81 
TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J8 TCGA-EE-A3JA 
       15.95        12.72         3.22        22.92        16.14        22.22 
TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 
        0.46        13.94        33.60        31.40        18.61        12.95 
TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D 
       38.40         5.72        76.41        25.18         3.78         3.52 
TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L 
       11.90        11.11       114.15        34.88         4.21        13.45 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W 
       28.60        42.84        34.68         9.57        36.07        17.72 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG 
       78.44        11.80         1.87         1.51        13.08        12.62 
TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN 
       11.74         9.04         6.58        22.49         1.71        18.41 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 
       85.74         4.90        64.47         3.45        11.01        23.80 
TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC 
       14.24        15.52         7.33         7.30         3.39        20.38 
TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ 
        8.22        19.53        11.08         7.17        30.87        12.92 
TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS 
       12.89        47.38        52.08         8.65         8.81        49.15 
TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 
       40.64         8.68        27.39         0.82         5.23        53.85 
TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD 
        7.36        28.73        14.20         5.98         6.41         2.27 
TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A6C8 
        0.20         0.13         0.16         0.43         9.90        12.85 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 
       24.85        31.33        84.72        10.13        16.24        15.42 
TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS 
       12.16        14.70         5.79 

  ITPR2 MUTATED ITPR2 WILD-TYPE 
           0.99            0.00 
  ITPR2 MUTATED ITPR2 WILD-TYPE 
         111.91          124.31 
  ITPR2 MUTATED ITPR2 WILD-TYPE 
          14.83           14.70 
[1] "1.0 - 111.9 (14.8)" "0.0 - 124.3 (14.7)"
[1] "hr=" "1.3"
D129V2, survival
                 sevent
clus2               0   1
  ITPR2 MUTATED     9   6
  ITPR2 WILD-TYPE 123 125
  ITPR2 MUTATED ITPR2 WILD-TYPE 
             15             248 
  ITPR2 MUTATED ITPR2 WILD-TYPE 
              6             125 
$`ITPR2 MUTATED`
TCGA-D3-A3C7 TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A3F8 TCGA-EE-A20C TCGA-EE-A29D 
       46.98        66.25        48.89        15.68       151.27        13.97 
TCGA-EE-A2A1 TCGA-EE-A2MD TCGA-EE-A2ML TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3JD 
      102.90        47.28       203.05        36.95        64.08        27.35 
TCGA-FS-A4F9 TCGA-FW-A3R5 TCGA-GF-A4EO 
       12.43        22.92         7.23 

$`ITPR2 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.57        16.67       112.04       112.57        71.80       133.25 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       28.08        31.59        90.90        95.74        43.43       103.10 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
       65.49        23.77       115.53       168.00        69.90        11.87 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       48.76       113.52        42.08        12.10       171.58        56.19 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C8 TCGA-D3-A3CB 
       66.08        45.11       130.72        58.06        46.32       166.52 
TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR 
       86.93        60.23        24.53        13.87         9.34       103.59 
TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J 
       39.75        21.47       161.85        43.69        40.14       131.90 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO 
       18.38        10.03        51.68        15.06       135.75       137.92 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW 
      166.19         7.43       125.19       151.53        54.67         3.65 
TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-DA-A1HW 
        6.41        11.34         3.25         9.90        25.18        36.03 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 
      117.21        20.38       194.83       176.55        35.93       107.34 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
       61.18        53.92        65.92        23.44        68.09        28.60 
TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH 
       10.49       215.44        13.87        10.16        45.11        35.01 
TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 
        3.55        52.01        29.82        27.22         8.65        94.98 
TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B 
       33.73        14.70        26.89        68.15         4.96       109.64 
TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C 
       78.87       168.26        13.55        63.35        80.61        47.84 
TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N 
       39.62        72.07        32.19         2.60        44.35        18.61 
TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W 
       56.42        37.35        14.47        55.92        25.87       171.55 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB 
       17.92        46.82        24.43        39.29        58.75        47.54 
TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ 
       67.43       314.56       135.95       208.04        48.72        89.33 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP 
       54.74        79.66        75.48        90.97       101.95        13.91 
TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 
       14.30        55.59        44.88        94.82        21.67       129.27 
TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH 
       28.83        19.76        61.51       103.27       103.20        16.96 
TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP 
      204.66        96.23       144.76       167.90        47.54       248.65 
TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA 
       43.23       103.56       136.47        41.59        53.26       124.31 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG 
      122.73        25.84         3.68        54.51        13.81        23.47 
TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JE 
      138.81       172.18       127.20        34.32        53.19        33.40 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 
      101.79       148.08        31.40        35.44        13.94        50.76 
TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E 
        9.17        77.75        98.40        48.89        12.59        13.02 
TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M 
       26.37       268.93       152.35         6.44       131.51        61.05 
TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 
       44.05       162.08        50.89        37.25       148.18        79.99 
TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH 
       43.82        23.34        20.15        16.37        31.27        32.05 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A 
      247.04        80.32        46.98        33.21        92.98       174.21 
TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
        4.90       216.92        48.59       228.59       202.65        20.91 
TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD 
       28.08         7.79        27.72        48.85       357.37        53.52 
TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK 
       40.27        15.45         9.70        32.75        47.38        23.93 
TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT 
      101.26        74.73       133.55        11.41       148.80        53.16 
TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 
       26.56        49.48        27.09        27.02        77.82        66.67 
TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 
       28.73       174.84        26.73        49.45        77.88         0.20 
TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GN-A262 
       47.54         0.16         2.40         9.90        14.04       120.46 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
      117.93        84.72        10.13        64.44        62.79        32.48 
TCGA-GN-A26D TCGA-QB-A6FS 
       39.58         6.67 

  ITPR2 MUTATED ITPR2 WILD-TYPE 
           7.23            0.16 
  ITPR2 MUTATED ITPR2 WILD-TYPE 
         203.05          357.37 
  ITPR2 MUTATED ITPR2 WILD-TYPE 
          46.98           48.74 
[1] "7.2 - 203.1 (47.0)" "0.2 - 357.4 (48.7)"
[1] "hr=" "1.1"
D129V3, continuous
                 vv
clus              DISTANT METASTASIS PRIMARY TUMOR
  ITPR2 MUTATED                    1             1
  ITPR2 WILD-TYPE                 34             3
                 vv
clus              REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  ITPR2 MUTATED                                           2                  11
  ITPR2 WILD-TYPE                                        56                 159
D129V4, multiclass
                                           clus
vv                                          ITPR2 MUTATED ITPR2 WILD-TYPE
  DISTANT METASTASIS                                    1              34
  PRIMARY TUMOR                                         1               3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE             2              56
  REGIONAL LYMPH NODE                                  11             159
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  ITPR2 MUTATED             0       1       1        0        1        2
  ITPR2 WILD-TYPE          10       5      21       10       23       15
                 vv
clus              STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  ITPR2 MUTATED           0         0         0         4          1          2
  ITPR2 WILD-TYPE        10        14         9        27         12         20
                 vv
clus              STAGE IIIC STAGE IV
  ITPR2 MUTATED            2        0
  ITPR2 WILD-TYPE         42       12
D129V5, multiclass
             clus
vv            ITPR2 MUTATED ITPR2 WILD-TYPE
  I OR II NOS             0              10
  STAGE 0                 1               5
  STAGE I                 1              21
  STAGE IA                0              10
  STAGE IB                1              23
  STAGE II                2              15
  STAGE IIA               0              10
  STAGE IIB               0              14
  STAGE IIC               0               9
  STAGE III               4              27
  STAGE IIIA              1              12
  STAGE IIIB              2              20
  STAGE IIIC              2              42
  STAGE IV                0              12
[1] 14  2
[1] 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
  ITPR2 MUTATED       2  3  4  2
  ITPR2 WILD-TYPE    49 55 49 53
D129V6, multiclass
       clus
vv      ITPR2 MUTATED ITPR2 WILD-TYPE
  T0+T1             2              49
  T2                3              55
  T3                4              49
  T4                2              53
[1] 4 2
[1] TRUE
[1] "dimension 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
  ITPR2 MUTATED     5   4   4   1
  ITPR2 WILD-TYPE 133  44  28  32
D129V7, multiclass
    clus
vv   ITPR2 MUTATED ITPR2 WILD-TYPE
  N0             5             133
  N1             4              44
  N2             4              28
  N3             1              32
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               M0  M1 M1A M1B M1C
  ITPR2 MUTATED    14   0   0   0   0
  ITPR2 WILD-TYPE 226   4   2   2   5
D129V8, multiclass
     clus
vv    ITPR2 MUTATED ITPR2 WILD-TYPE
  M0             14             226
  M1              0               4
  M1A             0               2
  M1B             0               2
  M1C             0               5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D129V9, binary
                 cls
clus               0  1
  ITPR2 MUTATED    5  4
  ITPR2 WILD-TYPE 97 63
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ITPR2 MUTATED      5    4
  ITPR2 WILD-TYPE   97   63
     clus
vv    ITPR2 MUTATED ITPR2 WILD-TYPE
  NO              5              97
  YES             4              63
[1] 2 2
[1] FALSE
D129V10, binary
                 cls
clus                0   1
  ITPR2 MUTATED     4  11
  ITPR2 WILD-TYPE  29 224
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ITPR2 MUTATED      4   11
  ITPR2 WILD-TYPE   29  224
     clus
vv    ITPR2 MUTATED ITPR2 WILD-TYPE
  NO              4              29
  YES            11             224
[1] 2 2
[1] FALSE
D129V11, continuous
D129V12, binary
                 cls
clus                0   1
  ITPR2 MUTATED     4  11
  ITPR2 WILD-TYPE  99 154
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ITPR2 MUTATED      4   11
  ITPR2 WILD-TYPE   99  154
        clus
vv       ITPR2 MUTATED ITPR2 WILD-TYPE
  FEMALE             4              99
  MALE              11             154
[1] 2 2
[1] FALSE
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ITPR2 MUTATED       0                         0    15
  ITPR2 WILD-TYPE     3                         1   249
D129V13, multiclass
                           clus
vv                          ITPR2 MUTATED ITPR2 WILD-TYPE
  ASIAN                                 0               3
  BLACK OR AFRICAN AMERICAN             0               1
  WHITE                                15             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"
D129V14, binary
                 cls
clus                0   1
  ITPR2 MUTATED     0  15
  ITPR2 WILD-TYPE   3 246
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ITPR2 MUTATED      0   15
  ITPR2 WILD-TYPE    3  246
                        clus
vv                       ITPR2 MUTATED ITPR2 WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO            15             246
[1] 2 2
[1] FALSE

Clustering(130) Variable = CRNKL1 MUTATION ANALYSIS
D130V1, survival
                  sevent
clus2                0   1
  CRNKL1 MUTATED     7   5
  CRNKL1 WILD-TYPE 121 125
  CRNKL1 MUTATED CRNKL1 WILD-TYPE 
              12              246 
  CRNKL1 MUTATED CRNKL1 WILD-TYPE 
               5              125 
$`CRNKL1 MUTATED`
TCGA-D3-A51J TCGA-D9-A6EC TCGA-EE-A182 TCGA-EE-A20C TCGA-EE-A2GB TCGA-EE-A2GU 
       41.10        13.22         1.35         4.34        39.39        36.33 
TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2MI TCGA-EE-A2MS TCGA-EE-A3AE TCGA-EE-A3JD 
        8.84        98.27        14.56        27.16        30.15        27.35 

$`CRNKL1 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.47         8.52       111.09        32.42        70.16       110.79 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       28.08        22.55        45.83        81.24        10.29        85.32 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
        8.38        21.14        88.50        68.22        69.90        11.41 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       30.87         7.50        36.16         6.31        92.42        56.19 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 
       64.44        45.11       114.67        15.25        46.98        46.32 
TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO 
       82.29        61.38        13.32        24.00         6.31         9.34 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H 
      103.59        26.37         5.39        80.22        42.71        15.09 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO 
       17.72         8.84        20.48        13.94        52.01        47.87 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 
        1.55         6.97        23.11         4.01         2.89         9.90 
TCGA-D9-A6EA TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 
       11.31        48.79        35.80        51.12        10.03        39.19 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA 
       13.68         9.99        44.52        36.69        25.15         4.93 
TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 
       22.36         6.64        19.36         7.00        17.56        14.83 
TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EE-A17X 
       13.15         0.20         0.00         0.00        13.22        11.57 
TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A184 
       10.55         6.31         8.12         1.12        12.20         5.13 
TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A 
        4.31        36.07         5.13         9.21         1.18         7.99 
TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H 
        9.90        37.97        11.15        38.63         8.55         4.41 
TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R 
        1.08        27.12         9.50        12.03         8.09         8.84 
TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 
        9.99         2.43         8.68         8.09        11.31        49.22 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE 
       23.90         9.67         8.94        34.29        17.98        34.92 
TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM 
       47.21        30.08        19.43        16.01        35.54        28.31 
TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT 
       33.83        30.84         5.42         1.15        13.02        34.98 
TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG 
        2.70         6.18        47.51         9.53        29.46        44.25 
TCGA-EE-A2MH TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN 
        7.96        63.42       111.78       111.91        56.02        25.08 
TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA 
       26.99        21.60        29.65        23.05         5.56       124.31 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH 
      122.73        25.84         3.68        13.81        15.95        12.72 
TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA 
        3.22        22.92        21.60        21.60        16.14        22.22 
TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 
        0.46        13.94        33.60        31.40        18.61        12.95 
TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D 
       38.40         5.72        76.41        25.18         3.78         3.52 
TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L 
       11.90        11.11       114.15        34.88         4.21        13.45 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W 
       28.60        42.84        34.68         9.57        36.07        17.72 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG 
       78.44        11.80         1.87         1.51        13.08        12.62 
TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN 
       11.74         9.04         6.58        22.49         1.71        18.41 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 
       85.74         4.90        64.47         3.45        11.01        23.80 
TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC 
       14.24        15.52         7.33         7.30         3.39        20.38 
TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ 
        8.22        19.53        11.08         7.17        30.87        12.92 
TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS 
       12.89        47.38        52.08         8.65         8.81        49.15 
TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 
       40.64         8.68        27.39         0.82         5.23        53.85 
TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC 
        7.36        28.73        14.20        10.78         5.98         6.41 
TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY 
        2.27         0.20         0.99         0.13         0.16         0.43 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        9.90         7.23        12.85        24.85        31.33        84.72 
TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS 
       10.13        16.24        15.42        12.16        14.70         5.79 

  CRNKL1 MUTATED CRNKL1 WILD-TYPE 
            1.35             0.00 
  CRNKL1 MUTATED CRNKL1 WILD-TYPE 
           98.27           124.31 
  CRNKL1 MUTATED CRNKL1 WILD-TYPE 
          27.255           14.470 
[1] "1.4 - 98.3 (27.3)"  "0.0 - 124.3 (14.5)"
[1] "hr=" "1.4"
D130V2, survival
                  sevent
clus2                0   1
  CRNKL1 MUTATED     7   5
  CRNKL1 WILD-TYPE 125 126
  CRNKL1 MUTATED CRNKL1 WILD-TYPE 
              12              251 
  CRNKL1 MUTATED CRNKL1 WILD-TYPE 
               5              126 
$`CRNKL1 MUTATED`
TCGA-D3-A51J TCGA-D9-A6EC TCGA-EE-A182 TCGA-EE-A20C TCGA-EE-A2GB TCGA-EE-A2GU 
      131.90        66.25        14.70       151.27        47.54        94.82 
TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2MI TCGA-EE-A2MS TCGA-EE-A3AE TCGA-EE-A3JD 
       21.67       129.27       204.66       136.47        54.51        27.35 

$`CRNKL1 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.57        16.67       112.04       112.57        71.80       133.25 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       28.08        31.59        90.90        95.74        43.43       103.10 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
       65.49        23.77       115.53       168.00        69.90        11.87 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       48.76       113.52        42.08        12.10       171.58        56.19 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 
       66.08        45.11       130.72        58.06        46.98        46.32 
TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO 
      166.52        86.93        60.23        24.53        13.87         9.34 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H 
      103.59        39.75        21.47       161.85        43.69        40.14 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO 
       18.38        10.03        51.68        15.06       135.75       137.92 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW 
      166.19         7.43       125.19       151.53        54.67         3.65 
TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-DA-A1HV 
        6.41        11.34         3.25         9.90        25.18        48.89 
TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 
       36.03       117.21        20.38       194.83       176.55        35.93 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC 
      107.34        61.18        53.92        65.92        23.44        68.09 
TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R 
       28.60        10.49       215.44        15.68        13.87        10.16 
TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y 
       45.11        35.01         3.55        52.01        29.82        27.22 
TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 
        8.65        94.98        33.73        26.89        68.15         4.96 
TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B 
      109.64        78.87       168.26        13.55        63.35        80.61 
TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L 
       47.84        13.97        39.62        72.07        32.19         2.60 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S 
       44.35        18.61        56.42        37.35        14.47        55.92 
TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 
       25.87       171.55        17.92        46.82       102.90        24.43 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH 
       39.29        58.75        67.43       314.56       135.95       208.04 
TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN 
       48.72        89.33        54.74        79.66        75.48        90.97 
TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2M7 
      101.95        13.91        14.30        55.59        44.88        28.83 
TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH 
       19.76        61.51        47.28       103.27       103.20        16.96 
TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP 
       96.23       144.76       203.05       167.90        47.54       248.65 
TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB 
       43.23       103.56        41.59        53.26       124.31       122.73 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 
       25.84         3.68        13.81        23.47       138.81       172.18 
TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JE 
      127.20        36.95        64.08        34.32        53.19        33.40 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 
      101.79       148.08        31.40        35.44        13.94        50.76 
TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E 
        9.17        77.75        98.40        48.89        12.59        13.02 
TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M 
       26.37       268.93       152.35         6.44       131.51        61.05 
TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 
       44.05       162.08        50.89        37.25       148.18        79.99 
TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH 
       43.82        23.34        20.15        16.37        31.27        32.05 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A 
      247.04        80.32        46.98        33.21        92.98       174.21 
TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
        4.90       216.92        48.59       228.59       202.65        20.91 
TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD 
       28.08         7.79        27.72        48.85       357.37        53.52 
TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK 
       40.27        15.45         9.70        32.75        47.38        23.93 
TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT 
      101.26        74.73       133.55        11.41       148.80        53.16 
TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 
       26.56        49.48        27.09        27.02        77.82        66.67 
TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD 
       28.73       174.84        12.43        26.73        49.45        77.88 
TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
        0.20        22.92        47.54         0.16         2.40         9.90 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 
        7.23        14.04       120.46       117.93        84.72        10.13 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS 
       64.44        62.79        32.48        39.58         6.67 

  CRNKL1 MUTATED CRNKL1 WILD-TYPE 
           14.70             0.16 
  CRNKL1 MUTATED CRNKL1 WILD-TYPE 
          204.66           357.37 
  CRNKL1 MUTATED CRNKL1 WILD-TYPE 
          80.535           47.540 
[1] "14.7 - 204.7 (80.5)" "0.2 - 357.4 (47.5)" 
[1] "hr=" "1.6"
D130V3, continuous
                  vv
clus               DISTANT METASTASIS PRIMARY TUMOR
  CRNKL1 MUTATED                    2             1
  CRNKL1 WILD-TYPE                 33             3
                  vv
clus               REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  CRNKL1 MUTATED                                           1
  CRNKL1 WILD-TYPE                                        57
                  vv
clus               REGIONAL LYMPH NODE
  CRNKL1 MUTATED                     8
  CRNKL1 WILD-TYPE                 162
D130V4, multiclass
                                           clus
vv                                          CRNKL1 MUTATED CRNKL1 WILD-TYPE
  DISTANT METASTASIS                                     2               33
  PRIMARY TUMOR                                          1                3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE              1               57
  REGIONAL LYMPH NODE                                    8              162
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  CRNKL1 MUTATED             0       1       2        2        0        1
  CRNKL1 WILD-TYPE          10       5      20        8       24       16
                  vv
clus               STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  CRNKL1 MUTATED           0         1         0         2          1
  CRNKL1 WILD-TYPE        10        13         9        29         12
                  vv
clus               STAGE IIIB STAGE IIIC STAGE IV
  CRNKL1 MUTATED            1          1        0
  CRNKL1 WILD-TYPE         21         43       12
D130V5, multiclass
             clus
vv            CRNKL1 MUTATED CRNKL1 WILD-TYPE
  I OR II NOS              0               10
  STAGE 0                  1                5
  STAGE I                  2               20
  STAGE IA                 2                8
  STAGE IB                 0               24
  STAGE II                 1               16
  STAGE IIA                0               10
  STAGE IIB                1               13
  STAGE IIC                0                9
  STAGE III                2               29
  STAGE IIIA               1               12
  STAGE IIIB               1               21
  STAGE IIIC               1               43
  STAGE IV                 0               12
[1] 14  2
[1] 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
  CRNKL1 MUTATED       4  2  2  2
  CRNKL1 WILD-TYPE    47 56 51 53
D130V6, multiclass
       clus
vv      CRNKL1 MUTATED CRNKL1 WILD-TYPE
  T0+T1              4               47
  T2                 2               56
  T3                 2               51
  T4                 2               53
[1] 4 2
[1] TRUE
[1] "dimension 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
  CRNKL1 MUTATED     7   4   1   0
  CRNKL1 WILD-TYPE 131  44  31  33
D130V7, multiclass
    clus
vv   CRNKL1 MUTATED CRNKL1 WILD-TYPE
  N0              7              131
  N1              4               44
  N2              1               31
  N3              0               33
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                M0  M1 M1A M1B M1C
  CRNKL1 MUTATED    12   0   0   0   0
  CRNKL1 WILD-TYPE 228   4   2   2   5
D130V8, multiclass
     clus
vv    CRNKL1 MUTATED CRNKL1 WILD-TYPE
  M0              12              228
  M1               0                4
  M1A              0                2
  M1B              0                2
  M1C              0                5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D130V9, binary
                  cls
clus                0  1
  CRNKL1 MUTATED    6  2
  CRNKL1 WILD-TYPE 96 65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CRNKL1 MUTATED      6    2
  CRNKL1 WILD-TYPE   96   65
     clus
vv    CRNKL1 MUTATED CRNKL1 WILD-TYPE
  NO               6               96
  YES              2               65
[1] 2 2
[1] FALSE
D130V10, binary
                  cls
clus                 0   1
  CRNKL1 MUTATED     2  10
  CRNKL1 WILD-TYPE  31 225
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CRNKL1 MUTATED      2   10
  CRNKL1 WILD-TYPE   31  225
     clus
vv    CRNKL1 MUTATED CRNKL1 WILD-TYPE
  NO               2               31
  YES             10              225
[1] 2 2
[1] FALSE
D130V11, continuous
D130V12, binary
                  cls
clus                 0   1
  CRNKL1 MUTATED     4   8
  CRNKL1 WILD-TYPE  99 157
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CRNKL1 MUTATED      4    8
  CRNKL1 WILD-TYPE   99  157
        clus
vv       CRNKL1 MUTATED CRNKL1 WILD-TYPE
  FEMALE              4               99
  MALE                8              157
[1] 2 2
[1] FALSE
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CRNKL1 MUTATED       0                         0    12
  CRNKL1 WILD-TYPE     3                         1   252
D130V13, multiclass
                           clus
vv                          CRNKL1 MUTATED CRNKL1 WILD-TYPE
  ASIAN                                  0                3
  BLACK OR AFRICAN AMERICAN              0                1
  WHITE                                 12              252
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D130V14, binary
                  cls
clus                 0   1
  CRNKL1 MUTATED     0  12
  CRNKL1 WILD-TYPE   3 249
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CRNKL1 MUTATED      0   12
  CRNKL1 WILD-TYPE    3  249
                        clus
vv                       CRNKL1 MUTATED CRNKL1 WILD-TYPE
  HISPANIC OR LATINO                  0                3
  NOT HISPANIC OR LATINO             12              249
[1] 2 2
[1] FALSE

Clustering(131) Variable = DSP MUTATION ANALYSIS
D131V1, survival
               sevent
clus2             0   1
  DSP MUTATED    24  31
  DSP WILD-TYPE 104  99
  DSP MUTATED DSP WILD-TYPE 
           55           203 
  DSP MUTATED DSP WILD-TYPE 
           31            99 
$`DSP MUTATED`
TCGA-D3-A2J8 TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JH TCGA-D3-A3ML TCGA-D3-A51T 
        8.38        11.41        30.87        36.16         6.31        13.94 
TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I5 TCGA-DA-A3F8 
       13.22        48.79        51.12        39.19        44.52        14.83 
TCGA-EE-A17X TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A20C TCGA-EE-A20H 
       11.57         1.12         1.35        12.20         4.34         9.21 
TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N 
       37.97        11.15        38.63         1.08        27.12         9.50 
TCGA-EE-A2A2 TCGA-EE-A2GC TCGA-EE-A2GI TCGA-EE-A2GL TCGA-EE-A2GP TCGA-EE-A2M5 
       23.90        34.29        30.08        35.54         5.42         8.84 
TCGA-EE-A2MD TCGA-EE-A2MJ TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS 
        9.53        63.42        26.99        21.60        29.65        27.16 
TCGA-EE-A3AC TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3J8 TCGA-EE-A3JA 
       25.84        30.15        13.81        15.95        16.14        22.22 
TCGA-ER-A193 TCGA-ER-A19W TCGA-FR-A69P TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1ZA 
       31.40        17.72         4.90        23.80        14.24         7.30 
TCGA-FS-A1ZK TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZZ TCGA-FS-A4FC TCGA-FW-A3R5 
       12.89         8.65         8.81         5.23         6.41         0.99 
TCGA-GN-A267 
       16.24 

$`DSP WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.47         8.52       111.09        32.42        70.16       110.79 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       28.08        22.55        45.83        81.24        10.29        85.32 
TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JG TCGA-D3-A2JK 
       21.14        88.50        68.22        69.90         7.50         6.31 
TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 
       92.42        56.19        64.44        45.11       114.67        15.25 
TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF 
       46.98        46.32        82.29        61.38        13.32        24.00 
TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F 
        9.34       103.59        26.37         5.39        80.22        42.71 
TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A5GN 
       15.09        41.10        17.72         8.84        20.48        52.01 
TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 
       47.87         1.55         6.97        23.11         4.01         2.89 
TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-DA-A1HW TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 
        9.90        11.31        35.80        10.03        13.68         9.99 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
       36.69        25.15         4.93        22.36         6.64        19.36 
TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH 
        7.00        17.56        13.15         0.20         0.00         0.00 
TCGA-EB-A5UN TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A184 TCGA-EE-A185 
       13.22        10.55         6.31         8.12         5.13         4.31 
TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29G 
       36.07         5.13         1.18         7.99         9.90         8.55 
TCGA-EE-A29H TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V 
        4.41        12.03         8.09         8.84         9.99         2.43 
TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A5 TCGA-EE-A2A6 
        8.68         8.09        11.31        49.22         9.67         8.94 
TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK 
       39.39        17.98        34.92        47.21        19.43        16.01 
TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT 
       28.31        33.83        30.84         1.15        13.02        34.98 
TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2ME 
       36.33        98.27         2.70         6.18        47.51        29.46 
TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM 
       44.25         7.96        14.56       111.78       111.91        56.02 
TCGA-EE-A2MN TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AD 
       25.08        23.05         5.56       124.31       122.73         3.68 
TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3JD 
       12.72         3.22        22.92        21.60        21.60        27.35 
TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 
        0.46        13.94        33.60        18.61        12.95        38.40 
TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E 
        5.72        76.41        25.18         3.78         3.52        11.90 
TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M 
       11.11       114.15        34.88         4.21        13.45        28.60 
TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A1A1 TCGA-ER-A2NC 
       42.84        34.68         9.57        36.07        78.44        11.80 
TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES 
        1.87         1.51        13.08        12.62        11.74         9.04 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A1YW 
        6.58        22.49         1.71        18.41        85.74        64.47 
TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZB TCGA-FS-A1ZC 
        3.45        11.01        15.52         7.33         3.39        20.38 
TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ 
        8.22        19.53        11.08         7.17        30.87        12.92 
TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW 
       47.38        52.08        49.15        40.64         8.68        27.39 
TCGA-FS-A1ZY TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 
        0.82        53.85         7.36        28.73        14.20        10.78 
TCGA-FS-A4FB TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY 
        5.98         2.27         0.20         0.13         0.16         0.43 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        9.90         7.23        12.85        24.85        31.33        84.72 
TCGA-GN-A266 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS 
       10.13        15.42        12.16        14.70         5.79 

  DSP MUTATED DSP WILD-TYPE 
         0.99          0.00 
  DSP MUTATED DSP WILD-TYPE 
        63.42        124.31 
  DSP MUTATED DSP WILD-TYPE 
        14.83         14.70 
[1] "1.0 - 63.4 (14.8)"  "0.0 - 124.3 (14.7)"
[1] "hr=" "1.3"
D131V2, survival
               sevent
clus2             0   1
  DSP MUTATED    24  31
  DSP WILD-TYPE 108 100
  DSP MUTATED DSP WILD-TYPE 
           55           208 
  DSP MUTATED DSP WILD-TYPE 
           31           100 
$`DSP MUTATED`
TCGA-D3-A2J8 TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JH TCGA-D3-A3ML TCGA-D3-A51T 
       65.49        11.87        48.76        42.08        13.87        15.06 
TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I5 TCGA-DA-A3F8 
       66.25        48.89       117.21       194.83       107.34        15.68 
TCGA-EE-A17X TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A20C TCGA-EE-A20H 
       29.82        33.73        14.70        26.89       151.27       168.26 
TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N 
       47.84        13.97        39.62         2.60        44.35        18.61 
TCGA-EE-A2A2 TCGA-EE-A2GC TCGA-EE-A2GI TCGA-EE-A2GL TCGA-EE-A2GP TCGA-EE-A2M5 
       24.43        67.43        48.72        79.66        13.91        21.67 
TCGA-EE-A2MD TCGA-EE-A2MJ TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS 
       47.28        96.23       248.65        43.23       103.56       136.47 
TCGA-EE-A3AC TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3J8 TCGA-EE-A3JA 
       25.84        54.51        13.81        23.47        34.32        53.19 
TCGA-ER-A193 TCGA-ER-A19W TCGA-FR-A69P TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1ZA 
       31.40       148.18         4.90       202.65        20.91        27.72 
TCGA-FS-A1ZK TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZZ TCGA-FS-A4FC TCGA-FW-A3R5 
       23.93       133.55        11.41        27.02        49.45        22.92 
TCGA-GN-A267 
       64.44 

$`DSP WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.57        16.67       112.04       112.57        71.80       133.25 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       28.08        31.59        90.90        95.74        43.43       103.10 
TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JG TCGA-D3-A2JK 
       23.77       115.53       168.00        69.90       113.52        12.10 
TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 
      171.58        56.19        66.08        45.11       130.72        58.06 
TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF 
       46.98        46.32       166.52        86.93        60.23        24.53 
TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F 
        9.34       103.59        39.75        21.47       161.85        43.69 
TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A5GN 
       40.14       131.90        18.38        10.03        51.68       135.75 
TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 
      137.92       166.19         7.43       125.19       151.53        54.67 
TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA 
        3.65         6.41        11.34         3.25         9.90        25.18 
TCGA-DA-A1HW TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I7 TCGA-DA-A1I8 
       36.03        20.38       176.55        35.93        61.18        53.92 
TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 
       65.92        23.44        68.09        28.60        10.49       215.44 
TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN 
       13.87        10.16        45.11        35.01         3.55        52.01 
TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B 
       27.22         8.65        94.98        68.15         4.96       109.64 
TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29G TCGA-EE-A29H 
       78.87        13.55        63.35        80.61        72.07        32.19 
TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W 
       56.42        37.35        14.47        55.92        25.87       171.55 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB 
       17.92        46.82       102.90        39.29        58.75        47.54 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GM 
      314.56       135.95       208.04        89.33        54.74        75.48 
TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU 
       90.97       101.95        14.30        55.59        44.88        94.82 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2ME TCGA-EE-A2MG 
      129.27        28.83        19.76        61.51       103.27       103.20 
TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN 
       16.96       204.66       144.76       203.05       167.90        47.54 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AH 
       41.59        53.26       124.31       122.73         3.68       138.81 
TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3JD TCGA-EE-A3JE 
      172.18       127.20        36.95        64.08        27.35        33.40 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 
      101.79       148.08        35.44        13.94        50.76         9.17 
TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F 
       77.75        98.40        48.89        12.59        13.02        26.37 
TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N 
      268.93       152.35         6.44       131.51        61.05        44.05 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
      162.08        50.89        37.25        79.99        43.82        23.34 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET 
       20.15        16.37        31.27        32.05       247.04        80.32 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A1YW TCGA-FS-A1YX 
       46.98        33.21        92.98       174.21       216.92        48.59 
TCGA-FS-A1YY TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD 
      228.59        28.08         7.79        48.85       357.37        53.52 
TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZM 
       40.27        15.45         9.70        32.75        47.38       101.26 
TCGA-FS-A1ZP TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY 
       74.73       148.80        53.16        26.56        49.48        27.09 
TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB 
       77.82        66.67        28.73       174.84        12.43        26.73 
TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
       77.88         0.20        47.54         0.16         2.40         9.90 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 
        7.23        14.04       120.46       117.93        84.72        10.13 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS 
       62.79        32.48        39.58         6.67 

  DSP MUTATED DSP WILD-TYPE 
         2.60          0.16 
  DSP MUTATED DSP WILD-TYPE 
       248.65        357.37 
  DSP MUTATED DSP WILD-TYPE 
       42.080        50.825 
[1] "2.6 - 248.7 (42.1)" "0.2 - 357.4 (50.8)"
[1] "hr=" "1.4"
D131V3, continuous
               vv
clus            DISTANT METASTASIS PRIMARY TUMOR
  DSP MUTATED                   11             1
  DSP WILD-TYPE                 24             3
               vv
clus            REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  DSP MUTATED                                           9                  35
  DSP WILD-TYPE                                        49                 135
D131V4, multiclass
                                           clus
vv                                          DSP MUTATED DSP WILD-TYPE
  DISTANT METASTASIS                                 11            24
  PRIMARY TUMOR                                       1             3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE           9            49
  REGIONAL LYMPH NODE                                35           135
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  DSP MUTATED             2       3       4        5        5        5
  DSP WILD-TYPE           8       3      18        5       19       12
               vv
clus            STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DSP MUTATED           2         3         0         4          5          5
  DSP WILD-TYPE         8        11         9        27          8         17
               vv
clus            STAGE IIIC STAGE IV
  DSP MUTATED           10        2
  DSP WILD-TYPE         34       10
D131V5, multiclass
             clus
vv            DSP MUTATED DSP WILD-TYPE
  I OR II NOS           2             8
  STAGE 0               3             3
  STAGE I               4            18
  STAGE IA              5             5
  STAGE IB              5            19
  STAGE II              5            12
  STAGE IIA             2             8
  STAGE IIB             3            11
  STAGE IIC             0             9
  STAGE III             4            27
  STAGE IIIA            5             8
  STAGE IIIB            5            17
  STAGE IIIC           10            34
  STAGE IV              2            10
[1] 14  2
[1] 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
  DSP MUTATED      12 11 13 11
  DSP WILD-TYPE    39 47 40 44
D131V6, multiclass
       clus
vv      DSP MUTATED DSP WILD-TYPE
  T0+T1          12            39
  T2             11            47
  T3             13            40
  T4             11            44
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             N0  N1  N2  N3
  DSP MUTATED    32  10   8   5
  DSP WILD-TYPE 106  38  24  28
D131V7, multiclass
    clus
vv   DSP MUTATED DSP WILD-TYPE
  N0          32           106
  N1          10            38
  N2           8            24
  N3           5            28
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             M0  M1 M1A M1B M1C
  DSP MUTATED    52   1   0   0   1
  DSP WILD-TYPE 188   3   2   2   4
D131V8, multiclass
     clus
vv    DSP MUTATED DSP WILD-TYPE
  M0           52           188
  M1            1             3
  M1A           0             2
  M1B           0             2
  M1C           1             4
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D131V9, binary
               cls
clus             0  1
  DSP MUTATED   26 12
  DSP WILD-TYPE 76 55
[1] "tbl2"
               cls
clus            [,1] [,2]
  DSP MUTATED     26   12
  DSP WILD-TYPE   76   55
     clus
vv    DSP MUTATED DSP WILD-TYPE
  NO           26            76
  YES          12            55
[1] 2 2
[1] FALSE
D131V10, binary
               cls
clus              0   1
  DSP MUTATED     7  49
  DSP WILD-TYPE  26 186
[1] "tbl2"
               cls
clus            [,1] [,2]
  DSP MUTATED      7   49
  DSP WILD-TYPE   26  186
     clus
vv    DSP MUTATED DSP WILD-TYPE
  NO            7            26
  YES          49           186
[1] 2 2
[1] FALSE
D131V11, continuous
D131V12, binary
               cls
clus              0   1
  DSP MUTATED    19  37
  DSP WILD-TYPE  84 128
[1] "tbl2"
               cls
clus            [,1] [,2]
  DSP MUTATED     19   37
  DSP WILD-TYPE   84  128
        clus
vv       DSP MUTATED DSP WILD-TYPE
  FEMALE          19            84
  MALE            37           128
[1] 2 2
[1] FALSE
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DSP MUTATED       0                         0    56
  DSP WILD-TYPE     3                         1   208
D131V13, multiclass
                           clus
vv                          DSP MUTATED DSP WILD-TYPE
  ASIAN                               0             3
  BLACK OR AFRICAN AMERICAN           0             1
  WHITE                              56           208
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D131V14, binary
               cls
clus              0   1
  DSP MUTATED     1  54
  DSP WILD-TYPE   2 207
[1] "tbl2"
               cls
clus            [,1] [,2]
  DSP MUTATED      1   54
  DSP WILD-TYPE    2  207
                        clus
vv                       DSP MUTATED DSP WILD-TYPE
  HISPANIC OR LATINO               1             2
  NOT HISPANIC OR LATINO          54           207
[1] 2 2
[1] FALSE

Clustering(132) Variable = SF3B1 MUTATION ANALYSIS
D132V1, survival
                 sevent
clus2               0   1
  SF3B1 MUTATED     7   6
  SF3B1 WILD-TYPE 121 124
  SF3B1 MUTATED SF3B1 WILD-TYPE 
             13             245 
  SF3B1 MUTATED SF3B1 WILD-TYPE 
              6             124 
$`SF3B1 MUTATED`
TCGA-D3-A2JL TCGA-DA-A1HV TCGA-DA-A3F8 TCGA-EE-A181 TCGA-EE-A29L TCGA-EE-A2MJ 
       92.42        48.79        14.83         1.12         1.08        63.42 
TCGA-EE-A3AE TCGA-ER-A19F TCGA-ER-A19S TCGA-ER-A2NF TCGA-ER-A3ES TCGA-FR-A3YN 
       30.15        11.11        36.07        13.08         9.04        18.41 
TCGA-FS-A4F5 
       28.73 

$`SF3B1 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.47         8.52       111.09        32.42        70.16       110.79 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       28.08        22.55        45.83        81.24        10.29        85.32 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
        8.38        21.14        88.50        68.22        69.90        11.41 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JN TCGA-D3-A2JO 
       30.87         7.50        36.16         6.31        56.19        64.44 
TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB 
       45.11       114.67        15.25        46.98        46.32        82.29 
TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR 
       61.38        13.32        24.00         6.31         9.34       103.59 
TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J 
       26.37         5.39        80.22        42.71        15.09        41.10 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO 
       17.72         8.84        20.48        13.94        52.01        47.87 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 
        1.55         6.97        23.11         4.01         2.89         9.90 
TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 
       11.31        13.22        35.80        51.12        10.03        39.19 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA 
       13.68         9.99        44.52        36.69        25.15         4.93 
TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-EB-A44Q 
       22.36         6.64        19.36         7.00        17.56        13.15 
TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y 
        0.20         0.00         0.00        13.22        11.57        10.55 
TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 
        6.31         8.12         1.35        12.20         5.13         4.31 
TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A 
       36.07         4.34         5.13         9.21         1.18         7.99 
TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H 
        9.90        37.97        11.15        38.63         8.55         4.41 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S 
       27.12         9.50        12.03         8.09         8.84         9.99 
TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 
        2.43         8.68         8.09        11.31        49.22        23.90 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE 
        9.67         8.94        39.39        34.29        17.98        34.92 
TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM 
       47.21        30.08        19.43        16.01        35.54        28.31 
TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT 
       33.83        30.84         5.42         1.15        13.02        34.98 
TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC 
       36.33         8.84        98.27         2.70         6.18        47.51 
TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MK 
        9.53        29.46        44.25         7.96        14.56       111.78 
TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR 
      111.91        56.02        25.08        26.99        21.60        29.65 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC 
       27.16        23.05         5.56       124.31       122.73        25.84 
TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 
        3.68        13.81        15.95        12.72         3.22        22.92 
TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE 
       21.60        21.60        16.14        22.22        27.35         0.46 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 
       13.94        33.60        31.40        18.61        12.95        38.40 
TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E 
        5.72        76.41        25.18         3.78         3.52        11.90 
TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N 
      114.15        34.88         4.21        13.45        28.60        42.84 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
       34.68         9.57        17.72        78.44        11.80         1.87 
TCGA-ER-A2NE TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL 
        1.51        12.62        11.74         6.58        22.49         1.71 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 
       85.74         4.90        64.47         3.45        11.01        23.80 
TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC 
       14.24        15.52         7.33         7.30         3.39        20.38 
TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ 
        8.22        19.53        11.08         7.17        30.87        12.92 
TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS 
       12.89        47.38        52.08         8.65         8.81        49.15 
TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 
       40.64         8.68        27.39         0.82         5.23        53.85 
TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD 
        7.36        14.20        10.78         5.98         6.41         2.27 
TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
        0.20         0.99         0.13         0.16         0.43         9.90 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 
        7.23        12.85        24.85        31.33        84.72        10.13 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS 
       16.24        15.42        12.16        14.70         5.79 

  SF3B1 MUTATED SF3B1 WILD-TYPE 
           1.08            0.00 
  SF3B1 MUTATED SF3B1 WILD-TYPE 
          92.42          124.31 
  SF3B1 MUTATED SF3B1 WILD-TYPE 
          18.41           14.56 
[1] "1.1 - 92.4 (18.4)"  "0.0 - 124.3 (14.6)"
[1] "hr=" "1.2"
D132V2, survival
                 sevent
clus2               0   1
  SF3B1 MUTATED     7   6
  SF3B1 WILD-TYPE 125 125
  SF3B1 MUTATED SF3B1 WILD-TYPE 
             13             250 
  SF3B1 MUTATED SF3B1 WILD-TYPE 
              6             125 
$`SF3B1 MUTATED`
TCGA-D3-A2JL TCGA-DA-A1HV TCGA-DA-A3F8 TCGA-EE-A181 TCGA-EE-A29L TCGA-EE-A2MJ 
      171.58        48.89        15.68        33.73         2.60        96.23 
TCGA-EE-A3AE TCGA-ER-A19F TCGA-ER-A19S TCGA-ER-A2NF TCGA-ER-A3ES TCGA-FR-A3YN 
       54.51        26.37        37.25        16.37       247.04        92.98 
TCGA-FS-A4F5 
       28.73 

$`SF3B1 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.57        16.67       112.04       112.57        71.80       133.25 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       28.08        31.59        90.90        95.74        43.43       103.10 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
       65.49        23.77       115.53       168.00        69.90        11.87 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JN TCGA-D3-A2JO 
       48.76       113.52        42.08        12.10        56.19        66.08 
TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB 
       45.11       130.72        58.06        46.98        46.32       166.52 
TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR 
       86.93        60.23        24.53        13.87         9.34       103.59 
TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J 
       39.75        21.47       161.85        43.69        40.14       131.90 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO 
       18.38        10.03        51.68        15.06       135.75       137.92 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW 
      166.19         7.43       125.19       151.53        54.67         3.65 
TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC 
        6.41        11.34         3.25         9.90        25.18        66.25 
TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 
       36.03       117.21        20.38       194.83       176.55        35.93 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC 
      107.34        61.18        53.92        65.92        23.44        68.09 
TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG 
       28.60        10.49       215.44        13.87        10.16        45.11 
TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z 
       35.01         3.55        52.01        29.82        27.22         8.65 
TCGA-EE-A180 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B 
       94.98        14.70        26.89        68.15         4.96       109.64 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B 
      151.27        78.87       168.26        13.55        63.35        80.61 
TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M 
       47.84        13.97        39.62        72.07        32.19        44.35 
TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V 
       18.61        56.42        37.35        14.47        55.92        25.87 
TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 
      171.55        17.92        46.82       102.90        24.43        39.29 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH 
       58.75        47.54        67.43       314.56       135.95       208.04 
TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN 
       48.72        89.33        54.74        79.66        75.48        90.97 
TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU 
      101.95        13.91        14.30        55.59        44.88        94.82 
TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD 
       21.67       129.27        28.83        19.76        61.51        47.28 
TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2ML 
      103.27       103.20        16.96       204.66       144.76       203.05 
TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS 
      167.90        47.54       248.65        43.23       103.56       136.47 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD 
       41.59        53.26       124.31       122.73        25.84         3.68 
TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 
       13.81        23.47       138.81       172.18       127.20        36.95 
TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH 
       64.08        34.32        53.19        27.35        33.40       101.79 
TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 
      148.08        31.40        35.44        13.94        50.76         9.17 
TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19G 
       77.75        98.40        48.89        12.59        13.02       268.93 
TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P 
      152.35         6.44       131.51        61.05        44.05       162.08 
TCGA-ER-A19Q TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE 
       50.89       148.18        79.99        43.82        23.34        20.15 
TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A44A 
       31.27        32.05        80.32        46.98        33.21       174.21 
TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
        4.90       216.92        48.59       228.59       202.65        20.91 
TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD 
       28.08         7.79        27.72        48.85       357.37        53.52 
TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK 
       40.27        15.45         9.70        32.75        47.38        23.93 
TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT 
      101.26        74.73       133.55        11.41       148.80        53.16 
TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 
       26.56        49.48        27.09        27.02        77.82        66.67 
TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 
      174.84        12.43        26.73        49.45        77.88         0.20 
TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
       22.92        47.54         0.16         2.40         9.90         7.23 
TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 
       14.04       120.46       117.93        84.72        10.13        64.44 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS 
       62.79        32.48        39.58         6.67 

  SF3B1 MUTATED SF3B1 WILD-TYPE 
           2.60            0.16 
  SF3B1 MUTATED SF3B1 WILD-TYPE 
         247.04          357.37 
  SF3B1 MUTATED SF3B1 WILD-TYPE 
         37.250          48.655 
[1] "2.6 - 247.0 (37.2)" "0.2 - 357.4 (48.7)"
[1] "hr=" "1.1"
D132V3, continuous
                 vv
clus              DISTANT METASTASIS PRIMARY TUMOR
  SF3B1 MUTATED                    1             1
  SF3B1 WILD-TYPE                 34             3
                 vv
clus              REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  SF3B1 MUTATED                                           1                  10
  SF3B1 WILD-TYPE                                        57                 160
D132V4, multiclass
                                           clus
vv                                          SF3B1 MUTATED SF3B1 WILD-TYPE
  DISTANT METASTASIS                                    1              34
  PRIMARY TUMOR                                         1               3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE             1              57
  REGIONAL LYMPH NODE                                  10             160
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  SF3B1 MUTATED             1       0       0        1        2        1
  SF3B1 WILD-TYPE           9       6      22        9       22       16
                 vv
clus              STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  SF3B1 MUTATED           0         0         0         1          0          2
  SF3B1 WILD-TYPE        10        14         9        30         13         20
                 vv
clus              STAGE IIIC STAGE IV
  SF3B1 MUTATED            2        0
  SF3B1 WILD-TYPE         42       12
D132V5, multiclass
             clus
vv            SF3B1 MUTATED SF3B1 WILD-TYPE
  I OR II NOS             1               9
  STAGE 0                 0               6
  STAGE I                 0              22
  STAGE IA                1               9
  STAGE IB                2              22
  STAGE II                1              16
  STAGE IIA               0              10
  STAGE IIB               0              14
  STAGE IIC               0               9
  STAGE III               1              30
  STAGE IIIA              0              13
  STAGE IIIB              2              20
  STAGE IIIC              2              42
  STAGE IV                0              12
[1] 14  2
[1] 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       2  3  1  3
  SF3B1 WILD-TYPE    49 55 52 52
D132V6, multiclass
       clus
vv      SF3B1 MUTATED SF3B1 WILD-TYPE
  T0+T1             2              49
  T2                3              55
  T3                1              52
  T4                3              52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  SF3B1 MUTATED     7   0   2   2
  SF3B1 WILD-TYPE 131  48  30  31
D132V7, multiclass
    clus
vv   SF3B1 MUTATED SF3B1 WILD-TYPE
  N0             7             131
  N1             0              48
  N2             2              30
  N3             2              31
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               M0  M1 M1A M1B M1C
  SF3B1 MUTATED    11   0   0   0   0
  SF3B1 WILD-TYPE 229   4   2   2   5
D132V8, multiclass
     clus
vv    SF3B1 MUTATED SF3B1 WILD-TYPE
  M0             11             229
  M1              0               4
  M1A             0               2
  M1B             0               2
  M1C             0               5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D132V9, binary
                 cls
clus               0  1
  SF3B1 MUTATED    5  2
  SF3B1 WILD-TYPE 97 65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SF3B1 MUTATED      5    2
  SF3B1 WILD-TYPE   97   65
     clus
vv    SF3B1 MUTATED SF3B1 WILD-TYPE
  NO              5              97
  YES             2              65
[1] 2 2
[1] FALSE
D132V10, binary
                 cls
clus                0   1
  SF3B1 MUTATED     2  11
  SF3B1 WILD-TYPE  31 224
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SF3B1 MUTATED      2   11
  SF3B1 WILD-TYPE   31  224
     clus
vv    SF3B1 MUTATED SF3B1 WILD-TYPE
  NO              2              31
  YES            11             224
[1] 2 2
[1] FALSE
D132V11, continuous
D132V12, binary
                 cls
clus                0   1
  SF3B1 MUTATED     6   7
  SF3B1 WILD-TYPE  97 158
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SF3B1 MUTATED      6    7
  SF3B1 WILD-TYPE   97  158
        clus
vv       SF3B1 MUTATED SF3B1 WILD-TYPE
  FEMALE             6              97
  MALE               7             158
[1] 2 2
[1] FALSE
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SF3B1 MUTATED       0                         0    13
  SF3B1 WILD-TYPE     3                         1   251
D132V13, multiclass
                           clus
vv                          SF3B1 MUTATED SF3B1 WILD-TYPE
  ASIAN                                 0               3
  BLACK OR AFRICAN AMERICAN             0               1
  WHITE                                13             251
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D132V14, binary
                 cls
clus                0   1
  SF3B1 MUTATED     0  13
  SF3B1 WILD-TYPE   3 248
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SF3B1 MUTATED      0   13
  SF3B1 WILD-TYPE    3  248
                        clus
vv                       SF3B1 MUTATED SF3B1 WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO            13             248
[1] 2 2
[1] FALSE

Clustering(133) Variable = CAGE1 MUTATION ANALYSIS
D133V1, survival
                 sevent
clus2               0   1
  CAGE1 MUTATED     6   5
  CAGE1 WILD-TYPE 122 125
  CAGE1 MUTATED CAGE1 WILD-TYPE 
             11             247 
  CAGE1 MUTATED CAGE1 WILD-TYPE 
              5             125 
$`CAGE1 MUTATED`
TCGA-D9-A6EC TCGA-DA-A1I4 TCGA-EE-A181 TCGA-EE-A20C TCGA-EE-A29S TCGA-EE-A2A6 
       13.22         9.99         1.12         4.34         9.99         8.94 
TCGA-EE-A2GI TCGA-EE-A2M5 TCGA-EE-A2MS TCGA-FS-A1ZK TCGA-FW-A3R5 
       30.08         8.84        27.16        12.89         0.99 

$`CAGE1 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.47         8.52       111.09        32.42        70.16       110.79 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       28.08        22.55        45.83        81.24        10.29        85.32 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
        8.38        21.14        88.50        68.22        69.90        11.41 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       30.87         7.50        36.16         6.31        92.42        56.19 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 
       64.44        45.11       114.67        15.25        46.98        46.32 
TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO 
       82.29        61.38        13.32        24.00         6.31         9.34 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H 
      103.59        26.37         5.39        80.22        42.71        15.09 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN 
       41.10        17.72         8.84        20.48        13.94        52.01 
TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 
       47.87         1.55         6.97        23.11         4.01         2.89 
TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 
        9.90        11.31        48.79        35.80        51.12        10.03 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA 
       39.19        13.68        44.52        36.69        25.15         4.93 
TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 
       22.36         6.64        19.36         7.00        17.56        14.83 
TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EE-A17X 
       13.15         0.20         0.00         0.00        13.22        11.57 
TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 
       10.55         6.31         8.12         1.35        12.20         5.13 
TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A 
        4.31        36.07         5.13         9.21         1.18         7.99 
TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H 
        9.90        37.97        11.15        38.63         8.55         4.41 
TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R 
        1.08        27.12         9.50        12.03         8.09         8.84 
TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 
        2.43         8.68         8.09        11.31        49.22        23.90 
TCGA-EE-A2A5 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH 
        9.67        39.39        34.29        17.98        34.92        47.21 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO 
       19.43        16.01        35.54        28.31        33.83        30.84 
TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M6 
        5.42         1.15        13.02        34.98        36.33        98.27 
TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG 
        2.70         6.18        47.51         9.53        29.46        44.25 
TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM 
        7.96        14.56        63.42       111.78       111.91        56.02 
TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MT TCGA-EE-A2MU 
       25.08        26.99        21.60        29.65        23.05         5.56 
TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF 
      124.31       122.73        25.84         3.68        30.15        13.81 
TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 
       15.95        12.72         3.22        22.92        21.60        21.60 
TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI 
       16.14        22.22        27.35         0.46        13.94        33.60 
TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A 
       31.40        18.61        12.95        38.40         5.72        76.41 
TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G 
       25.18         3.78         3.52        11.90        11.11       114.15 
TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P 
       34.88         4.21        13.45        28.60        42.84        34.68 
TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
        9.57        36.07        17.72        78.44        11.80         1.87 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET 
        1.51        13.08        12.62        11.74         9.04         6.58 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW 
       22.49         1.71        18.41        85.74         4.90        64.47 
TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 
        3.45        11.01        23.80        14.24        15.52         7.33 
TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF 
        7.30         3.39        20.38         8.22        19.53        11.08 
TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ 
        7.17        30.87        12.92        47.38        52.08         8.65 
TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY 
        8.81        49.15        40.64         8.68        27.39         0.82 
TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 
        5.23        53.85         7.36        28.73        14.20        10.78 
TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV 
        5.98         6.41         2.27         0.20         0.13         0.16 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 
        0.43         9.90         7.23        12.85        24.85        31.33 
TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D 
       84.72        10.13        16.24        15.42        12.16        14.70 
TCGA-QB-A6FS 
        5.79 

  CAGE1 MUTATED CAGE1 WILD-TYPE 
           0.99            0.00 
  CAGE1 MUTATED CAGE1 WILD-TYPE 
          30.08          124.31 
  CAGE1 MUTATED CAGE1 WILD-TYPE 
           9.99           15.42 
[1] "1.0 - 30.1 (10.0)"  "0.0 - 124.3 (15.4)"
[1] "hr=" "1.5"
D133V2, survival
                 sevent
clus2               0   1
  CAGE1 MUTATED     6   5
  CAGE1 WILD-TYPE 126 126
  CAGE1 MUTATED CAGE1 WILD-TYPE 
             11             252 
  CAGE1 MUTATED CAGE1 WILD-TYPE 
              5             126 
$`CAGE1 MUTATED`
TCGA-D9-A6EC TCGA-DA-A1I4 TCGA-EE-A181 TCGA-EE-A20C TCGA-EE-A29S TCGA-EE-A2A6 
       66.25        35.93        33.73       151.27        55.92        58.75 
TCGA-EE-A2GI TCGA-EE-A2M5 TCGA-EE-A2MS TCGA-FS-A1ZK TCGA-FW-A3R5 
       48.72        21.67       136.47        23.93        22.92 

$`CAGE1 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.57        16.67       112.04       112.57        71.80       133.25 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       28.08        31.59        90.90        95.74        43.43       103.10 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
       65.49        23.77       115.53       168.00        69.90        11.87 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       48.76       113.52        42.08        12.10       171.58        56.19 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 
       66.08        45.11       130.72        58.06        46.98        46.32 
TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO 
      166.52        86.93        60.23        24.53        13.87         9.34 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H 
      103.59        39.75        21.47       161.85        43.69        40.14 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN 
      131.90        18.38        10.03        51.68        15.06       135.75 
TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 
      137.92       166.19         7.43       125.19       151.53        54.67 
TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA 
        3.65         6.41        11.34         3.25         9.90        25.18 
TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 
       48.89        36.03       117.21        20.38       194.83       176.55 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC 
      107.34        61.18        53.92        65.92        23.44        68.09 
TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R 
       28.60        10.49       215.44        15.68        13.87        10.16 
TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y 
       45.11        35.01         3.55        52.01        29.82        27.22 
TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 
        8.65        94.98        14.70        26.89        68.15         4.96 
TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B 
      109.64        78.87       168.26        13.55        63.35        80.61 
TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L 
       47.84        13.97        39.62        72.07        32.19         2.60 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29V 
       44.35        18.61        56.42        37.35        14.47        25.87 
TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 
      171.55        17.92        46.82       102.90        24.43        39.29 
TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ 
       47.54        67.43       314.56       135.95       208.04        89.33 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP 
       54.74        79.66        75.48        90.97       101.95        13.91 
TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 
       14.30        55.59        44.88        94.82       129.27        28.83 
TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH 
       19.76        61.51        47.28       103.27       103.20        16.96 
TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN 
      204.66        96.23       144.76       203.05       167.90        47.54 
TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA 
      248.65        43.23       103.56        41.59        53.26       124.31 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG 
      122.73        25.84         3.68        54.51        13.81        23.47 
TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 
      138.81       172.18       127.20        36.95        64.08        34.32 
TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 
       53.19        27.35        33.40       101.79       148.08        31.40 
TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B 
       35.44        13.94        50.76         9.17        77.75        98.40 
TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H 
       48.89        12.59        13.02        26.37       268.93       152.35 
TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q 
        6.44       131.51        61.05        44.05       162.08        50.89 
TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE 
       37.25       148.18        79.99        43.82        23.34        20.15 
TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV 
       16.37        31.27        32.05       247.04        80.32        46.98 
TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX 
       33.21        92.98       174.21         4.90       216.92        48.59 
TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA 
      228.59       202.65        20.91        28.08         7.79        27.72 
TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG 
       48.85       357.37        53.52        40.27        15.45         9.70 
TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR 
       32.75        47.38       101.26        74.73       133.55        11.41 
TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ 
      148.80        53.16        26.56        49.48        27.09        27.02 
TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB 
       77.82        66.67        28.73       174.84        12.43        26.73 
TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY 
       49.45        77.88         0.20        47.54         0.16         2.40 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        9.90         7.23        14.04       120.46       117.93        84.72 
TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS 
       10.13        64.44        62.79        32.48        39.58         6.67 

  CAGE1 MUTATED CAGE1 WILD-TYPE 
          21.67            0.16 
  CAGE1 MUTATED CAGE1 WILD-TYPE 
         151.27          357.37 
  CAGE1 MUTATED CAGE1 WILD-TYPE 
         48.720          48.215 
[1] "21.7 - 151.3 (48.7)" "0.2 - 357.4 (48.2)" 
[1] "hr=" "1"  
D133V3, continuous
                 vv
clus              DISTANT METASTASIS PRIMARY TUMOR
  CAGE1 MUTATED                    2             1
  CAGE1 WILD-TYPE                 33             3
                 vv
clus              REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  CAGE1 MUTATED                                           1                   7
  CAGE1 WILD-TYPE                                        57                 163
D133V4, multiclass
                                           clus
vv                                          CAGE1 MUTATED CAGE1 WILD-TYPE
  DISTANT METASTASIS                                    2              33
  PRIMARY TUMOR                                         1               3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE             1              57
  REGIONAL LYMPH NODE                                   7             163
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  CAGE1 MUTATED             0       1       1        2        0        3
  CAGE1 WILD-TYPE          10       5      21        8       24       14
                 vv
clus              STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  CAGE1 MUTATED           1         0         0         1          1          0
  CAGE1 WILD-TYPE         9        14         9        30         12         22
                 vv
clus              STAGE IIIC STAGE IV
  CAGE1 MUTATED            1        0
  CAGE1 WILD-TYPE         43       12
D133V5, multiclass
             clus
vv            CAGE1 MUTATED CAGE1 WILD-TYPE
  I OR II NOS             0              10
  STAGE 0                 1               5
  STAGE I                 1              21
  STAGE IA                2               8
  STAGE IB                0              24
  STAGE II                3              14
  STAGE IIA               1               9
  STAGE IIB               0              14
  STAGE IIC               0               9
  STAGE III               1              30
  STAGE IIIA              1              12
  STAGE IIIB              0              22
  STAGE IIIC              1              43
  STAGE IV                0              12
[1] 14  2
[1] 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
  CAGE1 MUTATED       2  1  5  1
  CAGE1 WILD-TYPE    49 57 48 54
D133V6, multiclass
       clus
vv      CAGE1 MUTATED CAGE1 WILD-TYPE
  T0+T1             2              49
  T2                1              57
  T3                5              48
  T4                1              54
[1] 4 2
[1] TRUE
[1] "dimension 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
  CAGE1 MUTATED     8   1   2   0
  CAGE1 WILD-TYPE 130  47  30  33
D133V7, multiclass
    clus
vv   CAGE1 MUTATED CAGE1 WILD-TYPE
  N0             8             130
  N1             1              47
  N2             2              30
  N3             0              33
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               M0  M1 M1A M1B M1C
  CAGE1 MUTATED    11   0   0   0   0
  CAGE1 WILD-TYPE 229   4   2   2   5
D133V8, multiclass
     clus
vv    CAGE1 MUTATED CAGE1 WILD-TYPE
  M0             11             229
  M1              0               4
  M1A             0               2
  M1B             0               2
  M1C             0               5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D133V9, binary
                 cls
clus               0  1
  CAGE1 MUTATED    6  1
  CAGE1 WILD-TYPE 96 66
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CAGE1 MUTATED      6    1
  CAGE1 WILD-TYPE   96   66
     clus
vv    CAGE1 MUTATED CAGE1 WILD-TYPE
  NO              6              96
  YES             1              66
[1] 2 2
[1] FALSE
D133V10, binary
                 cls
clus                0   1
  CAGE1 MUTATED     0  11
  CAGE1 WILD-TYPE  33 224
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CAGE1 MUTATED      0   11
  CAGE1 WILD-TYPE   33  224
     clus
vv    CAGE1 MUTATED CAGE1 WILD-TYPE
  NO              0              33
  YES            11             224
[1] 2 2
[1] FALSE
D133V11, continuous
D133V12, binary
                 cls
clus                0   1
  CAGE1 MUTATED     2   9
  CAGE1 WILD-TYPE 101 156
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CAGE1 MUTATED      2    9
  CAGE1 WILD-TYPE  101  156
        clus
vv       CAGE1 MUTATED CAGE1 WILD-TYPE
  FEMALE             2             101
  MALE               9             156
[1] 2 2
[1] FALSE
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CAGE1 MUTATED       0                         0    11
  CAGE1 WILD-TYPE     3                         1   253
D133V13, multiclass
                           clus
vv                          CAGE1 MUTATED CAGE1 WILD-TYPE
  ASIAN                                 0               3
  BLACK OR AFRICAN AMERICAN             0               1
  WHITE                                11             253
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D133V14, binary
                 cls
clus                0   1
  CAGE1 MUTATED     0  11
  CAGE1 WILD-TYPE   3 250
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CAGE1 MUTATED      0   11
  CAGE1 WILD-TYPE    3  250
                        clus
vv                       CAGE1 MUTATED CAGE1 WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO            11             250
[1] 2 2
[1] FALSE

Clustering(134) Variable = DDX43 MUTATION ANALYSIS
D134V1, survival
                 sevent
clus2               0   1
  DDX43 MUTATED     4   6
  DDX43 WILD-TYPE 124 124
  DDX43 MUTATED DDX43 WILD-TYPE 
             10             248 
  DDX43 MUTATED DDX43 WILD-TYPE 
              6             124 
$`DDX43 MUTATED`
TCGA-EE-A181 TCGA-EE-A29D TCGA-EE-A2A0 TCGA-EE-A2MD TCGA-EE-A2MR TCGA-EE-A3JD 
        1.12        11.15        11.31         9.53        29.65        27.35 
TCGA-ER-A19D TCGA-FS-A1ZW TCGA-FS-A4FD TCGA-FW-A3R5 
        3.52        27.39         2.27         0.99 

$`DDX43 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.47         8.52       111.09        32.42        70.16       110.79 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       28.08        22.55        45.83        81.24        10.29        85.32 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
        8.38        21.14        88.50        68.22        69.90        11.41 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       30.87         7.50        36.16         6.31        92.42        56.19 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 
       64.44        45.11       114.67        15.25        46.98        46.32 
TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO 
       82.29        61.38        13.32        24.00         6.31         9.34 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H 
      103.59        26.37         5.39        80.22        42.71        15.09 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN 
       41.10        17.72         8.84        20.48        13.94        52.01 
TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 
       47.87         1.55         6.97        23.11         4.01         2.89 
TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY 
        9.90        11.31        13.22        48.79        35.80        51.12 
TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 
       10.03        39.19        13.68         9.99        44.52        36.69 
TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 
       25.15         4.93        22.36         6.64        19.36         7.00 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH 
       17.56        14.83        13.15         0.20         0.00         0.00 
TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A182 
       13.22        11.57        10.55         6.31         8.12         1.35 
TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F 
       12.20         5.13         4.31        36.07         4.34         5.13 
TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E 
        9.21         1.18         7.99         9.90        37.97        38.63 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P 
        8.55         4.41         1.08        27.12         9.50        12.03 
TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X 
        8.09         8.84         9.99         2.43         8.68         8.09 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC 
       49.22        23.90         9.67         8.94        39.39        34.29 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK 
       17.98        34.92        47.21        30.08        19.43        16.01 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR 
       35.54        28.31        33.83        30.84         5.42         1.15 
TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 
       13.02        34.98        36.33         8.84        98.27         2.70 
TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI 
        6.18        47.51        29.46        44.25         7.96        14.56 
TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP 
       63.42       111.78       111.91        56.02        25.08        26.99 
TCGA-EE-A2MQ TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB 
       21.60        27.16        23.05         5.56       124.31       122.73 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH 
       25.84         3.68        30.15        13.81        15.95        12.72 
TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA 
        3.22        22.92        21.60        21.60        16.14        22.22 
TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 
        0.46        13.94        33.60        31.40        18.61        12.95 
TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19E 
       38.40         5.72        76.41        25.18         3.78        11.90 
TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M 
       11.11       114.15        34.88         4.21        13.45        28.60 
TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 
       42.84        34.68         9.57        36.07        17.72        78.44 
TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH 
       11.80         1.87         1.51        13.08        12.62        11.74 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A 
        9.04         6.58        22.49         1.71        18.41        85.74 
TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
        4.90        64.47         3.45        11.01        23.80        14.24 
TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD 
       15.52         7.33         7.30         3.39        20.38         8.22 
TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK 
       19.53        11.08         7.17        30.87        12.92        12.89 
TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT 
       47.38        52.08         8.65         8.81        49.15        40.64 
TCGA-FS-A1ZU TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 
        8.68         0.82         5.23        53.85         7.36        28.73 
TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FW-A3I3 TCGA-FW-A3TU 
       14.20        10.78         5.98         6.41         0.20         0.13 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 
        0.16         0.43         9.90         7.23        12.85        24.85 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
       31.33        84.72        10.13        16.24        15.42        12.16 
TCGA-GN-A26D TCGA-QB-A6FS 
       14.70         5.79 

  DDX43 MUTATED DDX43 WILD-TYPE 
           0.99            0.00 
  DDX43 MUTATED DDX43 WILD-TYPE 
          29.65          124.31 
  DDX43 MUTATED DDX43 WILD-TYPE 
          10.34           15.17 
[1] "1.0 - 29.6 (10.3)"  "0.0 - 124.3 (15.2)"
[1] "hr=" "2"  
D134V2, survival
                 sevent
clus2               0   1
  DDX43 MUTATED     5   6
  DDX43 WILD-TYPE 127 125
  DDX43 MUTATED DDX43 WILD-TYPE 
             11             252 
  DDX43 MUTATED DDX43 WILD-TYPE 
              6             125 
$`DDX43 MUTATED`
TCGA-D9-A149 TCGA-EE-A181 TCGA-EE-A29D TCGA-EE-A2A0 TCGA-EE-A2MD TCGA-EE-A2MR 
       54.67        33.73        13.97        46.82        47.28       103.56 
TCGA-EE-A3JD TCGA-ER-A19D TCGA-FS-A1ZW TCGA-FS-A4FD TCGA-FW-A3R5 
       27.35        12.59        49.48        77.88        22.92 

$`DDX43 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.57        16.67       112.04       112.57        71.80       133.25 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       28.08        31.59        90.90        95.74        43.43       103.10 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
       65.49        23.77       115.53       168.00        69.90        11.87 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       48.76       113.52        42.08        12.10       171.58        56.19 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 
       66.08        45.11       130.72        58.06        46.98        46.32 
TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO 
      166.52        86.93        60.23        24.53        13.87         9.34 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H 
      103.59        39.75        21.47       161.85        43.69        40.14 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN 
      131.90        18.38        10.03        51.68        15.06       135.75 
TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A1JW 
      137.92       166.19         7.43       125.19       151.53         3.65 
TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC 
        6.41        11.34         3.25         9.90        25.18        66.25 
TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 
       48.89        36.03       117.21        20.38       194.83       176.55 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB 
       35.93       107.34        61.18        53.92        65.92        23.44 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q 
       68.09        28.60        10.49       215.44        15.68        13.87 
TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X 
       10.16        45.11        35.01         3.55        52.01        29.82 
TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 
       27.22         8.65        94.98        14.70        26.89        68.15 
TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I 
        4.96       109.64       151.27        78.87       168.26        13.55 
TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H 
       63.35        80.61        47.84        39.62        72.07        32.19 
TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R 
        2.60        44.35        18.61        56.42        37.35        14.47 
TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A1 TCGA-EE-A2A2 
       55.92        25.87       171.55        17.92       102.90        24.43 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE 
       39.29        58.75        47.54        67.43       314.56       135.95 
TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM 
      208.04        48.72        89.33        54.74        79.66        75.48 
TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT 
       90.97       101.95        13.91        14.30        55.59        44.88 
TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC 
       94.82        21.67       129.27        28.83        19.76        61.51 
TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK 
      103.27       103.20        16.96       204.66        96.23       144.76 
TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MS 
      203.05       167.90        47.54       248.65        43.23       136.47 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD 
       41.59        53.26       124.31       122.73        25.84         3.68 
TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 
       54.51        13.81        23.47       138.81       172.18       127.20 
TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JE TCGA-EE-A3JH 
       36.95        64.08        34.32        53.19        33.40       101.79 
TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 
      148.08        31.40        35.44        13.94        50.76         9.17 
TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G 
       77.75        98.40        48.89        13.02        26.37       268.93 
TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P 
      152.35         6.44       131.51        61.05        44.05       162.08 
TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
       50.89        37.25       148.18        79.99        43.82        23.34 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET 
       20.15        16.37        31.27        32.05       247.04        80.32 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW 
       46.98        33.21        92.98       174.21         4.90       216.92 
TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 
       48.59       228.59       202.65        20.91        28.08         7.79 
TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF 
       27.72        48.85       357.37        53.52        40.27        15.45 
TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP 
        9.70        32.75        47.38        23.93       101.26        74.73 
TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZY 
      133.55        11.41       148.80        53.16        26.56        27.09 
TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 
       27.02        77.82        66.67        28.73       174.84        12.43 
TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY 
       26.73        49.45         0.20        47.54         0.16         2.40 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        9.90         7.23        14.04       120.46       117.93        84.72 
TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS 
       10.13        64.44        62.79        32.48        39.58         6.67 

  DDX43 MUTATED DDX43 WILD-TYPE 
          12.59            0.16 
  DDX43 MUTATED DDX43 WILD-TYPE 
         103.56          357.37 
  DDX43 MUTATED DDX43 WILD-TYPE 
          46.82           48.74 
[1] "12.6 - 103.6 (46.8)" "0.2 - 357.4 (48.7)" 
[1] "hr=" "1.6"
D134V3, continuous
                 vv
clus              DISTANT METASTASIS PRIMARY TUMOR
  DDX43 MUTATED                    0             0
  DDX43 WILD-TYPE                 35             4
                 vv
clus              REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  DDX43 MUTATED                                           2                   9
  DDX43 WILD-TYPE                                        56                 161
D134V4, multiclass
                                           clus
vv                                          DDX43 MUTATED DDX43 WILD-TYPE
  DISTANT METASTASIS                                    0              35
  PRIMARY TUMOR                                         0               4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE             2              56
  REGIONAL LYMPH NODE                                   9             161
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  DDX43 MUTATED             0       0       1        0        1        2
  DDX43 WILD-TYPE          10       6      21       10       23       15
                 vv
clus              STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DDX43 MUTATED           1         0         0         2          0          1
  DDX43 WILD-TYPE         9        14         9        29         13         21
                 vv
clus              STAGE IIIC STAGE IV
  DDX43 MUTATED            2        0
  DDX43 WILD-TYPE         42       12
D134V5, multiclass
             clus
vv            DDX43 MUTATED DDX43 WILD-TYPE
  I OR II NOS             0              10
  STAGE 0                 0               6
  STAGE I                 1              21
  STAGE IA                0              10
  STAGE IB                1              23
  STAGE II                2              15
  STAGE IIA               1               9
  STAGE IIB               0              14
  STAGE IIC               0               9
  STAGE III               2              29
  STAGE IIIA              0              13
  STAGE IIIB              1              21
  STAGE IIIC              2              42
  STAGE IV                0              12
[1] 14  2
[1] 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
  DDX43 MUTATED       0  4  4  0
  DDX43 WILD-TYPE    51 54 49 55
D134V6, multiclass
       clus
vv      DDX43 MUTATED DDX43 WILD-TYPE
  T0+T1             0              51
  T2                4              54
  T3                4              49
  T4                0              55
[1] 4 2
[1] TRUE
[1] "dimension 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
  DDX43 MUTATED     5   3   2   1
  DDX43 WILD-TYPE 133  45  30  32
D134V7, multiclass
    clus
vv   DDX43 MUTATED DDX43 WILD-TYPE
  N0             5             133
  N1             3              45
  N2             2              30
  N3             1              32
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               M0  M1 M1A M1B M1C
  DDX43 MUTATED    11   0   0   0   0
  DDX43 WILD-TYPE 229   4   2   2   5
D134V8, multiclass
     clus
vv    DDX43 MUTATED DDX43 WILD-TYPE
  M0             11             229
  M1              0               4
  M1A             0               2
  M1B             0               2
  M1C             0               5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D134V9, binary
                 cls
clus               0  1
  DDX43 MUTATED    4  3
  DDX43 WILD-TYPE 98 64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX43 MUTATED      4    3
  DDX43 WILD-TYPE   98   64
     clus
vv    DDX43 MUTATED DDX43 WILD-TYPE
  NO              4              98
  YES             3              64
[1] 2 2
[1] FALSE
D134V10, binary
                 cls
clus                0   1
  DDX43 MUTATED     1  10
  DDX43 WILD-TYPE  32 225
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX43 MUTATED      1   10
  DDX43 WILD-TYPE   32  225
     clus
vv    DDX43 MUTATED DDX43 WILD-TYPE
  NO              1              32
  YES            10             225
[1] 2 2
[1] FALSE
D134V11, continuous
D134V12, binary
                 cls
clus                0   1
  DDX43 MUTATED     4   7
  DDX43 WILD-TYPE  99 158
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX43 MUTATED      4    7
  DDX43 WILD-TYPE   99  158
        clus
vv       DDX43 MUTATED DDX43 WILD-TYPE
  FEMALE             4              99
  MALE               7             158
[1] 2 2
[1] FALSE
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DDX43 MUTATED       0                         0    11
  DDX43 WILD-TYPE     3                         1   253
D134V13, multiclass
                           clus
vv                          DDX43 MUTATED DDX43 WILD-TYPE
  ASIAN                                 0               3
  BLACK OR AFRICAN AMERICAN             0               1
  WHITE                                11             253
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D134V14, binary
                 cls
clus                0   1
  DDX43 MUTATED     0  11
  DDX43 WILD-TYPE   3 250
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX43 MUTATED      0   11
  DDX43 WILD-TYPE    3  250
                        clus
vv                       DDX43 MUTATED DDX43 WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO            11             250
[1] 2 2
[1] FALSE

Clustering(135) Variable = CYP3A7 MUTATION ANALYSIS
D135V1, survival
                  sevent
clus2                0   1
  CYP3A7 MUTATED    10  12
  CYP3A7 WILD-TYPE 118 118
  CYP3A7 MUTATED CYP3A7 WILD-TYPE 
              22              236 
  CYP3A7 MUTATED CYP3A7 WILD-TYPE 
              12              118 
$`CYP3A7 MUTATED`
TCGA-D3-A2JF TCGA-D3-A3MR TCGA-D9-A3Z1 TCGA-DA-A1HV TCGA-DA-A1HW TCGA-EE-A180 
       30.87       103.59         4.01        48.79        35.80         8.12 
TCGA-EE-A181 TCGA-EE-A29E TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2GE TCGA-EE-A2GO 
        1.12        38.63         2.43         8.09        34.92        30.84 
TCGA-EE-A2MJ TCGA-EE-A3AA TCGA-EE-A3AC TCGA-ER-A2NH TCGA-FS-A1ZF TCGA-FS-A1ZK 
       63.42       124.31        25.84        11.74        11.08        12.89 
TCGA-FS-A1ZZ TCGA-FS-A4F8 TCGA-FW-A3R5 TCGA-GN-A266 
        5.23        14.20         0.99        10.13 

$`CYP3A7 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.47         8.52       111.09        32.42        70.16       110.79 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       28.08        22.55        45.83        81.24        10.29        85.32 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
        8.38        21.14        88.50        68.22        69.90        11.41 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO 
        7.50        36.16         6.31        92.42        56.19        64.44 
TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB 
       45.11       114.67        15.25        46.98        46.32        82.29 
TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MU 
       61.38        13.32        24.00         6.31         9.34        26.37 
TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K 
        5.39        80.22        42.71        15.09        41.10        17.72 
TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR 
        8.84        20.48        13.94        52.01        47.87         1.55 
TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC 
        6.97        23.11         2.89         9.90        11.31        13.22 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 
       51.12        10.03        39.19        13.68         9.99        44.52 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
       36.69        25.15         4.93        22.36         6.64        19.36 
TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG 
        7.00        17.56        14.83        13.15         0.20         0.00 
TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A182 
        0.00        13.22        11.57        10.55         6.31         1.35 
TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F 
       12.20         5.13         4.31        36.07         4.34         5.13 
TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D 
        9.21         1.18         7.99         9.90        37.97        11.15 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P 
        8.55         4.41         1.08        27.12         9.50        12.03 
TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29W TCGA-EE-A2A0 TCGA-EE-A2A1 
        8.09         8.84         9.99         8.68        11.31        49.22 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD 
       23.90         9.67         8.94        39.39        34.29        17.98 
TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM 
       47.21        30.08        19.43        16.01        35.54        28.31 
TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU 
       33.83         5.42         1.15        13.02        34.98        36.33 
TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD 
        8.84        98.27         2.70         6.18        47.51         9.53 
TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2ML 
       29.46        44.25         7.96        14.56       111.78       111.91 
TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS 
       56.02        25.08        26.99        21.60        29.65        27.16 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF 
       23.05         5.56       122.73         3.68        30.15        13.81 
TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 
       15.95        12.72         3.22        22.92        21.60        21.60 
TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI 
       16.14        22.22        27.35         0.46        13.94        33.60 
TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A 
       31.40        18.61        12.95        38.40         5.72        76.41 
TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G 
       25.18         3.78         3.52        11.90        11.11       114.15 
TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P 
       34.88         4.21        13.45        28.60        42.84        34.68 
TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
        9.57        36.07        17.72        78.44        11.80         1.87 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV 
        1.51        13.08        12.62         9.04         6.58        22.49 
TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX 
        1.71        18.41        85.74         4.90        64.47         3.45 
TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA 
       11.01        23.80        14.24        15.52         7.33         7.30 
TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZH 
        3.39        20.38         8.22        19.53         7.17        30.87 
TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS 
       12.92        47.38        52.08         8.65         8.81        49.15 
TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A4F0 TCGA-FS-A4F4 
       40.64         8.68        27.39         0.82        53.85         7.36 
TCGA-FS-A4F5 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 
       28.73        10.78         5.98         6.41         2.27         0.20 
TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 
        0.13         0.16         0.43         9.90         7.23        12.85 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
       24.85        31.33        84.72        16.24        15.42        12.16 
TCGA-GN-A26D TCGA-QB-A6FS 
       14.70         5.79 

  CYP3A7 MUTATED CYP3A7 WILD-TYPE 
            0.99             0.00 
  CYP3A7 MUTATED CYP3A7 WILD-TYPE 
          124.31           122.73 
  CYP3A7 MUTATED CYP3A7 WILD-TYPE 
          13.545           14.960 
[1] "1.0 - 124.3 (13.5)" "0.0 - 122.7 (15.0)"
[1] "hr=" "1"  
D135V2, survival
                  sevent
clus2                0   1
  CYP3A7 MUTATED    10  12
  CYP3A7 WILD-TYPE 122 119
  CYP3A7 MUTATED CYP3A7 WILD-TYPE 
              22              241 
  CYP3A7 MUTATED CYP3A7 WILD-TYPE 
              12              119 
$`CYP3A7 MUTATED`
TCGA-D3-A2JF TCGA-D3-A3MR TCGA-D9-A3Z1 TCGA-DA-A1HV TCGA-DA-A1HW TCGA-EE-A180 
       48.76       103.59        11.34        48.89        36.03        94.98 
TCGA-EE-A181 TCGA-EE-A29E TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2GE TCGA-EE-A2GO 
       33.73        39.62        25.87        17.92       135.95       101.95 
TCGA-EE-A2MJ TCGA-EE-A3AA TCGA-EE-A3AC TCGA-ER-A2NH TCGA-FS-A1ZF TCGA-FS-A1ZK 
       96.23       124.31        25.84        32.05        15.45        23.93 
TCGA-FS-A1ZZ TCGA-FS-A4F8 TCGA-FW-A3R5 TCGA-GN-A266 
       27.02       174.84        22.92        10.13 

$`CYP3A7 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.57        16.67       112.04       112.57        71.80       133.25 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       28.08        31.59        90.90        95.74        43.43       103.10 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
       65.49        23.77       115.53       168.00        69.90        11.87 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO 
      113.52        42.08        12.10       171.58        56.19        66.08 
TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB 
       45.11       130.72        58.06        46.98        46.32       166.52 
TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MU 
       86.93        60.23        24.53        13.87         9.34        39.75 
TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K 
       21.47       161.85        43.69        40.14       131.90        18.38 
TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR 
       10.03        51.68        15.06       135.75       137.92       166.19 
TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX 
        7.43       125.19       151.53        54.67         3.65         6.41 
TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1HY TCGA-DA-A1I0 
        3.25         9.90        25.18        66.25       117.21        20.38 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 
      194.83       176.55        35.93       107.34        61.18        53.92 
TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 
       65.92        23.44        68.09        28.60        10.49       215.44 
TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL 
       15.68        13.87        10.16        45.11        35.01         3.55 
TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A182 TCGA-EE-A183 
       52.01        29.82        27.22         8.65        14.70        26.89 
TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H 
       68.15         4.96       109.64       151.27        78.87       168.26 
TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29G 
       13.55        63.35        80.61        47.84        13.97        72.07 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
       32.19         2.60        44.35        18.61        56.42        37.35 
TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29W TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 
       14.47        55.92       171.55        46.82       102.90        24.43 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GH 
       39.29        58.75        47.54        67.43       314.56       208.04 
TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN 
       48.72        89.33        54.74        79.66        75.48        90.97 
TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 
       13.91        14.30        55.59        44.88        94.82        21.67 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME 
      129.27        28.83        19.76        61.51        47.28       103.27 
TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM 
      103.20        16.96       204.66       144.76       203.05       167.90 
TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT 
       47.54       248.65        43.23       103.56       136.47        41.59 
TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG 
       53.26       122.73         3.68        54.51        13.81        23.47 
TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 
      138.81       172.18       127.20        36.95        64.08        34.32 
TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 
       53.19        27.35        33.40       101.79       148.08        31.40 
TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B 
       35.44        13.94        50.76         9.17        77.75        98.40 
TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H 
       48.89        12.59        13.02        26.37       268.93       152.35 
TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q 
        6.44       131.51        61.05        44.05       162.08        50.89 
TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE 
       37.25       148.18        79.99        43.82        23.34        20.15 
TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL 
       16.37        31.27       247.04        80.32        46.98        33.21 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY 
       92.98       174.21         4.90       216.92        48.59       228.59 
TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB 
      202.65        20.91        28.08         7.79        27.72        48.85 
TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ 
      357.37        53.52        40.27         9.70        32.75        47.38 
TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT 
      101.26        74.73       133.55        11.41       148.80        53.16 
TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 
       26.56        49.48        27.09        77.82        66.67        28.73 
TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU 
       12.43        26.73        49.45        77.88         0.20        47.54 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 
        0.16         2.40         9.90         7.23        14.04       120.46 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D 
      117.93        84.72        64.44        62.79        32.48        39.58 
TCGA-QB-A6FS 
        6.67 

  CYP3A7 MUTATED CYP3A7 WILD-TYPE 
           10.13             0.16 
  CYP3A7 MUTATED CYP3A7 WILD-TYPE 
          174.84           357.37 
  CYP3A7 MUTATED CYP3A7 WILD-TYPE 
           34.88            48.85 
[1] "10.1 - 174.8 (34.9)" "0.2 - 357.4 (48.9)" 
[1] "hr=" "1.4"
D135V3, continuous
                  vv
clus               DISTANT METASTASIS PRIMARY TUMOR
  CYP3A7 MUTATED                    7             0
  CYP3A7 WILD-TYPE                 28             4
                  vv
clus               REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  CYP3A7 MUTATED                                           3
  CYP3A7 WILD-TYPE                                        55
                  vv
clus               REGIONAL LYMPH NODE
  CYP3A7 MUTATED                    13
  CYP3A7 WILD-TYPE                 157
D135V4, multiclass
                                           clus
vv                                          CYP3A7 MUTATED CYP3A7 WILD-TYPE
  DISTANT METASTASIS                                     7               28
  PRIMARY TUMOR                                          0                4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE              3               55
  REGIONAL LYMPH NODE                                   13              157
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  CYP3A7 MUTATED             1       0       2        1        1        3
  CYP3A7 WILD-TYPE           9       6      20        9       23       14
                  vv
clus               STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  CYP3A7 MUTATED           0         1         1         6          0
  CYP3A7 WILD-TYPE        10        13         8        25         13
                  vv
clus               STAGE IIIB STAGE IIIC STAGE IV
  CYP3A7 MUTATED            3          3        0
  CYP3A7 WILD-TYPE         19         41       12
D135V5, multiclass
             clus
vv            CYP3A7 MUTATED CYP3A7 WILD-TYPE
  I OR II NOS              1                9
  STAGE 0                  0                6
  STAGE I                  2               20
  STAGE IA                 1                9
  STAGE IB                 1               23
  STAGE II                 3               14
  STAGE IIA                0               10
  STAGE IIB                1               13
  STAGE IIC                1                8
  STAGE III                6               25
  STAGE IIIA               0               13
  STAGE IIIB               3               19
  STAGE IIIC               3               41
  STAGE IV                 0               12
[1] 14  2
[1] 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
  CYP3A7 MUTATED       7  4  5  5
  CYP3A7 WILD-TYPE    44 54 48 50
D135V6, multiclass
       clus
vv      CYP3A7 MUTATED CYP3A7 WILD-TYPE
  T0+T1              7               44
  T2                 4               54
  T3                 5               48
  T4                 5               50
[1] 4 2
[1] TRUE
[1] "dimension 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
  CYP3A7 MUTATED    12   5   3   2
  CYP3A7 WILD-TYPE 126  43  29  31
D135V7, multiclass
    clus
vv   CYP3A7 MUTATED CYP3A7 WILD-TYPE
  N0             12              126
  N1              5               43
  N2              3               29
  N3              2               31
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                M0  M1 M1A M1B M1C
  CYP3A7 MUTATED    22   0   0   0   0
  CYP3A7 WILD-TYPE 218   4   2   2   5
D135V8, multiclass
     clus
vv    CYP3A7 MUTATED CYP3A7 WILD-TYPE
  M0              22              218
  M1               0                4
  M1A              0                2
  M1B              0                2
  M1C              0                5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D135V9, binary
                  cls
clus                0  1
  CYP3A7 MUTATED    9  3
  CYP3A7 WILD-TYPE 93 64
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CYP3A7 MUTATED      9    3
  CYP3A7 WILD-TYPE   93   64
     clus
vv    CYP3A7 MUTATED CYP3A7 WILD-TYPE
  NO               9               93
  YES              3               64
[1] 2 2
[1] FALSE
D135V10, binary
                  cls
clus                 0   1
  CYP3A7 MUTATED     5  18
  CYP3A7 WILD-TYPE  28 217
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CYP3A7 MUTATED      5   18
  CYP3A7 WILD-TYPE   28  217
     clus
vv    CYP3A7 MUTATED CYP3A7 WILD-TYPE
  NO               5               28
  YES             18              217
[1] 2 2
[1] FALSE
D135V11, continuous
D135V12, binary
                  cls
clus                 0   1
  CYP3A7 MUTATED     8  15
  CYP3A7 WILD-TYPE  95 150
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CYP3A7 MUTATED      8   15
  CYP3A7 WILD-TYPE   95  150
        clus
vv       CYP3A7 MUTATED CYP3A7 WILD-TYPE
  FEMALE              8               95
  MALE               15              150
[1] 2 2
[1] FALSE
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CYP3A7 MUTATED       0                         0    23
  CYP3A7 WILD-TYPE     3                         1   241
D135V13, multiclass
                           clus
vv                          CYP3A7 MUTATED CYP3A7 WILD-TYPE
  ASIAN                                  0                3
  BLACK OR AFRICAN AMERICAN              0                1
  WHITE                                 23              241
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D135V14, binary
                  cls
clus                 0   1
  CYP3A7 MUTATED     1  22
  CYP3A7 WILD-TYPE   2 239
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CYP3A7 MUTATED      1   22
  CYP3A7 WILD-TYPE    2  239
                        clus
vv                       CYP3A7 MUTATED CYP3A7 WILD-TYPE
  HISPANIC OR LATINO                  1                2
  NOT HISPANIC OR LATINO             22              239
[1] 2 2
[1] FALSE

Clustering(136) Variable = VGLL1 MUTATION ANALYSIS
D136V1, survival
                 sevent
clus2               0   1
  VGLL1 MUTATED     4   2
  VGLL1 WILD-TYPE 124 128
  VGLL1 MUTATED VGLL1 WILD-TYPE 
              6             252 
  VGLL1 MUTATED VGLL1 WILD-TYPE 
              2             128 
$`VGLL1 MUTATED`
TCGA-EE-A2GP TCGA-EE-A2MS TCGA-ER-A1A1 TCGA-FW-A3R5 TCGA-FW-A5DY TCGA-GN-A266 
        5.42        27.16        78.44         0.99         0.43        10.13 

$`VGLL1 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.47         8.52       111.09        32.42        70.16       110.79 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       28.08        22.55        45.83        81.24        10.29        85.32 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
        8.38        21.14        88.50        68.22        69.90        11.41 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       30.87         7.50        36.16         6.31        92.42        56.19 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 
       64.44        45.11       114.67        15.25        46.98        46.32 
TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO 
       82.29        61.38        13.32        24.00         6.31         9.34 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H 
      103.59        26.37         5.39        80.22        42.71        15.09 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN 
       41.10        17.72         8.84        20.48        13.94        52.01 
TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 
       47.87         1.55         6.97        23.11         4.01         2.89 
TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY 
        9.90        11.31        13.22        48.79        35.80        51.12 
TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 
       10.03        39.19        13.68         9.99        44.52        36.69 
TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 
       25.15         4.93        22.36         6.64        19.36         7.00 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH 
       17.56        14.83        13.15         0.20         0.00         0.00 
TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 
       13.22        11.57        10.55         6.31         8.12         1.12 
TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C 
        1.35        12.20         5.13         4.31        36.07         4.34 
TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C 
        5.13         9.21         1.18         7.99         9.90        37.97 
TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M 
       11.15        38.63         8.55         4.41         1.08        27.12 
TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V 
        9.50        12.03         8.09         8.84         9.99         2.43 
TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 
        8.68         8.09        11.31        49.22        23.90         9.67 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH 
        8.94        39.39        34.29        17.98        34.92        47.21 
TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN 
       30.08        19.43        16.01        35.54        28.31        33.83 
TCGA-EE-A2GO TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 
       30.84         1.15        13.02        34.98        36.33         8.84 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME 
       98.27         2.70         6.18        47.51         9.53        29.46 
TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML 
       44.25         7.96        14.56        63.42       111.78       111.91 
TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MT 
       56.02        25.08        26.99        21.60        29.65        23.05 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE 
        5.56       124.31       122.73        25.84         3.68        30.15 
TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 
       13.81        15.95        12.72         3.22        22.92        21.60 
TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH 
       21.60        16.14        22.22        27.35         0.46        13.94 
TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 
       33.60        31.40        18.61        12.95        38.40         5.72 
TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F 
       76.41        25.18         3.78         3.52        11.90        11.11 
TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N 
      114.15        34.88         4.21        13.45        28.60        42.84 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A2NC TCGA-ER-A2ND 
       34.68         9.57        36.07        17.72        11.80         1.87 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET 
        1.51        13.08        12.62        11.74         9.04         6.58 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW 
       22.49         1.71        18.41        85.74         4.90        64.47 
TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 
        3.45        11.01        23.80        14.24        15.52         7.33 
TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF 
        7.30         3.39        20.38         8.22        19.53        11.08 
TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP 
        7.17        30.87        12.92        12.89        47.38        52.08 
TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW 
        8.65         8.81        49.15        40.64         8.68        27.39 
TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 
        0.82         5.23        53.85         7.36        28.73        14.20 
TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU 
       10.78         5.98         6.41         2.27         0.20         0.13 
TCGA-FW-A3TV TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 
        0.16         9.90         7.23        12.85        24.85        31.33 
TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS 
       84.72        16.24        15.42        12.16        14.70         5.79 

  VGLL1 MUTATED VGLL1 WILD-TYPE 
           0.43            0.00 
  VGLL1 MUTATED VGLL1 WILD-TYPE 
          78.44          124.31 
  VGLL1 MUTATED VGLL1 WILD-TYPE 
          7.775          14.960 
[1] "0.4 - 78.4 (7.8)"   "0.0 - 124.3 (15.0)"
[1] "hr=" "1.1"
D136V2, survival
                 sevent
clus2               0   1
  VGLL1 MUTATED     4   2
  VGLL1 WILD-TYPE 128 129
  VGLL1 MUTATED VGLL1 WILD-TYPE 
              6             257 
  VGLL1 MUTATED VGLL1 WILD-TYPE 
              2             129 
$`VGLL1 MUTATED`
TCGA-EE-A2GP TCGA-EE-A2MS TCGA-ER-A1A1 TCGA-FW-A3R5 TCGA-FW-A5DY TCGA-GN-A266 
       13.91       136.47        79.99        22.92         2.40        10.13 

$`VGLL1 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.57        16.67       112.04       112.57        71.80       133.25 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       28.08        31.59        90.90        95.74        43.43       103.10 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
       65.49        23.77       115.53       168.00        69.90        11.87 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       48.76       113.52        42.08        12.10       171.58        56.19 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 
       66.08        45.11       130.72        58.06        46.98        46.32 
TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO 
      166.52        86.93        60.23        24.53        13.87         9.34 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H 
      103.59        39.75        21.47       161.85        43.69        40.14 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN 
      131.90        18.38        10.03        51.68        15.06       135.75 
TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 
      137.92       166.19         7.43       125.19       151.53        54.67 
TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA 
        3.65         6.41        11.34         3.25         9.90        25.18 
TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 
       66.25        48.89        36.03       117.21        20.38       194.83 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA 
      176.55        35.93       107.34        61.18        53.92        65.92 
TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 
       23.44        68.09        28.60        10.49       215.44        15.68 
TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN 
       13.87        10.16        45.11        35.01         3.55        52.01 
TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 
       29.82        27.22         8.65        94.98        33.73        14.70 
TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F 
       26.89        68.15         4.96       109.64       151.27        78.87 
TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D 
      168.26        13.55        63.35        80.61        47.84        13.97 
TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N 
       39.62        72.07        32.19         2.60        44.35        18.61 
TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W 
       56.42        37.35        14.47        55.92        25.87       171.55 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 
       17.92        46.82       102.90        24.43        39.29        58.75 
TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI 
       47.54        67.43       314.56       135.95       208.04        48.72 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO 
       89.33        54.74        79.66        75.48        90.97       101.95 
TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 
       14.30        55.59        44.88        94.82        21.67       129.27 
TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG 
       28.83        19.76        61.51        47.28       103.27       103.20 
TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM 
       16.96       204.66        96.23       144.76       203.05       167.90 
TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MT TCGA-EE-A2MU 
       47.54       248.65        43.23       103.56        41.59        53.26 
TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF 
      124.31       122.73        25.84         3.68        54.51        13.81 
TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 
       23.47       138.81       172.18       127.20        36.95        64.08 
TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI 
       34.32        53.19        27.35        33.40       101.79       148.08 
TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A 
       31.40        35.44        13.94        50.76         9.17        77.75 
TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G 
       98.40        48.89        12.59        13.02        26.37       268.93 
TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P 
      152.35         6.44       131.51        61.05        44.05       162.08 
TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE 
       50.89        37.25       148.18        43.82        23.34        20.15 
TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV 
       16.37        31.27        32.05       247.04        80.32        46.98 
TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX 
       33.21        92.98       174.21         4.90       216.92        48.59 
TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA 
      228.59       202.65        20.91        28.08         7.79        27.72 
TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG 
       48.85       357.37        53.52        40.27        15.45         9.70 
TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ 
       32.75        47.38        23.93       101.26        74.73       133.55 
TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY 
       11.41       148.80        53.16        26.56        49.48        27.09 
TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 
       27.02        77.82        66.67        28.73       174.84        12.43 
TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV 
       26.73        49.45        77.88         0.20        47.54         0.16 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        9.90         7.23        14.04       120.46       117.93        84.72 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS 
       64.44        62.79        32.48        39.58         6.67 

  VGLL1 MUTATED VGLL1 WILD-TYPE 
           2.40            0.16 
  VGLL1 MUTATED VGLL1 WILD-TYPE 
         136.47          357.37 
  VGLL1 MUTATED VGLL1 WILD-TYPE 
         18.415          48.720 
[1] "2.4 - 136.5 (18.4)" "0.2 - 357.4 (48.7)"
[1] "hr=" "1.1"
D136V3, continuous
                 vv
clus              DISTANT METASTASIS PRIMARY TUMOR
  VGLL1 MUTATED                    0             0
  VGLL1 WILD-TYPE                 35             4
                 vv
clus              REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  VGLL1 MUTATED                                           2                   4
  VGLL1 WILD-TYPE                                        56                 166
D136V4, multiclass
                                           clus
vv                                          VGLL1 MUTATED VGLL1 WILD-TYPE
  DISTANT METASTASIS                                    0              35
  PRIMARY TUMOR                                         0               4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE             2              56
  REGIONAL LYMPH NODE                                   4             166
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  VGLL1 MUTATED             0       0       0        0        0        1
  VGLL1 WILD-TYPE          10       6      22       10       24       16
                 vv
clus              STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  VGLL1 MUTATED           0         0         0         2          0          1
  VGLL1 WILD-TYPE        10        14         9        29         13         21
                 vv
clus              STAGE IIIC STAGE IV
  VGLL1 MUTATED            1        0
  VGLL1 WILD-TYPE         43       12
D136V5, multiclass
             clus
vv            VGLL1 MUTATED VGLL1 WILD-TYPE
  I OR II NOS             0              10
  STAGE 0                 0               6
  STAGE I                 0              22
  STAGE IA                0              10
  STAGE IB                0              24
  STAGE II                1              16
  STAGE IIA               0              10
  STAGE IIB               0              14
  STAGE IIC               0               9
  STAGE III               2              29
  STAGE IIIA              0              13
  STAGE IIIB              1              21
  STAGE IIIC              1              43
  STAGE IV                0              12
[1] 14  2
[1] 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
  VGLL1 MUTATED       0  0  2  1
  VGLL1 WILD-TYPE    51 58 51 54
D136V6, multiclass
       clus
vv      VGLL1 MUTATED VGLL1 WILD-TYPE
  T0+T1             0              51
  T2                0              58
  T3                2              51
  T4                1              54
[1] 4 2
[1] TRUE
[1] "dimension 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
  VGLL1 MUTATED     1   2   1   1
  VGLL1 WILD-TYPE 137  46  31  32
D136V7, multiclass
    clus
vv   VGLL1 MUTATED VGLL1 WILD-TYPE
  N0             1             137
  N1             2              46
  N2             1              31
  N3             1              32
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               M0  M1 M1A M1B M1C
  VGLL1 MUTATED     4   0   0   0   0
  VGLL1 WILD-TYPE 236   4   2   2   5
D136V8, multiclass
     clus
vv    VGLL1 MUTATED VGLL1 WILD-TYPE
  M0              4             236
  M1              0               4
  M1A             0               2
  M1B             0               2
  M1C             0               5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D136V9, binary
                 cls
clus                0   1
  VGLL1 MUTATED     1   1
  VGLL1 WILD-TYPE 101  66
[1] "tbl2"
                 cls
clus              [,1] [,2]
  VGLL1 MUTATED      1    1
  VGLL1 WILD-TYPE  101   66
     clus
vv    VGLL1 MUTATED VGLL1 WILD-TYPE
  NO              1             101
  YES             1              66
[1] 2 2
[1] FALSE
D136V10, binary
                 cls
clus                0   1
  VGLL1 MUTATED     2   4
  VGLL1 WILD-TYPE  31 231
[1] "tbl2"
                 cls
clus              [,1] [,2]
  VGLL1 MUTATED      2    4
  VGLL1 WILD-TYPE   31  231
     clus
vv    VGLL1 MUTATED VGLL1 WILD-TYPE
  NO              2              31
  YES             4             231
[1] 2 2
[1] FALSE
D136V11, continuous
[1] "Remove cluster labels:" "VGLL1 MUTATED"         
clus
  VGLL1 MUTATED VGLL1 WILD-TYPE 
              2             198 
     TCGA-D3-A1Q1      TCGA-D3-A1Q3      TCGA-D3-A1Q4      TCGA-D3-A1Q6 
"VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" 
     TCGA-D3-A1Q7      TCGA-D3-A1Q9      TCGA-D3-A1QA      TCGA-D3-A2J6 
"VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" 
     TCGA-D3-A2J7      TCGA-D3-A2J8      TCGA-D3-A2J9      TCGA-D3-A2JA 
"VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" 
     TCGA-D3-A2JD      TCGA-D3-A2JF      TCGA-D3-A2JG      TCGA-D3-A2JH 
"VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" 
     TCGA-D3-A2JK      TCGA-D3-A3BZ      TCGA-D3-A3C6      TCGA-D3-A3CB 
"VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" 
     TCGA-D3-A3CC      TCGA-D3-A3CF      TCGA-D3-A3ML      TCGA-D3-A3MU 
"VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" 
     TCGA-D3-A3MV      TCGA-D3-A51E      TCGA-D3-A51F      TCGA-D3-A51G 
"VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" 
     TCGA-D3-A51H      TCGA-D3-A51K      TCGA-D3-A51R      TCGA-D3-A51T 
"VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" 
     TCGA-D3-A5GN      TCGA-D3-A5GO      TCGA-D3-A5GR      TCGA-D3-A5GS 
"VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" 
     TCGA-D3-A5GU      TCGA-D9-A3Z1      TCGA-D9-A3Z3      TCGA-D9-A6E9 
"VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" 
     TCGA-D9-A6EA      TCGA-D9-A6EC      TCGA-DA-A1HW      TCGA-DA-A1HY 
"VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" 
     TCGA-DA-A1I0      TCGA-DA-A1I4      TCGA-DA-A1I5      TCGA-DA-A1I8 
"VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" 
     TCGA-DA-A1IA      TCGA-DA-A1IB      TCGA-DA-A1IC      TCGA-DA-A3F2 
"VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" 
     TCGA-DA-A3F5      TCGA-DA-A3F8      TCGA-EB-A5SH      TCGA-EB-A5UL 
"VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" 
     TCGA-EB-A5UN      TCGA-EE-A17X      TCGA-EE-A17Y      TCGA-EE-A17Z 
"VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" 
     TCGA-EE-A180      TCGA-EE-A181      TCGA-EE-A182      TCGA-EE-A184 
"VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" 
     TCGA-EE-A185      TCGA-EE-A20B      TCGA-EE-A20F      TCGA-EE-A20H 
"VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" 
     TCGA-EE-A29A      TCGA-EE-A29B      TCGA-EE-A29C      TCGA-EE-A29D 
"VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" 
     TCGA-EE-A29E      TCGA-EE-A29G      TCGA-EE-A29H      TCGA-EE-A29L 
"VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" 
     TCGA-EE-A29M      TCGA-EE-A29P      TCGA-EE-A29Q      TCGA-EE-A29R 
"VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" 
     TCGA-EE-A29S      TCGA-EE-A29V      TCGA-EE-A29W      TCGA-EE-A29X 
"VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" 
     TCGA-EE-A2A0      TCGA-EE-A2A1      TCGA-EE-A2A2      TCGA-EE-A2A5 
"VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" 
     TCGA-EE-A2A6      TCGA-EE-A2GB      TCGA-EE-A2GC      TCGA-EE-A2GD 
"VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" 
     TCGA-EE-A2GE      TCGA-EE-A2GH      TCGA-EE-A2GI      TCGA-EE-A2GJ 
"VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" 
     TCGA-EE-A2GK      TCGA-EE-A2GL      TCGA-EE-A2GM      TCGA-EE-A2GN 
"VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" 
     TCGA-EE-A2GO      TCGA-EE-A2GR      TCGA-EE-A2GS      TCGA-EE-A2GT 
"VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" 
     TCGA-EE-A2GU      TCGA-EE-A2M5      TCGA-EE-A2M6      TCGA-EE-A2M7 
"VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" 
     TCGA-EE-A2M8      TCGA-EE-A2MC      TCGA-EE-A2MD      TCGA-EE-A2ME 
"VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" 
     TCGA-EE-A2MG      TCGA-EE-A2MH      TCGA-EE-A2MI      TCGA-EE-A2MJ 
"VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" 
     TCGA-EE-A2MK      TCGA-EE-A2ML      TCGA-EE-A2MM      TCGA-EE-A2MN 
"VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" 
     TCGA-EE-A2MP      TCGA-EE-A2MQ      TCGA-EE-A2MR      TCGA-EE-A2MT 
"VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" 
     TCGA-EE-A2MU      TCGA-EE-A3AE      TCGA-EE-A3AH      TCGA-EE-A3J3 
"VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" 
     TCGA-EE-A3J4      TCGA-EE-A3J5      TCGA-EE-A3J7      TCGA-EE-A3J8 
"VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" 
     TCGA-EE-A3JA      TCGA-EE-A3JE      TCGA-EE-A3JH      TCGA-EE-A3JI 
"VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" 
     TCGA-ER-A197      TCGA-ER-A198      TCGA-ER-A199      TCGA-ER-A19C 
"VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" 
     TCGA-ER-A19D      TCGA-ER-A19E      TCGA-ER-A19F      TCGA-ER-A19G 
"VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" 
     TCGA-ER-A19H      TCGA-ER-A19M      TCGA-ER-A19Q      TCGA-ER-A19W 
"VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" 
     TCGA-ER-A2NC      TCGA-ER-A2ND      TCGA-ER-A2NF      TCGA-ER-A2NG 
"VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" 
     TCGA-ER-A2NH      TCGA-ER-A3ET      TCGA-ER-A3EV      TCGA-ER-A3PL 
"VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" 
     TCGA-FR-A3YN      TCGA-FR-A44A      TCGA-FS-A1YW      TCGA-FS-A1YX 
"VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" 
     TCGA-FS-A1YY      TCGA-FS-A1Z0      TCGA-FS-A1Z4      TCGA-FS-A1Z7 
"VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" 
     TCGA-FS-A1ZA      TCGA-FS-A1ZB      TCGA-FS-A1ZD      TCGA-FS-A1ZE 
"VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" 
     TCGA-FS-A1ZF      TCGA-FS-A1ZG      TCGA-FS-A1ZH      TCGA-FS-A1ZJ 
"VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" 
     TCGA-FS-A1ZK      TCGA-FS-A1ZM      TCGA-FS-A1ZP      TCGA-FS-A1ZR 
"VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" 
     TCGA-FS-A1ZS      TCGA-FS-A1ZT      TCGA-FS-A1ZU      TCGA-FS-A1ZW 
"VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" 
     TCGA-FS-A1ZY      TCGA-FS-A1ZZ      TCGA-FS-A4F0      TCGA-FS-A4F4 
"VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" 
     TCGA-FS-A4F5      TCGA-FS-A4F8      TCGA-FS-A4F9      TCGA-FS-A4FB 
"VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" 
     TCGA-FS-A4FC      TCGA-FS-A4FD      TCGA-FW-A3TV      TCGA-GF-A6C8 
"VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" 
     TCGA-GN-A262      TCGA-GN-A264      TCGA-GN-A267      TCGA-GN-A268 
"VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" 
     TCGA-GN-A26A      TCGA-GN-A26D 
"VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" 
D136V12, binary
                 cls
clus                0   1
  VGLL1 MUTATED     1   5
  VGLL1 WILD-TYPE 102 160
[1] "tbl2"
                 cls
clus              [,1] [,2]
  VGLL1 MUTATED      1    5
  VGLL1 WILD-TYPE  102  160
        clus
vv       VGLL1 MUTATED VGLL1 WILD-TYPE
  FEMALE             1             102
  MALE               5             160
[1] 2 2
[1] FALSE
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  VGLL1 MUTATED       0                         0     6
  VGLL1 WILD-TYPE     3                         1   258
D136V13, multiclass
                           clus
vv                          VGLL1 MUTATED VGLL1 WILD-TYPE
  ASIAN                                 0               3
  BLACK OR AFRICAN AMERICAN             0               1
  WHITE                                 6             258
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D136V14, binary
                 cls
clus                0   1
  VGLL1 MUTATED     0   6
  VGLL1 WILD-TYPE   3 255
[1] "tbl2"
                 cls
clus              [,1] [,2]
  VGLL1 MUTATED      0    6
  VGLL1 WILD-TYPE    3  255
                        clus
vv                       VGLL1 MUTATED VGLL1 WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO             6             255
[1] 2 2
[1] FALSE

Clustering(137) Variable = GML MUTATION ANALYSIS
D137V1, survival
               sevent
clus2             0   1
  GML MUTATED     4   4
  GML WILD-TYPE 124 126
  GML MUTATED GML WILD-TYPE 
            8           250 
  GML MUTATED GML WILD-TYPE 
            4           126 
$`GML MUTATED`
TCGA-D3-A2JC TCGA-DA-A1I7 TCGA-EE-A29D TCGA-EE-A2GJ TCGA-EE-A2MI TCGA-EE-A2MJ 
       69.90        36.69        11.15        19.43        14.56        63.42 
TCGA-EE-A2MT TCGA-FS-A1Z3 
       23.05        14.24 

$`GML WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.47         8.52       111.09        32.42        70.16       110.79 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       28.08        22.55        45.83        81.24        10.29        85.32 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JD TCGA-D3-A2JF 
        8.38        21.14        88.50        68.22        11.41        30.87 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO 
        7.50        36.16         6.31        92.42        56.19        64.44 
TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB 
       45.11       114.67        15.25        46.98        46.32        82.29 
TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR 
       61.38        13.32        24.00         6.31         9.34       103.59 
TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J 
       26.37         5.39        80.22        42.71        15.09        41.10 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO 
       17.72         8.84        20.48        13.94        52.01        47.87 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 
        1.55         6.97        23.11         4.01         2.89         9.90 
TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 
       11.31        13.22        48.79        35.80        51.12        10.03 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I8 TCGA-DA-A1IA 
       39.19        13.68         9.99        44.52        25.15         4.93 
TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 
       22.36         6.64        19.36         7.00        17.56        14.83 
TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EE-A17X 
       13.15         0.20         0.00         0.00        13.22        11.57 
TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 
       10.55         6.31         8.12         1.12         1.35        12.20 
TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H 
        5.13         4.31        36.07         4.34         5.13         9.21 
TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G 
        1.18         7.99         9.90        37.97        38.63         8.55 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
        4.41         1.08        27.12         9.50        12.03         8.09 
TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 
        8.84         9.99         2.43         8.68         8.09        11.31 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC 
       49.22        23.90         9.67         8.94        39.39        34.29 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GK TCGA-EE-A2GL 
       17.98        34.92        47.21        30.08        16.01        35.54 
TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS 
       28.31        33.83        30.84         5.42         1.15        13.02 
TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 
       34.98        36.33         8.84        98.27         2.70         6.18 
TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MK 
       47.51         9.53        29.46        44.25         7.96       111.78 
TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR 
      111.91        56.02        25.08        26.99        21.60        29.65 
TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD 
       27.16         5.56       124.31       122.73        25.84         3.68 
TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 
       30.15        13.81        15.95        12.72         3.22        22.92 
TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE 
       21.60        21.60        16.14        22.22        27.35         0.46 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 
       13.94        33.60        31.40        18.61        12.95        38.40 
TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E 
        5.72        76.41        25.18         3.78         3.52        11.90 
TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M 
       11.11       114.15        34.88         4.21        13.45        28.60 
TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 
       42.84        34.68         9.57        36.07        17.72        78.44 
TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH 
       11.80         1.87         1.51        13.08        12.62        11.74 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A 
        9.04         6.58        22.49         1.71        18.41        85.74 
TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z4 
        4.90        64.47         3.45        11.01        23.80        15.52 
TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE 
        7.33         7.30         3.39        20.38         8.22        19.53 
TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM 
       11.08         7.17        30.87        12.92        12.89        47.38 
TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU 
       52.08         8.65         8.81        49.15        40.64         8.68 
TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 
       27.39         0.82         5.23        53.85         7.36        28.73 
TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 
       14.20        10.78         5.98         6.41         2.27         0.20 
TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
        0.99         0.13         0.16         0.43         9.90         7.23 
TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 
       12.85        24.85        31.33        84.72        10.13        16.24 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS 
       15.42        12.16        14.70         5.79 

  GML MUTATED GML WILD-TYPE 
        11.15          0.00 
  GML MUTATED GML WILD-TYPE 
        69.90        124.31 
  GML MUTATED GML WILD-TYPE 
        21.24         14.45 
[1] "11.2 - 69.9 (21.2)" "0.0 - 124.3 (14.4)"
[1] "hr=" "1.3"
D137V2, survival
               sevent
clus2             0   1
  GML MUTATED     6   4
  GML WILD-TYPE 126 127
  GML MUTATED GML WILD-TYPE 
           10           253 
  GML MUTATED GML WILD-TYPE 
            4           127 
$`GML MUTATED`
TCGA-D3-A2JC TCGA-D9-A1JW TCGA-DA-A1I7 TCGA-EB-A5UL TCGA-EE-A29D TCGA-EE-A2GJ 
       69.90         3.65        61.18         3.55        13.97        89.33 
TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MT TCGA-FS-A1Z3 
      204.66        96.23        41.59        20.91 

$`GML WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.57        16.67       112.04       112.57        71.80       133.25 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       28.08        31.59        90.90        95.74        43.43       103.10 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JD TCGA-D3-A2JF 
       65.49        23.77       115.53       168.00        11.87        48.76 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO 
      113.52        42.08        12.10       171.58        56.19        66.08 
TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB 
       45.11       130.72        58.06        46.98        46.32       166.52 
TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR 
       86.93        60.23        24.53        13.87         9.34       103.59 
TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J 
       39.75        21.47       161.85        43.69        40.14       131.90 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO 
       18.38        10.03        51.68        15.06       135.75       137.92 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JX 
      166.19         7.43       125.19       151.53        54.67         6.41 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1HV 
       11.34         3.25         9.90        25.18        66.25        48.89 
TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 
       36.03       117.21        20.38       194.83       176.55        35.93 
TCGA-DA-A1I5 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
      107.34        53.92        65.92        23.44        68.09        28.60 
TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG 
       10.49       215.44        15.68        13.87        10.16        45.11 
TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 
       35.01        52.01        29.82        27.22         8.65        94.98 
TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B 
       33.73        14.70        26.89        68.15         4.96       109.64 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B 
      151.27        78.87       168.26        13.55        63.35        80.61 
TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M 
       47.84        39.62        72.07        32.19         2.60        44.35 
TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V 
       18.61        56.42        37.35        14.47        55.92        25.87 
TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 
      171.55        17.92        46.82       102.90        24.43        39.29 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH 
       58.75        47.54        67.43       314.56       135.95       208.04 
TCGA-EE-A2GI TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO 
       48.72        54.74        79.66        75.48        90.97       101.95 
TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 
       13.91        14.30        55.59        44.88        94.82        21.67 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME 
      129.27        28.83        19.76        61.51        47.28       103.27 
TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN 
      103.20        16.96       144.76       203.05       167.90        47.54 
TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3AA 
      248.65        43.23       103.56       136.47        53.26       124.31 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG 
      122.73        25.84         3.68        54.51        13.81        23.47 
TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 
      138.81       172.18       127.20        36.95        64.08        34.32 
TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 
       53.19        27.35        33.40       101.79       148.08        31.40 
TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B 
       35.44        13.94        50.76         9.17        77.75        98.40 
TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H 
       48.89        12.59        13.02        26.37       268.93       152.35 
TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q 
        6.44       131.51        61.05        44.05       162.08        50.89 
TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE 
       37.25       148.18        79.99        43.82        23.34        20.15 
TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV 
       16.37        31.27        32.05       247.04        80.32        46.98 
TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX 
       33.21        92.98       174.21         4.90       216.92        48.59 
TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB 
      228.59       202.65        28.08         7.79        27.72        48.85 
TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH 
      357.37        53.52        40.27        15.45         9.70        32.75 
TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR 
       47.38        23.93       101.26        74.73       133.55        11.41 
TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ 
      148.80        53.16        26.56        49.48        27.09        27.02 
TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB 
       77.82        66.67        28.73       174.84        12.43        26.73 
TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV 
       49.45        77.88         0.20        22.92        47.54         0.16 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 
        2.40         9.90         7.23        14.04       120.46       117.93 
TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D 
       84.72        10.13        64.44        62.79        32.48        39.58 
TCGA-QB-A6FS 
        6.67 

  GML MUTATED GML WILD-TYPE 
         3.55          0.16 
  GML MUTATED GML WILD-TYPE 
       204.66        357.37 
  GML MUTATED GML WILD-TYPE 
       51.385        48.590 
[1] "3.5 - 204.7 (51.4)" "0.2 - 357.4 (48.6)"
[1] "hr=" "1.2"
D137V3, continuous
               vv
clus            DISTANT METASTASIS PRIMARY TUMOR
  GML MUTATED                    1             0
  GML WILD-TYPE                 34             4
               vv
clus            REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  GML MUTATED                                           1                   8
  GML WILD-TYPE                                        57                 162
D137V4, multiclass
                                           clus
vv                                          GML MUTATED GML WILD-TYPE
  DISTANT METASTASIS                                  1            34
  PRIMARY TUMOR                                       0             4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE           1            57
  REGIONAL LYMPH NODE                                 8           162
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  GML MUTATED             0       0       0        1        1        0
  GML WILD-TYPE          10       6      22        9       23       17
               vv
clus            STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  GML MUTATED           0         1         0         3          0          1
  GML WILD-TYPE        10        13         9        28         13         21
               vv
clus            STAGE IIIC STAGE IV
  GML MUTATED            1        1
  GML WILD-TYPE         43       11
D137V5, multiclass
             clus
vv            GML MUTATED GML WILD-TYPE
  I OR II NOS           0            10
  STAGE 0               0             6
  STAGE I               0            22
  STAGE IA              1             9
  STAGE IB              1            23
  STAGE II              0            17
  STAGE IIA             0            10
  STAGE IIB             1            13
  STAGE IIC             0             9
  STAGE III             3            28
  STAGE IIIA            0            13
  STAGE IIIB            1            21
  STAGE IIIC            1            43
  STAGE IV              1            11
[1] 14  2
[1] 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
  GML MUTATED       4  1  1  2
  GML WILD-TYPE    47 57 52 53
D137V6, multiclass
       clus
vv      GML MUTATED GML WILD-TYPE
  T0+T1           4            47
  T2              1            57
  T3              1            52
  T4              2            53
[1] 4 2
[1] TRUE
[1] "dimension 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
  GML MUTATED     5   2   3   0
  GML WILD-TYPE 133  46  29  33
D137V7, multiclass
    clus
vv   GML MUTATED GML WILD-TYPE
  N0           5           133
  N1           2            46
  N2           3            29
  N3           0            33
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             M0  M1 M1A M1B M1C
  GML MUTATED     9   1   0   0   0
  GML WILD-TYPE 231   3   2   2   5
D137V8, multiclass
     clus
vv    GML MUTATED GML WILD-TYPE
  M0            9           231
  M1            1             3
  M1A           0             2
  M1B           0             2
  M1C           0             5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D137V9, binary
               cls
clus             0  1
  GML MUTATED    4  1
  GML WILD-TYPE 98 66
[1] "tbl2"
               cls
clus            [,1] [,2]
  GML MUTATED      4    1
  GML WILD-TYPE   98   66
     clus
vv    GML MUTATED GML WILD-TYPE
  NO            4            98
  YES           1            66
[1] 2 2
[1] FALSE
D137V10, binary
               cls
clus              0   1
  GML MUTATED     3   7
  GML WILD-TYPE  30 228
[1] "tbl2"
               cls
clus            [,1] [,2]
  GML MUTATED      3    7
  GML WILD-TYPE   30  228
     clus
vv    GML MUTATED GML WILD-TYPE
  NO            3            30
  YES           7           228
[1] 2 2
[1] FALSE
D137V11, continuous
D137V12, binary
               cls
clus              0   1
  GML MUTATED     2   8
  GML WILD-TYPE 101 157
[1] "tbl2"
               cls
clus            [,1] [,2]
  GML MUTATED      2    8
  GML WILD-TYPE  101  157
        clus
vv       GML MUTATED GML WILD-TYPE
  FEMALE           2           101
  MALE             8           157
[1] 2 2
[1] FALSE
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  GML MUTATED       0                         0    10
  GML WILD-TYPE     3                         1   254
D137V13, multiclass
                           clus
vv                          GML MUTATED GML WILD-TYPE
  ASIAN                               0             3
  BLACK OR AFRICAN AMERICAN           0             1
  WHITE                              10           254
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D137V14, binary
               cls
clus              0   1
  GML MUTATED     0  10
  GML WILD-TYPE   3 251
[1] "tbl2"
               cls
clus            [,1] [,2]
  GML MUTATED      0   10
  GML WILD-TYPE    3  251
                        clus
vv                       GML MUTATED GML WILD-TYPE
  HISPANIC OR LATINO               0             3
  NOT HISPANIC OR LATINO          10           251
[1] 2 2
[1] FALSE

Clustering(138) Variable = GZMA MUTATION ANALYSIS
D138V1, survival
                sevent
clus2              0   1
  GZMA MUTATED     8   3
  GZMA WILD-TYPE 120 127
  GZMA MUTATED GZMA WILD-TYPE 
            11            247 
  GZMA MUTATED GZMA WILD-TYPE 
             3            127 
$`GZMA MUTATED`
TCGA-D3-A3CB TCGA-DA-A1I8 TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A2A2 TCGA-EE-A2GC 
       82.29        25.15        38.63         4.41        23.90        34.29 
TCGA-EE-A2GI TCGA-EE-A2GR TCGA-FS-A4F5 TCGA-FW-A3R5 TCGA-GN-A266 
       30.08         1.15        28.73         0.99        10.13 

$`GZMA WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.47         8.52       111.09        32.42        70.16       110.79 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       28.08        22.55        45.83        81.24        10.29        85.32 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
        8.38        21.14        88.50        68.22        69.90        11.41 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       30.87         7.50        36.16         6.31        92.42        56.19 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 
       64.44        45.11       114.67        15.25        46.98        46.32 
TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR 
       61.38        13.32        24.00         6.31         9.34       103.59 
TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J 
       26.37         5.39        80.22        42.71        15.09        41.10 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO 
       17.72         8.84        20.48        13.94        52.01        47.87 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 
        1.55         6.97        23.11         4.01         2.89         9.90 
TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 
       11.31        13.22        48.79        35.80        51.12        10.03 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA 
       39.19        13.68         9.99        44.52        36.69         4.93 
TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 
       22.36         6.64        19.36         7.00        17.56        14.83 
TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EE-A17X 
       13.15         0.20         0.00         0.00        13.22        11.57 
TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 
       10.55         6.31         8.12         1.12         1.35        12.20 
TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H 
        5.13         4.31        36.07         4.34         5.13         9.21 
TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29G 
        1.18         7.99         9.90        37.97        11.15         8.55 
TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R 
        1.08        27.12         9.50        12.03         8.09         8.84 
TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 
        9.99         2.43         8.68         8.09        11.31        49.22 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH 
        9.67         8.94        39.39        17.98        34.92        47.21 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO 
       19.43        16.01        35.54        28.31        33.83        30.84 
TCGA-EE-A2GP TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 
        5.42        13.02        34.98        36.33         8.84        98.27 
TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG 
        2.70         6.18        47.51         9.53        29.46        44.25 
TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM 
        7.96        14.56        63.42       111.78       111.91        56.02 
TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT 
       25.08        26.99        21.60        29.65        27.16        23.05 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE 
        5.56       124.31       122.73        25.84         3.68        30.15 
TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 
       13.81        15.95        12.72         3.22        22.92        21.60 
TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH 
       21.60        16.14        22.22        27.35         0.46        13.94 
TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 
       33.60        31.40        18.61        12.95        38.40         5.72 
TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F 
       76.41        25.18         3.78         3.52        11.90        11.11 
TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N 
      114.15        34.88         4.21        13.45        28.60        42.84 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
       34.68         9.57        36.07        17.72        78.44        11.80 
TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES 
        1.87         1.51        13.08        12.62        11.74         9.04 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
        6.58        22.49         1.71        18.41        85.74         4.90 
TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 
       64.47         3.45        11.01        23.80        14.24        15.52 
TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE 
        7.33         7.30         3.39        20.38         8.22        19.53 
TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM 
       11.08         7.17        30.87        12.92        12.89        47.38 
TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU 
       52.08         8.65         8.81        49.15        40.64         8.68 
TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 
       27.39         0.82         5.23        53.85         7.36        14.20 
TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU 
       10.78         5.98         6.41         2.27         0.20         0.13 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 
        0.16         0.43         9.90         7.23        12.85        24.85 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D 
       31.33        84.72        16.24        15.42        12.16        14.70 
TCGA-QB-A6FS 
        5.79 

  GZMA MUTATED GZMA WILD-TYPE 
          0.99           0.00 
  GZMA MUTATED GZMA WILD-TYPE 
         82.29         124.31 
  GZMA MUTATED GZMA WILD-TYPE 
         25.15          14.56 
[1] "1.0 - 82.3 (25.1)"  "0.0 - 124.3 (14.6)"
[1] "hr=" "2"  
D138V2, survival
                sevent
clus2              0   1
  GZMA MUTATED     8   3
  GZMA WILD-TYPE 124 128
  GZMA MUTATED GZMA WILD-TYPE 
            11            252 
  GZMA MUTATED GZMA WILD-TYPE 
             3            128 
$`GZMA MUTATED`
TCGA-D3-A3CB TCGA-DA-A1I8 TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A2A2 TCGA-EE-A2GC 
      166.52        53.92        39.62        32.19        24.43        67.43 
TCGA-EE-A2GI TCGA-EE-A2GR TCGA-FS-A4F5 TCGA-FW-A3R5 TCGA-GN-A266 
       48.72        14.30        28.73        22.92        10.13 

$`GZMA WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.57        16.67       112.04       112.57        71.80       133.25 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       28.08        31.59        90.90        95.74        43.43       103.10 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
       65.49        23.77       115.53       168.00        69.90        11.87 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       48.76       113.52        42.08        12.10       171.58        56.19 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 
       66.08        45.11       130.72        58.06        46.98        46.32 
TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR 
       86.93        60.23        24.53        13.87         9.34       103.59 
TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J 
       39.75        21.47       161.85        43.69        40.14       131.90 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO 
       18.38        10.03        51.68        15.06       135.75       137.92 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW 
      166.19         7.43       125.19       151.53        54.67         3.65 
TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC 
        6.41        11.34         3.25         9.90        25.18        66.25 
TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 
       48.89        36.03       117.21        20.38       194.83       176.55 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC 
       35.93       107.34        61.18        65.92        23.44        68.09 
TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R 
       28.60        10.49       215.44        15.68        13.87        10.16 
TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y 
       45.11        35.01         3.55        52.01        29.82        27.22 
TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 
        8.65        94.98        33.73        14.70        26.89        68.15 
TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I 
        4.96       109.64       151.27        78.87       168.26        13.55 
TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29L 
       63.35        80.61        47.84        13.97        72.07         2.60 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S 
       44.35        18.61        56.42        37.35        14.47        55.92 
TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A5 
       25.87       171.55        17.92        46.82       102.90        39.29 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ 
       58.75        47.54       314.56       135.95       208.04        89.33 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP 
       54.74        79.66        75.48        90.97       101.95        13.91 
TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 
       55.59        44.88        94.82        21.67       129.27        28.83 
TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH 
       19.76        61.51        47.28       103.27       103.20        16.96 
TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN 
      204.66        96.23       144.76       203.05       167.90        47.54 
TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU 
      248.65        43.23       103.56       136.47        41.59        53.26 
TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF 
      124.31       122.73        25.84         3.68        54.51        13.81 
TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 
       23.47       138.81       172.18       127.20        36.95        64.08 
TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI 
       34.32        53.19        27.35        33.40       101.79       148.08 
TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A 
       31.40        35.44        13.94        50.76         9.17        77.75 
TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G 
       98.40        48.89        12.59        13.02        26.37       268.93 
TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P 
      152.35         6.44       131.51        61.05        44.05       162.08 
TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
       50.89        37.25       148.18        79.99        43.82        23.34 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET 
       20.15        16.37        31.27        32.05       247.04        80.32 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW 
       46.98        33.21        92.98       174.21         4.90       216.92 
TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 
       48.59       228.59       202.65        20.91        28.08         7.79 
TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF 
       27.72        48.85       357.37        53.52        40.27        15.45 
TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP 
        9.70        32.75        47.38        23.93       101.26        74.73 
TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW 
      133.55        11.41       148.80        53.16        26.56        49.48 
TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 
       27.09        27.02        77.82        66.67       174.84        12.43 
TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV 
       26.73        49.45        77.88         0.20        47.54         0.16 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 
        2.40         9.90         7.23        14.04       120.46       117.93 
TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS 
       84.72        64.44        62.79        32.48        39.58         6.67 

  GZMA MUTATED GZMA WILD-TYPE 
         10.13           0.16 
  GZMA MUTATED GZMA WILD-TYPE 
        166.52         357.37 
  GZMA MUTATED GZMA WILD-TYPE 
        32.190         48.805 
[1] "10.1 - 166.5 (32.2)" "0.2 - 357.4 (48.8)" 
[1] "hr=" "1.3"
D138V3, continuous
                vv
clus             DISTANT METASTASIS PRIMARY TUMOR
  GZMA MUTATED                    0             0
  GZMA WILD-TYPE                 35             4
                vv
clus             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  GZMA MUTATED                                           4                   7
  GZMA WILD-TYPE                                        54                 163
D138V4, multiclass
                                           clus
vv                                          GZMA MUTATED GZMA WILD-TYPE
  DISTANT METASTASIS                                   0             35
  PRIMARY TUMOR                                        0              4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE            4             54
  REGIONAL LYMPH NODE                                  7            163
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  GZMA MUTATED             1       0       0        2        1        1
  GZMA WILD-TYPE           9       6      22        8       23       16
                vv
clus             STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  GZMA MUTATED           0         1         0         1          0          1
  GZMA WILD-TYPE        10        13         9        30         13         21
                vv
clus             STAGE IIIC STAGE IV
  GZMA MUTATED            2        0
  GZMA WILD-TYPE         42       12
D138V5, multiclass
             clus
vv            GZMA MUTATED GZMA WILD-TYPE
  I OR II NOS            1              9
  STAGE 0                0              6
  STAGE I                0             22
  STAGE IA               2              8
  STAGE IB               1             23
  STAGE II               1             16
  STAGE IIA              0             10
  STAGE IIB              1             13
  STAGE IIC              0              9
  STAGE III              1             30
  STAGE IIIA             0             13
  STAGE IIIB             1             21
  STAGE IIIC             2             42
  STAGE IV               0             12
[1] 14  2
[1] 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
  GZMA MUTATED       2  2  2  3
  GZMA WILD-TYPE    49 56 51 52
D138V6, multiclass
       clus
vv      GZMA MUTATED GZMA WILD-TYPE
  T0+T1            2             49
  T2               2             56
  T3               2             51
  T4               3             52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  GZMA MUTATED     6   2   1   1
  GZMA WILD-TYPE 132  46  31  32
D138V7, multiclass
    clus
vv   GZMA MUTATED GZMA WILD-TYPE
  N0            6            132
  N1            2             46
  N2            1             31
  N3            1             32
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              M0  M1 M1A M1B M1C
  GZMA MUTATED    10   0   0   0   0
  GZMA WILD-TYPE 230   4   2   2   5
D138V8, multiclass
     clus
vv    GZMA MUTATED GZMA WILD-TYPE
  M0            10            230
  M1             0              4
  M1A            0              2
  M1B            0              2
  M1C            0              5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D138V9, binary
                cls
clus              0  1
  GZMA MUTATED    4  3
  GZMA WILD-TYPE 98 64
[1] "tbl2"
                cls
clus             [,1] [,2]
  GZMA MUTATED      4    3
  GZMA WILD-TYPE   98   64
     clus
vv    GZMA MUTATED GZMA WILD-TYPE
  NO             4             98
  YES            3             64
[1] 2 2
[1] FALSE
D138V10, binary
                cls
clus               0   1
  GZMA MUTATED     1  10
  GZMA WILD-TYPE  32 225
[1] "tbl2"
                cls
clus             [,1] [,2]
  GZMA MUTATED      1   10
  GZMA WILD-TYPE   32  225
     clus
vv    GZMA MUTATED GZMA WILD-TYPE
  NO             1             32
  YES           10            225
[1] 2 2
[1] FALSE
D138V11, continuous
D138V12, binary
                cls
clus               0   1
  GZMA MUTATED     3   8
  GZMA WILD-TYPE 100 157
[1] "tbl2"
                cls
clus             [,1] [,2]
  GZMA MUTATED      3    8
  GZMA WILD-TYPE  100  157
        clus
vv       GZMA MUTATED GZMA WILD-TYPE
  FEMALE            3            100
  MALE              8            157
[1] 2 2
[1] FALSE
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  GZMA MUTATED       0                         0    11
  GZMA WILD-TYPE     3                         1   253
D138V13, multiclass
                           clus
vv                          GZMA MUTATED GZMA WILD-TYPE
  ASIAN                                0              3
  BLACK OR AFRICAN AMERICAN            0              1
  WHITE                               11            253
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D138V14, binary
                cls
clus               0   1
  GZMA MUTATED     0  11
  GZMA WILD-TYPE   3 250
[1] "tbl2"
                cls
clus             [,1] [,2]
  GZMA MUTATED      0   11
  GZMA WILD-TYPE    3  250
                        clus
vv                       GZMA MUTATED GZMA WILD-TYPE
  HISPANIC OR LATINO                0              3
  NOT HISPANIC OR LATINO           11            250
[1] 2 2
[1] FALSE

Clustering(139) Variable = NPTX1 MUTATION ANALYSIS
D139V1, survival
                 sevent
clus2               0   1
  NPTX1 MUTATED     6   2
  NPTX1 WILD-TYPE 122 128
  NPTX1 MUTATED NPTX1 WILD-TYPE 
              8             250 
  NPTX1 MUTATED NPTX1 WILD-TYPE 
              2             128 
$`NPTX1 MUTATED`
TCGA-D3-A2JF TCGA-D9-A6EC TCGA-EE-A29D TCGA-EE-A29L TCGA-EE-A2GI TCGA-EE-A2MR 
       30.87        13.22        11.15         1.08        30.08        29.65 
TCGA-EE-A3AE TCGA-FW-A3R5 
       30.15         0.99 

$`NPTX1 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.47         8.52       111.09        32.42        70.16       110.79 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       28.08        22.55        45.83        81.24        10.29        85.32 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
        8.38        21.14        88.50        68.22        69.90        11.41 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO 
        7.50        36.16         6.31        92.42        56.19        64.44 
TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB 
       45.11       114.67        15.25        46.98        46.32        82.29 
TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR 
       61.38        13.32        24.00         6.31         9.34       103.59 
TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J 
       26.37         5.39        80.22        42.71        15.09        41.10 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO 
       17.72         8.84        20.48        13.94        52.01        47.87 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 
        1.55         6.97        23.11         4.01         2.89         9.90 
TCGA-D9-A6EA TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 
       11.31        48.79        35.80        51.12        10.03        39.19 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA 
       13.68         9.99        44.52        36.69        25.15         4.93 
TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 
       22.36         6.64        19.36         7.00        17.56        14.83 
TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EE-A17X 
       13.15         0.20         0.00         0.00        13.22        11.57 
TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 
       10.55         6.31         8.12         1.12         1.35        12.20 
TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H 
        5.13         4.31        36.07         4.34         5.13         9.21 
TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G 
        1.18         7.99         9.90        37.97        38.63         8.55 
TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R 
        4.41        27.12         9.50        12.03         8.09         8.84 
TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 
        9.99         2.43         8.68         8.09        11.31        49.22 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD 
       23.90         9.67         8.94        39.39        34.29        17.98 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM 
       34.92        47.21        19.43        16.01        35.54        28.31 
TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT 
       33.83        30.84         5.42         1.15        13.02        34.98 
TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC 
       36.33         8.84        98.27         2.70         6.18        47.51 
TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ 
        9.53        29.46        44.25         7.96        14.56        63.42 
TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ 
      111.78       111.91        56.02        25.08        26.99        21.60 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC 
       27.16        23.05         5.56       124.31       122.73        25.84 
TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 
        3.68        13.81        15.95        12.72         3.22        22.92 
TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE 
       21.60        21.60        16.14        22.22        27.35         0.46 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 
       13.94        33.60        31.40        18.61        12.95        38.40 
TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E 
        5.72        76.41        25.18         3.78         3.52        11.90 
TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M 
       11.11       114.15        34.88         4.21        13.45        28.60 
TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 
       42.84        34.68         9.57        36.07        17.72        78.44 
TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH 
       11.80         1.87         1.51        13.08        12.62        11.74 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A 
        9.04         6.58        22.49         1.71        18.41        85.74 
TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
        4.90        64.47         3.45        11.01        23.80        14.24 
TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD 
       15.52         7.33         7.30         3.39        20.38         8.22 
TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK 
       19.53        11.08         7.17        30.87        12.92        12.89 
TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT 
       47.38        52.08         8.65         8.81        49.15        40.64 
TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 
        8.68        27.39         0.82         5.23        53.85         7.36 
TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD 
       28.73        14.20        10.78         5.98         6.41         2.27 
TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
        0.20         0.13         0.16         0.43         9.90         7.23 
TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 
       12.85        24.85        31.33        84.72        10.13        16.24 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS 
       15.42        12.16        14.70         5.79 

  NPTX1 MUTATED NPTX1 WILD-TYPE 
           0.99            0.00 
  NPTX1 MUTATED NPTX1 WILD-TYPE 
          30.87          124.31 
  NPTX1 MUTATED NPTX1 WILD-TYPE 
         21.435          14.765 
[1] "1.0 - 30.9 (21.4)"  "0.0 - 124.3 (14.8)"
[1] "hr=" "1.8"
D139V2, survival
                 sevent
clus2               0   1
  NPTX1 MUTATED     6   2
  NPTX1 WILD-TYPE 126 129
  NPTX1 MUTATED NPTX1 WILD-TYPE 
              8             255 
  NPTX1 MUTATED NPTX1 WILD-TYPE 
              2             129 
$`NPTX1 MUTATED`
TCGA-D3-A2JF TCGA-D9-A6EC TCGA-EE-A29D TCGA-EE-A29L TCGA-EE-A2GI TCGA-EE-A2MR 
       48.76        66.25        13.97         2.60        48.72       103.56 
TCGA-EE-A3AE TCGA-FW-A3R5 
       54.51        22.92 

$`NPTX1 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.57        16.67       112.04       112.57        71.80       133.25 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       28.08        31.59        90.90        95.74        43.43       103.10 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
       65.49        23.77       115.53       168.00        69.90        11.87 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO 
      113.52        42.08        12.10       171.58        56.19        66.08 
TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB 
       45.11       130.72        58.06        46.98        46.32       166.52 
TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR 
       86.93        60.23        24.53        13.87         9.34       103.59 
TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J 
       39.75        21.47       161.85        43.69        40.14       131.90 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO 
       18.38        10.03        51.68        15.06       135.75       137.92 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW 
      166.19         7.43       125.19       151.53        54.67         3.65 
TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-DA-A1HV 
        6.41        11.34         3.25         9.90        25.18        48.89 
TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 
       36.03       117.21        20.38       194.83       176.55        35.93 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC 
      107.34        61.18        53.92        65.92        23.44        68.09 
TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R 
       28.60        10.49       215.44        15.68        13.87        10.16 
TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y 
       45.11        35.01         3.55        52.01        29.82        27.22 
TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 
        8.65        94.98        33.73        14.70        26.89        68.15 
TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I 
        4.96       109.64       151.27        78.87       168.26        13.55 
TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H 
       63.35        80.61        47.84        39.62        72.07        32.19 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S 
       44.35        18.61        56.42        37.35        14.47        55.92 
TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 
       25.87       171.55        17.92        46.82       102.90        24.43 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE 
       39.29        58.75        47.54        67.43       314.56       135.95 
TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN 
      208.04        89.33        54.74        79.66        75.48        90.97 
TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU 
      101.95        13.91        14.30        55.59        44.88        94.82 
TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD 
       21.67       129.27        28.83        19.76        61.51        47.28 
TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK 
      103.27       103.20        16.96       204.66        96.23       144.76 
TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MS 
      203.05       167.90        47.54       248.65        43.23       136.47 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD 
       41.59        53.26       124.31       122.73        25.84         3.68 
TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 
       13.81        23.47       138.81       172.18       127.20        36.95 
TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH 
       64.08        34.32        53.19        27.35        33.40       101.79 
TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 
      148.08        31.40        35.44        13.94        50.76         9.17 
TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F 
       77.75        98.40        48.89        12.59        13.02        26.37 
TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N 
      268.93       152.35         6.44       131.51        61.05        44.05 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
      162.08        50.89        37.25       148.18        79.99        43.82 
TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES 
       23.34        20.15        16.37        31.27        32.05       247.04 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
       80.32        46.98        33.21        92.98       174.21         4.90 
TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 
      216.92        48.59       228.59       202.65        20.91        28.08 
TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE 
        7.79        27.72        48.85       357.37        53.52        40.27 
TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM 
       15.45         9.70        32.75        47.38        23.93       101.26 
TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU 
       74.73       133.55        11.41       148.80        53.16        26.56 
TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 
       49.48        27.09        27.02        77.82        66.67        28.73 
TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 
      174.84        12.43        26.73        49.45        77.88         0.20 
TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 
       47.54         0.16         2.40         9.90         7.23        14.04 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 
      120.46       117.93        84.72        10.13        64.44        62.79 
TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS 
       32.48        39.58         6.67 

  NPTX1 MUTATED NPTX1 WILD-TYPE 
           2.60            0.16 
  NPTX1 MUTATED NPTX1 WILD-TYPE 
         103.56          357.37 
  NPTX1 MUTATED NPTX1 WILD-TYPE 
          48.74           47.84 
[1] "2.6 - 103.6 (48.7)" "0.2 - 357.4 (47.8)"
[1] "hr=" "1.4"
D139V3, continuous
                 vv
clus              DISTANT METASTASIS PRIMARY TUMOR
  NPTX1 MUTATED                    1             1
  NPTX1 WILD-TYPE                 34             3
                 vv
clus              REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  NPTX1 MUTATED                                           0                   6
  NPTX1 WILD-TYPE                                        58                 164
D139V4, multiclass
                                           clus
vv                                          NPTX1 MUTATED NPTX1 WILD-TYPE
  DISTANT METASTASIS                                    1              34
  PRIMARY TUMOR                                         1               3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE             0              58
  REGIONAL LYMPH NODE                                   6             164
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  NPTX1 MUTATED             0       0       1        3        0        0
  NPTX1 WILD-TYPE          10       6      21        7       24       17
                 vv
clus              STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  NPTX1 MUTATED           0         0         0         1          1          0
  NPTX1 WILD-TYPE        10        14         9        30         12         22
                 vv
clus              STAGE IIIC STAGE IV
  NPTX1 MUTATED            2        0
  NPTX1 WILD-TYPE         42       12
D139V5, multiclass
             clus
vv            NPTX1 MUTATED NPTX1 WILD-TYPE
  I OR II NOS             0              10
  STAGE 0                 0               6
  STAGE I                 1              21
  STAGE IA                3               7
  STAGE IB                0              24
  STAGE II                0              17
  STAGE IIA               0              10
  STAGE IIB               0              14
  STAGE IIC               0               9
  STAGE III               1              30
  STAGE IIIA              1              12
  STAGE IIIB              0              22
  STAGE IIIC              2              42
  STAGE IV                0              12
[1] 14  2
[1] 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
  NPTX1 MUTATED       3  1  2  1
  NPTX1 WILD-TYPE    48 57 51 54
D139V6, multiclass
       clus
vv      NPTX1 MUTATED NPTX1 WILD-TYPE
  T0+T1             3              48
  T2                1              57
  T3                2              51
  T4                1              54
[1] 4 2
[1] TRUE
[1] "dimension 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
  NPTX1 MUTATED     4   2   1   1
  NPTX1 WILD-TYPE 134  46  31  32
D139V7, multiclass
    clus
vv   NPTX1 MUTATED NPTX1 WILD-TYPE
  N0             4             134
  N1             2              46
  N2             1              31
  N3             1              32
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               M0  M1 M1A M1B M1C
  NPTX1 MUTATED     8   0   0   0   0
  NPTX1 WILD-TYPE 232   4   2   2   5
D139V8, multiclass
     clus
vv    NPTX1 MUTATED NPTX1 WILD-TYPE
  M0              8             232
  M1              0               4
  M1A             0               2
  M1B             0               2
  M1C             0               5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D139V9, binary
                 cls
clus               0  1
  NPTX1 MUTATED    5  2
  NPTX1 WILD-TYPE 97 65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NPTX1 MUTATED      5    2
  NPTX1 WILD-TYPE   97   65
     clus
vv    NPTX1 MUTATED NPTX1 WILD-TYPE
  NO              5              97
  YES             2              65
[1] 2 2
[1] FALSE
D139V10, binary
                 cls
clus                0   1
  NPTX1 MUTATED     0   8
  NPTX1 WILD-TYPE  33 227
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NPTX1 MUTATED      0    8
  NPTX1 WILD-TYPE   33  227
     clus
vv    NPTX1 MUTATED NPTX1 WILD-TYPE
  NO              0              33
  YES             8             227
[1] 2 2
[1] FALSE
D139V11, continuous
D139V12, binary
                 cls
clus                0   1
  NPTX1 MUTATED     2   6
  NPTX1 WILD-TYPE 101 159
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NPTX1 MUTATED      2    6
  NPTX1 WILD-TYPE  101  159
        clus
vv       NPTX1 MUTATED NPTX1 WILD-TYPE
  FEMALE             2             101
  MALE               6             159
[1] 2 2
[1] FALSE
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  NPTX1 MUTATED       0                         0     8
  NPTX1 WILD-TYPE     3                         1   256
D139V13, multiclass
                           clus
vv                          NPTX1 MUTATED NPTX1 WILD-TYPE
  ASIAN                                 0               3
  BLACK OR AFRICAN AMERICAN             0               1
  WHITE                                 8             256
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D139V14, binary
                 cls
clus                0   1
  NPTX1 MUTATED     0   8
  NPTX1 WILD-TYPE   3 253
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NPTX1 MUTATED      0    8
  NPTX1 WILD-TYPE    3  253
                        clus
vv                       NPTX1 MUTATED NPTX1 WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO             8             253
[1] 2 2
[1] FALSE

Clustering(140) Variable = DACT1 MUTATION ANALYSIS
D140V1, survival
                 sevent
clus2               0   1
  DACT1 MUTATED     5   5
  DACT1 WILD-TYPE 123 125
  DACT1 MUTATED DACT1 WILD-TYPE 
             10             248 
  DACT1 MUTATED DACT1 WILD-TYPE 
              5             125 
$`DACT1 MUTATED`
TCGA-D3-A3MR TCGA-EE-A2GN TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A3AF TCGA-EE-A3JD 
      103.59        33.83        14.56        63.42        13.81        27.35 
TCGA-EE-A3JH TCGA-FS-A1YY TCGA-FW-A3R5 TCGA-FW-A5DY 
       13.94        11.01         0.99         0.43 

$`DACT1 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.47         8.52       111.09        32.42        70.16       110.79 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       28.08        22.55        45.83        81.24        10.29        85.32 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
        8.38        21.14        88.50        68.22        69.90        11.41 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       30.87         7.50        36.16         6.31        92.42        56.19 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 
       64.44        45.11       114.67        15.25        46.98        46.32 
TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO 
       82.29        61.38        13.32        24.00         6.31         9.34 
TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J 
       26.37         5.39        80.22        42.71        15.09        41.10 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO 
       17.72         8.84        20.48        13.94        52.01        47.87 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 
        1.55         6.97        23.11         4.01         2.89         9.90 
TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 
       11.31        13.22        48.79        35.80        51.12        10.03 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 
       39.19        13.68         9.99        44.52        36.69        25.15 
TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 
        4.93        22.36         6.64        19.36         7.00        17.56 
TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN 
       14.83        13.15         0.20         0.00         0.00        13.22 
TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 
       11.57        10.55         6.31         8.12         1.12         1.35 
TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F 
       12.20         5.13         4.31        36.07         4.34         5.13 
TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D 
        9.21         1.18         7.99         9.90        37.97        11.15 
TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N 
       38.63         8.55         4.41         1.08        27.12         9.50 
TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W 
       12.03         8.09         8.84         9.99         2.43         8.68 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 
        8.09        11.31        49.22        23.90         9.67         8.94 
TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI 
       39.39        34.29        17.98        34.92        47.21        30.08 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GO TCGA-EE-A2GP 
       19.43        16.01        35.54        28.31        30.84         5.42 
TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 
        1.15        13.02        34.98        36.33         8.84        98.27 
TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG 
        2.70         6.18        47.51         9.53        29.46        44.25 
TCGA-EE-A2MH TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP 
        7.96       111.78       111.91        56.02        25.08        26.99 
TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA 
       21.60        29.65        27.16        23.05         5.56       124.31 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AG TCGA-EE-A3AH 
      122.73        25.84         3.68        30.15        15.95        12.72 
TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA 
        3.22        22.92        21.60        21.60        16.14        22.22 
TCGA-EE-A3JE TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 
        0.46        33.60        31.40        18.61        12.95        38.40 
TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E 
        5.72        76.41        25.18         3.78         3.52        11.90 
TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M 
       11.11       114.15        34.88         4.21        13.45        28.60 
TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 
       42.84        34.68         9.57        36.07        17.72        78.44 
TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH 
       11.80         1.87         1.51        13.08        12.62        11.74 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A 
        9.04         6.58        22.49         1.71        18.41        85.74 
TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 
        4.90        64.47         3.45        23.80        14.24        15.52 
TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE 
        7.33         7.30         3.39        20.38         8.22        19.53 
TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM 
       11.08         7.17        30.87        12.92        12.89        47.38 
TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU 
       52.08         8.65         8.81        49.15        40.64         8.68 
TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 
       27.39         0.82         5.23        53.85         7.36        28.73 
TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 
       14.20        10.78         5.98         6.41         2.27         0.20 
TCGA-FW-A3TU TCGA-FW-A3TV TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 
        0.13         0.16         9.90         7.23        12.85        24.85 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
       31.33        84.72        10.13        16.24        15.42        12.16 
TCGA-GN-A26D TCGA-QB-A6FS 
       14.70         5.79 

  DACT1 MUTATED DACT1 WILD-TYPE 
           0.43            0.00 
  DACT1 MUTATED DACT1 WILD-TYPE 
         103.59          124.31 
  DACT1 MUTATED DACT1 WILD-TYPE 
          14.25           14.96 
[1] "0.4 - 103.6 (14.2)" "0.0 - 124.3 (15.0)"
[1] "hr=" "1.1"
D140V2, survival
                 sevent
clus2               0   1
  DACT1 MUTATED     5   5
  DACT1 WILD-TYPE 127 126
  DACT1 MUTATED DACT1 WILD-TYPE 
             10             253 
  DACT1 MUTATED DACT1 WILD-TYPE 
              5             126 
$`DACT1 MUTATED`
TCGA-D3-A3MR TCGA-EE-A2GN TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A3AF TCGA-EE-A3JD 
      103.59        90.97       204.66        96.23        13.81        27.35 
TCGA-EE-A3JH TCGA-FS-A1YY TCGA-FW-A3R5 TCGA-FW-A5DY 
      101.79       228.59        22.92         2.40 

$`DACT1 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.57        16.67       112.04       112.57        71.80       133.25 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       28.08        31.59        90.90        95.74        43.43       103.10 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
       65.49        23.77       115.53       168.00        69.90        11.87 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       48.76       113.52        42.08        12.10       171.58        56.19 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 
       66.08        45.11       130.72        58.06        46.98        46.32 
TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO 
      166.52        86.93        60.23        24.53        13.87         9.34 
TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J 
       39.75        21.47       161.85        43.69        40.14       131.90 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO 
       18.38        10.03        51.68        15.06       135.75       137.92 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW 
      166.19         7.43       125.19       151.53        54.67         3.65 
TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC 
        6.41        11.34         3.25         9.90        25.18        66.25 
TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 
       48.89        36.03       117.21        20.38       194.83       176.55 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB 
       35.93       107.34        61.18        53.92        65.92        23.44 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q 
       68.09        28.60        10.49       215.44        15.68        13.87 
TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X 
       10.16        45.11        35.01         3.55        52.01        29.82 
TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 
       27.22         8.65        94.98        33.73        14.70        26.89 
TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H 
       68.15         4.96       109.64       151.27        78.87       168.26 
TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E 
       13.55        63.35        80.61        47.84        13.97        39.62 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P 
       72.07        32.19         2.60        44.35        18.61        56.42 
TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X 
       37.35        14.47        55.92        25.87       171.55        17.92 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB 
       46.82       102.90        24.43        39.29        58.75        47.54 
TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ 
       67.43       314.56       135.95       208.04        48.72        89.33 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR 
       54.74        79.66        75.48       101.95        13.91        14.30 
TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 
       55.59        44.88        94.82        21.67       129.27        28.83 
TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH 
       19.76        61.51        47.28       103.27       103.20        16.96 
TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ 
      144.76       203.05       167.90        47.54       248.65        43.23 
TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB 
      103.56       136.47        41.59        53.26       124.31       122.73 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 
       25.84         3.68        54.51        23.47       138.81       172.18 
TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JE 
      127.20        36.95        64.08        34.32        53.19        33.40 
TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 
      148.08        31.40        35.44        13.94        50.76         9.17 
TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F 
       77.75        98.40        48.89        12.59        13.02        26.37 
TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N 
      268.93       152.35         6.44       131.51        61.05        44.05 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
      162.08        50.89        37.25       148.18        79.99        43.82 
TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES 
       23.34        20.15        16.37        31.27        32.05       247.04 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
       80.32        46.98        33.21        92.98       174.21         4.90 
TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 
      216.92        48.59       202.65        20.91        28.08         7.79 
TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF 
       27.72        48.85       357.37        53.52        40.27        15.45 
TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP 
        9.70        32.75        47.38        23.93       101.26        74.73 
TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW 
      133.55        11.41       148.80        53.16        26.56        49.48 
TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 
       27.09        27.02        77.82        66.67        28.73       174.84 
TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU 
       12.43        26.73        49.45        77.88         0.20        47.54 
TCGA-FW-A3TV TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 
        0.16         9.90         7.23        14.04       120.46       117.93 
TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D 
       84.72        10.13        64.44        62.79        32.48        39.58 
TCGA-QB-A6FS 
        6.67 

  DACT1 MUTATED DACT1 WILD-TYPE 
           2.40            0.16 
  DACT1 MUTATED DACT1 WILD-TYPE 
         228.59          357.37 
  DACT1 MUTATED DACT1 WILD-TYPE 
          93.60           47.84 
[1] "2.4 - 228.6 (93.6)" "0.2 - 357.4 (47.8)"
[1] "hr=" "1.4"
D140V3, continuous
                 vv
clus              DISTANT METASTASIS PRIMARY TUMOR
  DACT1 MUTATED                    1             0
  DACT1 WILD-TYPE                 34             4
                 vv
clus              REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  DACT1 MUTATED                                           3                   7
  DACT1 WILD-TYPE                                        55                 163
D140V4, multiclass
                                           clus
vv                                          DACT1 MUTATED DACT1 WILD-TYPE
  DISTANT METASTASIS                                    1              34
  PRIMARY TUMOR                                         0               4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE             3              55
  REGIONAL LYMPH NODE                                   7             163
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  DACT1 MUTATED             0       1       0        0        1        0
  DACT1 WILD-TYPE          10       5      22       10       23       17
                 vv
clus              STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DACT1 MUTATED           2         1         0         5          0          0
  DACT1 WILD-TYPE         8        13         9        26         13         22
                 vv
clus              STAGE IIIC STAGE IV
  DACT1 MUTATED            1        0
  DACT1 WILD-TYPE         43       12
D140V5, multiclass
             clus
vv            DACT1 MUTATED DACT1 WILD-TYPE
  I OR II NOS             0              10
  STAGE 0                 1               5
  STAGE I                 0              22
  STAGE IA                0              10
  STAGE IB                1              23
  STAGE II                0              17
  STAGE IIA               2               8
  STAGE IIB               1              13
  STAGE IIC               0               9
  STAGE III               5              26
  STAGE IIIA              0              13
  STAGE IIIB              0              22
  STAGE IIIC              1              43
  STAGE IV                0              12
[1] 14  2
[1] 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
  DACT1 MUTATED       2  2  2  2
  DACT1 WILD-TYPE    49 56 51 53
D140V6, multiclass
       clus
vv      DACT1 MUTATED DACT1 WILD-TYPE
  T0+T1             2              49
  T2                2              56
  T3                2              51
  T4                2              53
[1] 4 2
[1] TRUE
[1] "dimension 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
  DACT1 MUTATED     6   2   2   1
  DACT1 WILD-TYPE 132  46  30  32
D140V7, multiclass
    clus
vv   DACT1 MUTATED DACT1 WILD-TYPE
  N0             6             132
  N1             2              46
  N2             2              30
  N3             1              32
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               M0  M1 M1A M1B M1C
  DACT1 MUTATED    10   0   0   0   0
  DACT1 WILD-TYPE 230   4   2   2   5
D140V8, multiclass
     clus
vv    DACT1 MUTATED DACT1 WILD-TYPE
  M0             10             230
  M1              0               4
  M1A             0               2
  M1B             0               2
  M1C             0               5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D140V9, binary
                 cls
clus                0   1
  DACT1 MUTATED     2   1
  DACT1 WILD-TYPE 100  66
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DACT1 MUTATED      2    1
  DACT1 WILD-TYPE  100   66
     clus
vv    DACT1 MUTATED DACT1 WILD-TYPE
  NO              2             100
  YES             1              66
[1] 2 2
[1] FALSE
D140V10, binary
                 cls
clus                0   1
  DACT1 MUTATED     3   8
  DACT1 WILD-TYPE  30 227
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DACT1 MUTATED      3    8
  DACT1 WILD-TYPE   30  227
     clus
vv    DACT1 MUTATED DACT1 WILD-TYPE
  NO              3              30
  YES             8             227
[1] 2 2
[1] FALSE
D140V11, continuous
D140V12, binary
                 cls
clus                0   1
  DACT1 MUTATED     3   8
  DACT1 WILD-TYPE 100 157
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DACT1 MUTATED      3    8
  DACT1 WILD-TYPE  100  157
        clus
vv       DACT1 MUTATED DACT1 WILD-TYPE
  FEMALE             3             100
  MALE               8             157
[1] 2 2
[1] FALSE
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DACT1 MUTATED       0                         0    11
  DACT1 WILD-TYPE     3                         1   253
D140V13, multiclass
                           clus
vv                          DACT1 MUTATED DACT1 WILD-TYPE
  ASIAN                                 0               3
  BLACK OR AFRICAN AMERICAN             0               1
  WHITE                                11             253
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D140V14, binary
                 cls
clus                0   1
  DACT1 MUTATED     0  11
  DACT1 WILD-TYPE   3 250
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DACT1 MUTATED      0   11
  DACT1 WILD-TYPE    3  250
                        clus
vv                       DACT1 MUTATED DACT1 WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO            11             250
[1] 2 2
[1] FALSE

Clustering(141) Variable = STK19 MUTATION ANALYSIS
D141V1, survival
                 sevent
clus2               0   1
  STK19 MUTATED     6   6
  STK19 WILD-TYPE 122 124
  STK19 MUTATED STK19 WILD-TYPE 
             12             246 
  STK19 MUTATED STK19 WILD-TYPE 
              6             124 
$`STK19 MUTATED`
TCGA-D9-A3Z3 TCGA-D9-A6EC TCGA-DA-A1HV TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A185 
        2.89        13.22        48.79         1.12        12.20         4.31 
TCGA-EE-A2GD TCGA-EE-A2GI TCGA-EE-A2MG TCGA-EE-A3JI TCGA-FS-A1ZA TCGA-GN-A266 
       17.98        30.08        44.25        33.60         7.30        10.13 

$`STK19 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.47         8.52       111.09        32.42        70.16       110.79 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       28.08        22.55        45.83        81.24        10.29        85.32 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
        8.38        21.14        88.50        68.22        69.90        11.41 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       30.87         7.50        36.16         6.31        92.42        56.19 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 
       64.44        45.11       114.67        15.25        46.98        46.32 
TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO 
       82.29        61.38        13.32        24.00         6.31         9.34 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H 
      103.59        26.37         5.39        80.22        42.71        15.09 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN 
       41.10        17.72         8.84        20.48        13.94        52.01 
TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A6E9 
       47.87         1.55         6.97        23.11         4.01         9.90 
TCGA-D9-A6EA TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 
       11.31        35.80        51.12        10.03        39.19        13.68 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB 
        9.99        44.52        36.69        25.15         4.93        22.36 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q 
        6.64        19.36         7.00        17.56        14.83        13.15 
TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y 
        0.20         0.00         0.00        13.22        11.57        10.55 
TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A182 TCGA-EE-A184 TCGA-EE-A20B TCGA-EE-A20C 
        6.31         8.12         1.35         5.13        36.07         4.34 
TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C 
        5.13         9.21         1.18         7.99         9.90        37.97 
TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M 
       11.15        38.63         8.55         4.41         1.08        27.12 
TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V 
        9.50        12.03         8.09         8.84         9.99         2.43 
TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 
        8.68         8.09        11.31        49.22        23.90         9.67 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ 
        8.94        39.39        34.29        34.92        47.21        19.43 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP 
       16.01        35.54        28.31        33.83        30.84         5.42 
TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 
        1.15        13.02        34.98        36.33         8.84        98.27 
TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MH 
        2.70         6.18        47.51         9.53        29.46         7.96 
TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN 
       14.56        63.42       111.78       111.91        56.02        25.08 
TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU 
       26.99        21.60        29.65        27.16        23.05         5.56 
TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF 
      124.31       122.73        25.84         3.68        30.15        13.81 
TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 
       15.95        12.72         3.22        22.92        21.60        21.60 
TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A193 
       16.14        22.22        27.35         0.46        13.94        31.40 
TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B 
       18.61        12.95        38.40         5.72        76.41        25.18 
TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H 
        3.78         3.52        11.90        11.11       114.15        34.88 
TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q 
        4.21        13.45        28.60        42.84        34.68         9.57 
TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE 
       36.07        17.72        78.44        11.80         1.87         1.51 
TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV 
       13.08        12.62        11.74         9.04         6.58        22.49 
TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX 
        1.71        18.41        85.74         4.90        64.47         3.45 
TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZB 
       11.01        23.80        14.24        15.52         7.33         3.39 
TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH 
       20.38         8.22        19.53        11.08         7.17        30.87 
TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR 
       12.92        12.89        47.38        52.08         8.65         8.81 
TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ 
       49.15        40.64         8.68        27.39         0.82         5.23 
TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB 
       53.85         7.36        28.73        14.20        10.78         5.98 
TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV 
        6.41         2.27         0.20         0.99         0.13         0.16 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 
        0.43         9.90         7.23        12.85        24.85        31.33 
TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS 
       84.72        16.24        15.42        12.16        14.70         5.79 

  STK19 MUTATED STK19 WILD-TYPE 
           1.12            0.00 
  STK19 MUTATED STK19 WILD-TYPE 
          48.79          124.31 
  STK19 MUTATED STK19 WILD-TYPE 
          12.71           14.96 
[1] "1.1 - 48.8 (12.7)"  "0.0 - 124.3 (15.0)"
[1] "hr=" "1.2"
D141V2, survival
                 sevent
clus2               0   1
  STK19 MUTATED     6   6
  STK19 WILD-TYPE 126 125
  STK19 MUTATED STK19 WILD-TYPE 
             12             251 
  STK19 MUTATED STK19 WILD-TYPE 
              6             125 
$`STK19 MUTATED`
TCGA-D9-A3Z3 TCGA-D9-A6EC TCGA-DA-A1HV TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A185 
        3.25        66.25        48.89        33.73        26.89         4.96 
TCGA-EE-A2GD TCGA-EE-A2GI TCGA-EE-A2MG TCGA-EE-A3JI TCGA-FS-A1ZA TCGA-GN-A266 
      314.56        48.72       103.20       148.08        27.72        10.13 

$`STK19 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.57        16.67       112.04       112.57        71.80       133.25 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       28.08        31.59        90.90        95.74        43.43       103.10 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
       65.49        23.77       115.53       168.00        69.90        11.87 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       48.76       113.52        42.08        12.10       171.58        56.19 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 
       66.08        45.11       130.72        58.06        46.98        46.32 
TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO 
      166.52        86.93        60.23        24.53        13.87         9.34 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H 
      103.59        39.75        21.47       161.85        43.69        40.14 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN 
      131.90        18.38        10.03        51.68        15.06       135.75 
TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 
      137.92       166.19         7.43       125.19       151.53        54.67 
TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-DA-A1HW 
        3.65         6.41        11.34         9.90        25.18        36.03 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 
      117.21        20.38       194.83       176.55        35.93       107.34 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
       61.18        53.92        65.92        23.44        68.09        28.60 
TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG 
       10.49       215.44        15.68        13.87        10.16        45.11 
TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z 
       35.01         3.55        52.01        29.82        27.22         8.65 
TCGA-EE-A180 TCGA-EE-A182 TCGA-EE-A184 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F 
       94.98        14.70        68.15       109.64       151.27        78.87 
TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D 
      168.26        13.55        63.35        80.61        47.84        13.97 
TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N 
       39.62        72.07        32.19         2.60        44.35        18.61 
TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W 
       56.42        37.35        14.47        55.92        25.87       171.55 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 
       17.92        46.82       102.90        24.43        39.29        58.75 
TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK 
       47.54        67.43       135.95       208.04        89.33        54.74 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR 
       79.66        75.48        90.97       101.95        13.91        14.30 
TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 
       55.59        44.88        94.82        21.67       129.27        28.83 
TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MH TCGA-EE-A2MI 
       19.76        61.51        47.28       103.27        16.96       204.66 
TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP 
       96.23       144.76       203.05       167.90        47.54       248.65 
TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA 
       43.23       103.56       136.47        41.59        53.26       124.31 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG 
      122.73        25.84         3.68        54.51        13.81        23.47 
TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 
      138.81       172.18       127.20        36.95        64.08        34.32 
TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A195 
       53.19        27.35        33.40       101.79        31.40        35.44 
TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C 
       13.94        50.76         9.17        77.75        98.40        48.89 
TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J 
       12.59        13.02        26.37       268.93       152.35         6.44 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S 
      131.51        61.05        44.05       162.08        50.89        37.25 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF 
      148.18        79.99        43.82        23.34        20.15        16.37 
TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL 
       31.27        32.05       247.04        80.32        46.98        33.21 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY 
       92.98       174.21         4.90       216.92        48.59       228.59 
TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZB TCGA-FS-A1ZC 
      202.65        20.91        28.08         7.79        48.85       357.37 
TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ 
       53.52        40.27        15.45         9.70        32.75        47.38 
TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS 
       23.93       101.26        74.73       133.55        11.41       148.80 
TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 
       53.16        26.56        49.48        27.09        27.02        77.82 
TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC 
       66.67        28.73       174.84        12.43        26.73        49.45 
TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY 
       77.88         0.20        22.92        47.54         0.16         2.40 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        9.90         7.23        14.04       120.46       117.93        84.72 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS 
       64.44        62.79        32.48        39.58         6.67 

  STK19 MUTATED STK19 WILD-TYPE 
           3.25            0.16 
  STK19 MUTATED STK19 WILD-TYPE 
         314.56          357.37 
  STK19 MUTATED STK19 WILD-TYPE 
         41.225          48.590 
[1] "3.2 - 314.6 (41.2)" "0.2 - 357.4 (48.6)"
[1] "hr=" "1"  
D141V3, continuous
                 vv
clus              DISTANT METASTASIS PRIMARY TUMOR
  STK19 MUTATED                    1             1
  STK19 WILD-TYPE                 34             3
                 vv
clus              REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  STK19 MUTATED                                           2                   8
  STK19 WILD-TYPE                                        56                 162
D141V4, multiclass
                                           clus
vv                                          STK19 MUTATED STK19 WILD-TYPE
  DISTANT METASTASIS                                    1              34
  PRIMARY TUMOR                                         1               3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE             2              56
  REGIONAL LYMPH NODE                                   8             162
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  STK19 MUTATED             0       1       2        1        0        1
  STK19 WILD-TYPE          10       5      20        9       24       16
                 vv
clus              STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  STK19 MUTATED           0         1         0         0          1          3
  STK19 WILD-TYPE        10        13         9        31         12         19
                 vv
clus              STAGE IIIC STAGE IV
  STK19 MUTATED            1        0
  STK19 WILD-TYPE         43       12
D141V5, multiclass
             clus
vv            STK19 MUTATED STK19 WILD-TYPE
  I OR II NOS             0              10
  STAGE 0                 1               5
  STAGE I                 2              20
  STAGE IA                1               9
  STAGE IB                0              24
  STAGE II                1              16
  STAGE IIA               0              10
  STAGE IIB               1              13
  STAGE IIC               0               9
  STAGE III               0              31
  STAGE IIIA              1              12
  STAGE IIIB              3              19
  STAGE IIIC              1              43
  STAGE IV                0              12
[1] 14  2
[1] 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
  STK19 MUTATED       2  2  3  3
  STK19 WILD-TYPE    49 56 50 52
D141V6, multiclass
       clus
vv      STK19 MUTATED STK19 WILD-TYPE
  T0+T1             2              49
  T2                2              56
  T3                3              50
  T4                3              52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  STK19 MUTATED     6   2   2   1
  STK19 WILD-TYPE 132  46  30  32
D141V7, multiclass
    clus
vv   STK19 MUTATED STK19 WILD-TYPE
  N0             6             132
  N1             2              46
  N2             2              30
  N3             1              32
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               M0  M1 M1A M1B M1C
  STK19 MUTATED    11   0   0   0   0
  STK19 WILD-TYPE 229   4   2   2   5
D141V8, multiclass
     clus
vv    STK19 MUTATED STK19 WILD-TYPE
  M0             11             229
  M1              0               4
  M1A             0               2
  M1B             0               2
  M1C             0               5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D141V9, binary
                 cls
clus               0  1
  STK19 MUTATED    4  3
  STK19 WILD-TYPE 98 64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STK19 MUTATED      4    3
  STK19 WILD-TYPE   98   64
     clus
vv    STK19 MUTATED STK19 WILD-TYPE
  NO              4              98
  YES             3              64
[1] 2 2
[1] FALSE
D141V10, binary
                 cls
clus                0   1
  STK19 MUTATED     2  10
  STK19 WILD-TYPE  31 225
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STK19 MUTATED      2   10
  STK19 WILD-TYPE   31  225
     clus
vv    STK19 MUTATED STK19 WILD-TYPE
  NO              2              31
  YES            10             225
[1] 2 2
[1] FALSE
D141V11, continuous
D141V12, binary
                 cls
clus                0   1
  STK19 MUTATED     7   5
  STK19 WILD-TYPE  96 160
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STK19 MUTATED      7    5
  STK19 WILD-TYPE   96  160
        clus
vv       STK19 MUTATED STK19 WILD-TYPE
  FEMALE             7              96
  MALE               5             160
[1] 2 2
[1] FALSE
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  STK19 MUTATED       0                         0    12
  STK19 WILD-TYPE     3                         1   252
D141V13, multiclass
                           clus
vv                          STK19 MUTATED STK19 WILD-TYPE
  ASIAN                                 0               3
  BLACK OR AFRICAN AMERICAN             0               1
  WHITE                                12             252
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D141V14, binary
                 cls
clus                0   1
  STK19 MUTATED     0  12
  STK19 WILD-TYPE   3 249
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STK19 MUTATED      0   12
  STK19 WILD-TYPE    3  249
                        clus
vv                       STK19 MUTATED STK19 WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO            12             249
[1] 2 2
[1] FALSE

Clustering(142) Variable = STK31 MUTATION ANALYSIS
D142V1, survival
                 sevent
clus2               0   1
  STK31 MUTATED    20  13
  STK31 WILD-TYPE 108 117
  STK31 MUTATED STK31 WILD-TYPE 
             33             225 
  STK31 MUTATED STK31 WILD-TYPE 
             13             117 
$`STK31 MUTATED`
TCGA-D3-A3ML TCGA-D3-A3MR TCGA-D3-A5GO TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A3F8 
        6.31       103.59        47.87        48.79        35.80        14.83 
TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A29E TCGA-EE-A29M TCGA-EE-A29X 
        1.12         1.35        12.20        38.63        27.12         8.09 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2GC TCGA-EE-A2GI TCGA-EE-A2GO TCGA-EE-A2M5 
       49.22        23.90        34.29        30.08        30.84         8.84 
TCGA-EE-A2MD TCGA-EE-A2MR TCGA-EE-A3AA TCGA-EE-A3AE TCGA-EE-A3J7 TCGA-EE-A3JA 
        9.53        29.65       124.31        30.15        21.60        22.22 
TCGA-EE-A3JD TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A19A TCGA-ER-A19N TCGA-FS-A1ZZ 
       27.35        33.60        31.40        76.41        42.84         5.23 
TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-GN-A266 
        0.99         0.13        10.13 

$`STK31 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.47         8.52       111.09        32.42        70.16       110.79 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       28.08        22.55        45.83        81.24        10.29        85.32 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
        8.38        21.14        88.50        68.22        69.90        11.41 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       30.87         7.50        36.16         6.31        92.42        56.19 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 
       64.44        45.11       114.67        15.25        46.98        46.32 
TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MU 
       82.29        61.38        13.32        24.00         9.34        26.37 
TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K 
        5.39        80.22        42.71        15.09        41.10        17.72 
TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS 
        8.84        20.48        13.94        52.01         1.55         6.97 
TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC 
       23.11         4.01         2.89         9.90        11.31        13.22 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 
       51.12        10.03        39.19        13.68         9.99        44.52 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
       36.69        25.15         4.93        22.36         6.64        19.36 
TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH 
        7.00        17.56        13.15         0.20         0.00         0.00 
TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A184 
       13.22        11.57        10.55         6.31         8.12         5.13 
TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I 
        4.31        36.07         4.34         5.13         9.21         1.18 
TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29H 
        7.99         9.90        37.97        11.15         8.55         4.41 
TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S 
        1.08         9.50        12.03         8.09         8.84         9.99 
TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A2A0 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB 
        2.43         8.68        11.31         9.67         8.94        39.39 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
       17.98        34.92        47.21        19.43        16.01        35.54 
TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT 
       28.31        33.83         5.42         1.15        13.02        34.98 
TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2ME 
       36.33        98.27         2.70         6.18        47.51        29.46 
TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML 
       44.25         7.96        14.56        63.42       111.78       111.91 
TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MS TCGA-EE-A2MT 
       56.02        25.08        26.99        21.60        27.16        23.05 
TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AG 
        5.56       122.73        25.84         3.68        13.81        15.95 
TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J8 TCGA-EE-A3JE 
       12.72         3.22        22.92        21.60        16.14         0.46 
TCGA-EE-A3JH TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19B 
       13.94        18.61        12.95        38.40         5.72        25.18 
TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H 
        3.78         3.52        11.90        11.11       114.15        34.88 
TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S 
        4.21        13.45        28.60        34.68         9.57        36.07 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF 
       17.72        78.44        11.80         1.87         1.51        13.08 
TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL 
       12.62        11.74         9.04         6.58        22.49         1.71 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY 
       18.41        85.74         4.90        64.47         3.45        11.01 
TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB 
       23.80        14.24        15.52         7.33         7.30         3.39 
TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH 
       20.38         8.22        19.53        11.08         7.17        30.87 
TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR 
       12.92        12.89        47.38        52.08         8.65         8.81 
TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A4F0 
       49.15        40.64         8.68        27.39         0.82        53.85 
TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC 
        7.36        28.73        14.20        10.78         5.98         6.41 
TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
        2.27         0.20         0.16         0.43         9.90         7.23 
TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 
       12.85        24.85        31.33        84.72        16.24        15.42 
TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS 
       12.16        14.70         5.79 

  STK31 MUTATED STK31 WILD-TYPE 
           0.13            0.00 
  STK31 MUTATED STK31 WILD-TYPE 
         124.31          122.73 
  STK31 MUTATED STK31 WILD-TYPE 
          27.35           13.94 
[1] "0.1 - 124.3 (27.4)" "0.0 - 122.7 (13.9)"
[1] "hr=" "1.6"
D142V2, survival
                 sevent
clus2               0   1
  STK31 MUTATED    21  13
  STK31 WILD-TYPE 111 118
  STK31 MUTATED STK31 WILD-TYPE 
             34             229 
  STK31 MUTATED STK31 WILD-TYPE 
             13             118 
$`STK31 MUTATED`
TCGA-D3-A3ML TCGA-D3-A3MR TCGA-D3-A5GO TCGA-D9-A148 TCGA-DA-A1HV TCGA-DA-A1HW 
       13.87       103.59       137.92       151.53        48.89        36.03 
TCGA-DA-A3F8 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A29E TCGA-EE-A29M 
       15.68        33.73        14.70        26.89        39.62        44.35 
TCGA-EE-A29X TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2GC TCGA-EE-A2GI TCGA-EE-A2GO 
       17.92       102.90        24.43        67.43        48.72       101.95 
TCGA-EE-A2M5 TCGA-EE-A2MD TCGA-EE-A2MR TCGA-EE-A3AA TCGA-EE-A3AE TCGA-EE-A3J7 
       21.67        47.28       103.56       124.31        54.51        64.08 
TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A19A TCGA-ER-A19N 
       53.19        27.35       148.08        31.40        77.75        44.05 
TCGA-FS-A1ZZ TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-GN-A266 
       27.02        22.92        47.54        10.13 

$`STK31 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.57        16.67       112.04       112.57        71.80       133.25 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       28.08        31.59        90.90        95.74        43.43       103.10 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
       65.49        23.77       115.53       168.00        69.90        11.87 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       48.76       113.52        42.08        12.10       171.58        56.19 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 
       66.08        45.11       130.72        58.06        46.98        46.32 
TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MU 
      166.52        86.93        60.23        24.53         9.34        39.75 
TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K 
       21.47       161.85        43.69        40.14       131.90        18.38 
TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS 
       10.03        51.68        15.06       135.75       166.19         7.43 
TCGA-D3-A5GU TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 
      125.19        54.67         3.65         6.41        11.34         3.25 
TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 
        9.90        25.18        66.25       117.21        20.38       194.83 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA 
      176.55        35.93       107.34        61.18        53.92        65.92 
TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-EB-A44Q 
       23.44        68.09        28.60        10.49       215.44        13.87 
TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X 
       10.16        45.11        35.01         3.55        52.01        29.82 
TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B 
       27.22         8.65        94.98        68.15         4.96       109.64 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B 
      151.27        78.87       168.26        13.55        63.35        80.61 
TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29N 
       47.84        13.97        72.07        32.19         2.60        18.61 
TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W 
       56.42        37.35        14.47        55.92        25.87       171.55 
TCGA-EE-A2A0 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE 
       46.82        39.29        58.75        47.54       314.56       135.95 
TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN 
      208.04        89.33        54.74        79.66        75.48        90.97 
TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M6 
       13.91        14.30        55.59        44.88        94.82       129.27 
TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH 
       28.83        19.76        61.51       103.27       103.20        16.96 
TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN 
      204.66        96.23       144.76       203.05       167.90        47.54 
TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AB 
      248.65        43.23       136.47        41.59        53.26       122.73 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 
       25.84         3.68        13.81        23.47       138.81       172.18 
TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J8 TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A195 
      127.20        36.95        34.32        33.40       101.79        35.44 
TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D 
       13.94        50.76         9.17        98.40        48.89        12.59 
TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L 
       13.02        26.37       268.93       152.35         6.44       131.51 
TCGA-ER-A19M TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 
       61.05       162.08        50.89        37.25       148.18        79.99 
TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH 
       43.82        23.34        20.15        16.37        31.27        32.05 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A 
      247.04        80.32        46.98        33.21        92.98       174.21 
TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
        4.90       216.92        48.59       228.59       202.65        20.91 
TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD 
       28.08         7.79        27.72        48.85       357.37        53.52 
TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK 
       40.27        15.45         9.70        32.75        47.38        23.93 
TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT 
      101.26        74.73       133.55        11.41       148.80        53.16 
TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 
       26.56        49.48        27.09        77.82        66.67        28.73 
TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 
      174.84        12.43        26.73        49.45        77.88         0.20 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 
        0.16         2.40         9.90         7.23        14.04       120.46 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D 
      117.93        84.72        64.44        62.79        32.48        39.58 
TCGA-QB-A6FS 
        6.67 

  STK31 MUTATED STK31 WILD-TYPE 
          10.13            0.16 
  STK31 MUTATED STK31 WILD-TYPE 
         151.53          357.37 
  STK31 MUTATED STK31 WILD-TYPE 
         45.815          48.850 
[1] "10.1 - 151.5 (45.8)" "0.2 - 357.4 (48.9)" 
[1] "hr=" "1.1"
D142V3, continuous
                 vv
clus              DISTANT METASTASIS PRIMARY TUMOR
  STK31 MUTATED                    4             0
  STK31 WILD-TYPE                 31             4
                 vv
clus              REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  STK31 MUTATED                                           5                  25
  STK31 WILD-TYPE                                        53                 145
D142V4, multiclass
                                           clus
vv                                          STK31 MUTATED STK31 WILD-TYPE
  DISTANT METASTASIS                                    4              31
  PRIMARY TUMOR                                         0               4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE             5              53
  REGIONAL LYMPH NODE                                  25             145
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  STK31 MUTATED             0       1       4        2        4        4
  STK31 WILD-TYPE          10       5      18        8       20       13
                 vv
clus              STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  STK31 MUTATED           0         3         0         4          1          4
  STK31 WILD-TYPE        10        11         9        27         12         18
                 vv
clus              STAGE IIIC STAGE IV
  STK31 MUTATED            2        1
  STK31 WILD-TYPE         42       11
D142V5, multiclass
             clus
vv            STK31 MUTATED STK31 WILD-TYPE
  I OR II NOS             0              10
  STAGE 0                 1               5
  STAGE I                 4              18
  STAGE IA                2               8
  STAGE IB                4              20
  STAGE II                4              13
  STAGE IIA               0              10
  STAGE IIB               3              11
  STAGE IIC               0               9
  STAGE III               4              27
  STAGE IIIA              1              12
  STAGE IIIB              4              18
  STAGE IIIC              2              42
  STAGE IV                1              11
[1] 14  2
[1] 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
  STK31 MUTATED       6  9  8  3
  STK31 WILD-TYPE    45 49 45 52
D142V6, multiclass
       clus
vv      STK31 MUTATED STK31 WILD-TYPE
  T0+T1             6              45
  T2                9              49
  T3                8              45
  T4                3              52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  STK31 MUTATED    19   6   5   1
  STK31 WILD-TYPE 119  42  27  32
D142V7, multiclass
    clus
vv   STK31 MUTATED STK31 WILD-TYPE
  N0            19             119
  N1             6              42
  N2             5              27
  N3             1              32
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               M0  M1 M1A M1B M1C
  STK31 MUTATED    29   1   0   1   0
  STK31 WILD-TYPE 211   3   2   1   5
D142V8, multiclass
     clus
vv    STK31 MUTATED STK31 WILD-TYPE
  M0             29             211
  M1              1               3
  M1A             0               2
  M1B             1               1
  M1C             0               5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D142V9, binary
                 cls
clus               0  1
  STK31 MUTATED   16  6
  STK31 WILD-TYPE 86 61
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STK31 MUTATED     16    6
  STK31 WILD-TYPE   86   61
     clus
vv    STK31 MUTATED STK31 WILD-TYPE
  NO             16              86
  YES             6              61
[1] 2 2
[1] FALSE
D142V10, binary
                 cls
clus                0   1
  STK31 MUTATED     7  27
  STK31 WILD-TYPE  26 208
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STK31 MUTATED      7   27
  STK31 WILD-TYPE   26  208
     clus
vv    STK31 MUTATED STK31 WILD-TYPE
  NO              7              26
  YES            27             208
[1] 2 2
[1] FALSE
D142V11, continuous
D142V12, binary
                 cls
clus                0   1
  STK31 MUTATED    10  24
  STK31 WILD-TYPE  93 141
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STK31 MUTATED     10   24
  STK31 WILD-TYPE   93  141
        clus
vv       STK31 MUTATED STK31 WILD-TYPE
  FEMALE            10              93
  MALE              24             141
[1] 2 2
[1] FALSE
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  STK31 MUTATED       0                         0    34
  STK31 WILD-TYPE     3                         1   230
D142V13, multiclass
                           clus
vv                          STK31 MUTATED STK31 WILD-TYPE
  ASIAN                                 0               3
  BLACK OR AFRICAN AMERICAN             0               1
  WHITE                                34             230
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D142V14, binary
                 cls
clus                0   1
  STK31 MUTATED     1  33
  STK31 WILD-TYPE   2 228
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STK31 MUTATED      1   33
  STK31 WILD-TYPE    2  228
                        clus
vv                       STK31 MUTATED STK31 WILD-TYPE
  HISPANIC OR LATINO                 1               2
  NOT HISPANIC OR LATINO            33             228
[1] 2 2
[1] FALSE

Clustering(143) Variable = ROS1 MUTATION ANALYSIS
D143V1, survival
                sevent
clus2              0   1
  ROS1 MUTATED    29  23
  ROS1 WILD-TYPE  99 107
  ROS1 MUTATED ROS1 WILD-TYPE 
            52            206 
  ROS1 MUTATED ROS1 WILD-TYPE 
            23            107 
$`ROS1 MUTATED`
TCGA-D3-A1Q8 TCGA-D3-A2JP TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51R TCGA-D3-A51T 
       28.08        45.11       103.59        26.37        20.48        13.94 
TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D9-A3Z1 TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1I7 
       52.01         1.55         4.01        13.22        48.79        36.69 
TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A184 TCGA-EE-A20F TCGA-EE-A29C TCGA-EE-A29D 
        1.12         1.35         5.13         5.13        37.97        11.15 
TCGA-EE-A29E TCGA-EE-A29L TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A2A2 TCGA-EE-A2GC 
       38.63         1.08         2.43         8.68        23.90        34.29 
TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GM TCGA-EE-A2GO TCGA-EE-A2GR TCGA-EE-A2MD 
       30.08        19.43        28.31        30.84         1.15         9.53 
TCGA-EE-A2MJ TCGA-EE-A2MS TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J5 TCGA-EE-A3J7 
       63.42        27.16        15.95        12.72        21.60        21.60 
TCGA-EE-A3J8 TCGA-EE-A3JD TCGA-ER-A19C TCGA-ER-A19G TCGA-ER-A19M TCGA-FR-A3YN 
       16.14        27.35         3.78       114.15        28.60        18.41 
TCGA-FR-A44A TCGA-FS-A1ZA TCGA-FS-A1ZF TCGA-FS-A1ZQ TCGA-FS-A1ZZ TCGA-FS-A4F5 
       85.74         7.30        11.08         8.65         5.23        28.73 
TCGA-FS-A4FC TCGA-FW-A3R5 TCGA-GN-A266 TCGA-QB-A6FS 
        6.41         0.99        10.13         5.79 

$`ROS1 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.47         8.52       111.09        32.42        70.16       110.79 
TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 
       22.55        45.83        81.24        10.29        85.32         8.38 
TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF 
       21.14        88.50        68.22        69.90        11.41        30.87 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO 
        7.50        36.16         6.31        92.42        56.19        64.44 
TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC 
      114.67        15.25        46.98        46.32        82.29        61.38 
TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MV TCGA-D3-A51E 
       13.32        24.00         6.31         9.34         5.39        80.22 
TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A5GO 
       42.71        15.09        41.10        17.72         8.84        47.87 
TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-DA-A1HW 
        6.97        23.11         2.89         9.90        11.31        35.80 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 
       51.12        10.03        39.19        13.68         9.99        44.52 
TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 
       25.15         4.93        22.36         6.64        19.36         7.00 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH 
       17.56        14.83        13.15         0.20         0.00         0.00 
TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A183 
       13.22        11.57        10.55         6.31         8.12        12.20 
TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A 
        4.31        36.07         4.34         9.21         1.18         7.99 
TCGA-EE-A29B TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P 
        9.90         8.55         4.41        27.12         9.50        12.03 
TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 
        8.09         8.84         9.99         8.09        11.31        49.22 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH 
        9.67         8.94        39.39        17.98        34.92        47.21 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GS TCGA-EE-A2GT 
       16.01        35.54        33.83         5.42        13.02        34.98 
TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC 
       36.33         8.84        98.27         2.70         6.18        47.51 
TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2ML 
       29.46        44.25         7.96        14.56       111.78       111.91 
TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MT 
       56.02        25.08        26.99        21.60        29.65        23.05 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE 
        5.56       124.31       122.73        25.84         3.68        30.15 
TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3JA TCGA-EE-A3JE TCGA-EE-A3JH 
       13.81         3.22        22.92        22.22         0.46        13.94 
TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 
       33.60        31.40        18.61        12.95        38.40         5.72 
TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19H 
       76.41        25.18         3.52        11.90        11.11        34.88 
TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S 
        4.21        13.45        42.84        34.68         9.57        36.07 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF 
       17.72        78.44        11.80         1.87         1.51        13.08 
TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL 
       12.62        11.74         9.04         6.58        22.49         1.71 
TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
        4.90        64.47         3.45        11.01        23.80        14.24 
TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE 
       15.52         7.33         3.39        20.38         8.22        19.53 
TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP 
        7.17        30.87        12.92        12.89        47.38        52.08 
TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY 
        8.81        49.15        40.64         8.68        27.39         0.82 
TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FD 
       53.85         7.36        14.20        10.78         5.98         2.27 
TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
        0.20         0.13         0.16         0.43         9.90         7.23 
TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 
       12.85        24.85        31.33        84.72        16.24        15.42 
TCGA-GN-A26A TCGA-GN-A26D 
       12.16        14.70 

  ROS1 MUTATED ROS1 WILD-TYPE 
          0.99           0.00 
  ROS1 MUTATED ROS1 WILD-TYPE 
        114.15         124.31 
  ROS1 MUTATED ROS1 WILD-TYPE 
        17.275         14.400 
[1] "1.0 - 114.2 (17.3)" "0.0 - 124.3 (14.4)"
[1] "hr=" "1.1"
D143V2, survival
                sevent
clus2              0   1
  ROS1 MUTATED    29  23
  ROS1 WILD-TYPE 103 108
  ROS1 MUTATED ROS1 WILD-TYPE 
            52            211 
  ROS1 MUTATED ROS1 WILD-TYPE 
            23            108 
$`ROS1 MUTATED`
TCGA-D3-A1Q8 TCGA-D3-A2JP TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51R TCGA-D3-A51T 
       28.08        45.11       103.59        39.75        51.68        15.06 
TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D9-A3Z1 TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1I7 
      135.75       166.19        11.34        66.25        48.89        61.18 
TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A184 TCGA-EE-A20F TCGA-EE-A29C TCGA-EE-A29D 
       33.73        14.70        68.15        78.87        47.84        13.97 
TCGA-EE-A29E TCGA-EE-A29L TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A2A2 TCGA-EE-A2GC 
       39.62         2.60        25.87       171.55        24.43        67.43 
TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GM TCGA-EE-A2GO TCGA-EE-A2GR TCGA-EE-A2MD 
       48.72        89.33        75.48       101.95        14.30        47.28 
TCGA-EE-A2MJ TCGA-EE-A2MS TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J5 TCGA-EE-A3J7 
       96.23       136.47        23.47       138.81        36.95        64.08 
TCGA-EE-A3J8 TCGA-EE-A3JD TCGA-ER-A19C TCGA-ER-A19G TCGA-ER-A19M TCGA-FR-A3YN 
       34.32        27.35        48.89       268.93        61.05        92.98 
TCGA-FR-A44A TCGA-FS-A1ZA TCGA-FS-A1ZF TCGA-FS-A1ZQ TCGA-FS-A1ZZ TCGA-FS-A4F5 
      174.21        27.72        15.45       133.55        27.02        28.73 
TCGA-FS-A4FC TCGA-FW-A3R5 TCGA-GN-A266 TCGA-QB-A6FS 
       49.45        22.92        10.13         6.67 

$`ROS1 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.57        16.67       112.04       112.57        71.80       133.25 
TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 
       31.59        90.90        95.74        43.43       103.10        65.49 
TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF 
       23.77       115.53       168.00        69.90        11.87        48.76 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO 
      113.52        42.08        12.10       171.58        56.19        66.08 
TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC 
      130.72        58.06        46.98        46.32       166.52        86.93 
TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MV TCGA-D3-A51E 
       60.23        24.53        13.87         9.34        21.47       161.85 
TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A5GO 
       43.69        40.14       131.90        18.38        10.03       137.92 
TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX 
        7.43       125.19       151.53        54.67         3.65         6.41 
TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 
        3.25         9.90        25.18        36.03       117.21        20.38 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I8 TCGA-DA-A1IA 
      194.83       176.55        35.93       107.34        53.92        65.92 
TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 
       23.44        68.09        28.60        10.49       215.44        15.68 
TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN 
       13.87        10.16        45.11        35.01         3.55        52.01 
TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A183 TCGA-EE-A185 
       29.82        27.22         8.65        94.98        26.89         4.96 
TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B 
      109.64       151.27       168.26        13.55        63.35        80.61 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
       72.07        32.19        44.35        18.61        56.42        37.35 
TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A5 
       14.47        55.92        17.92        46.82       102.90        39.29 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GK 
       58.75        47.54       314.56       135.95       208.04        54.74 
TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU 
       79.66        90.97        13.91        55.59        44.88        94.82 
TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2ME 
       21.67       129.27        28.83        19.76        61.51       103.27 
TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM 
      103.20        16.96       204.66       144.76       203.05       167.90 
TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MT TCGA-EE-A2MU 
       47.54       248.65        43.23       103.56        41.59        53.26 
TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF 
      124.31       122.73        25.84         3.68        54.51        13.81 
TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3JA TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI 
      172.18       127.20        53.19        33.40       101.79       148.08 
TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A 
       31.40        35.44        13.94        50.76         9.17        77.75 
TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19H TCGA-ER-A19J 
       98.40        12.59        13.02        26.37       152.35         6.44 
TCGA-ER-A19L TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W 
      131.51        44.05       162.08        50.89        37.25       148.18 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG 
       79.99        43.82        23.34        20.15        16.37        31.27 
TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A69P 
       32.05       247.04        80.32        46.98        33.21         4.90 
TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 
      216.92        48.59       228.59       202.65        20.91        28.08 
TCGA-FS-A1Z7 TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG 
        7.79        48.85       357.37        53.52        40.27         9.70 
TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZR 
       32.75        47.38        23.93       101.26        74.73        11.41 
TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A4F0 
      148.80        53.16        26.56        49.48        27.09        77.82 
TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FD TCGA-FW-A3I3 
       66.67       174.84        12.43        26.73        77.88         0.20 
TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 
       47.54         0.16         2.40         9.90         7.23        14.04 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
      120.46       117.93        84.72        64.44        62.79        32.48 
TCGA-GN-A26D 
       39.58 

  ROS1 MUTATED ROS1 WILD-TYPE 
          2.60           0.16 
  ROS1 MUTATED ROS1 WILD-TYPE 
        268.93         357.37 
  ROS1 MUTATED ROS1 WILD-TYPE 
         48.28          48.59 
[1] "2.6 - 268.9 (48.3)" "0.2 - 357.4 (48.6)"
[1] "hr=" "1.1"
D143V3, continuous
                vv
clus             DISTANT METASTASIS PRIMARY TUMOR
  ROS1 MUTATED                    7             1
  ROS1 WILD-TYPE                 28             3
                vv
clus             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  ROS1 MUTATED                                          13                  33
  ROS1 WILD-TYPE                                        45                 137
D143V4, multiclass
                                           clus
vv                                          ROS1 MUTATED ROS1 WILD-TYPE
  DISTANT METASTASIS                                   7             28
  PRIMARY TUMOR                                        1              3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE           13             45
  REGIONAL LYMPH NODE                                 33            137
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  ROS1 MUTATED             1       2       4        2        5        7
  ROS1 WILD-TYPE           9       4      18        8       19       10
                vv
clus             STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  ROS1 MUTATED           2         2         2         7          3          5
  ROS1 WILD-TYPE         8        12         7        24         10         17
                vv
clus             STAGE IIIC STAGE IV
  ROS1 MUTATED            9        1
  ROS1 WILD-TYPE         35       11
D143V5, multiclass
             clus
vv            ROS1 MUTATED ROS1 WILD-TYPE
  I OR II NOS            1              9
  STAGE 0                2              4
  STAGE I                4             18
  STAGE IA               2              8
  STAGE IB               5             19
  STAGE II               7             10
  STAGE IIA              2              8
  STAGE IIB              2             12
  STAGE IIC              2              7
  STAGE III              7             24
  STAGE IIIA             3             10
  STAGE IIIB             5             17
  STAGE IIIC             9             35
  STAGE IV               1             11
[1] 14  2
[1] 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
  ROS1 MUTATED      12  8 16 11
  ROS1 WILD-TYPE    39 50 37 44
D143V6, multiclass
       clus
vv      ROS1 MUTATED ROS1 WILD-TYPE
  T0+T1           12             39
  T2               8             50
  T3              16             37
  T4              11             44
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  ROS1 MUTATED    28  12   7   5
  ROS1 WILD-TYPE 110  36  25  28
D143V7, multiclass
    clus
vv   ROS1 MUTATED ROS1 WILD-TYPE
  N0           28            110
  N1           12             36
  N2            7             25
  N3            5             28
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              M0  M1 M1A M1B M1C
  ROS1 MUTATED    52   0   0   1   0
  ROS1 WILD-TYPE 188   4   2   1   5
D143V8, multiclass
     clus
vv    ROS1 MUTATED ROS1 WILD-TYPE
  M0            52            188
  M1             0              4
  M1A            0              2
  M1B            1              1
  M1C            0              5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D143V9, binary
                cls
clus              0  1
  ROS1 MUTATED   21 13
  ROS1 WILD-TYPE 81 54
[1] "tbl2"
                cls
clus             [,1] [,2]
  ROS1 MUTATED     21   13
  ROS1 WILD-TYPE   81   54
     clus
vv    ROS1 MUTATED ROS1 WILD-TYPE
  NO            21             81
  YES           13             54
[1] 2 2
[1] FALSE
D143V10, binary
                cls
clus               0   1
  ROS1 MUTATED     9  45
  ROS1 WILD-TYPE  24 190
[1] "tbl2"
                cls
clus             [,1] [,2]
  ROS1 MUTATED      9   45
  ROS1 WILD-TYPE   24  190
     clus
vv    ROS1 MUTATED ROS1 WILD-TYPE
  NO             9             24
  YES           45            190
[1] 2 2
[1] FALSE
D143V11, continuous
D143V12, binary
                cls
clus               0   1
  ROS1 MUTATED    16  38
  ROS1 WILD-TYPE  87 127
[1] "tbl2"
                cls
clus             [,1] [,2]
  ROS1 MUTATED     16   38
  ROS1 WILD-TYPE   87  127
        clus
vv       ROS1 MUTATED ROS1 WILD-TYPE
  FEMALE           16             87
  MALE             38            127
[1] 2 2
[1] FALSE
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ROS1 MUTATED       0                         0    54
  ROS1 WILD-TYPE     3                         1   210
D143V13, multiclass
                           clus
vv                          ROS1 MUTATED ROS1 WILD-TYPE
  ASIAN                                0              3
  BLACK OR AFRICAN AMERICAN            0              1
  WHITE                               54            210
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D143V14, binary
                cls
clus               0   1
  ROS1 MUTATED     1  53
  ROS1 WILD-TYPE   2 208
[1] "tbl2"
                cls
clus             [,1] [,2]
  ROS1 MUTATED      1   53
  ROS1 WILD-TYPE    2  208
                        clus
vv                       ROS1 MUTATED ROS1 WILD-TYPE
  HISPANIC OR LATINO                1              2
  NOT HISPANIC OR LATINO           53            208
[1] 2 2
[1] FALSE

Clustering(144) Variable = KCNB2 MUTATION ANALYSIS
D144V1, survival
                 sevent
clus2               0   1
  KCNB2 MUTATED    24  31
  KCNB2 WILD-TYPE 104  99
  KCNB2 MUTATED KCNB2 WILD-TYPE 
             55             203 
  KCNB2 MUTATED KCNB2 WILD-TYPE 
             31              99 
$`KCNB2 MUTATED`
TCGA-D3-A1Q6 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A2JD TCGA-D3-A2JL TCGA-D3-A2JO 
       70.16        22.55        45.83        11.41        92.42        64.44 
TCGA-D3-A3MV TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A6EC 
        5.39        20.48        13.94        23.11         4.01        13.22 
TCGA-DA-A1I0 TCGA-DA-A3F8 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A181 TCGA-EE-A182 
       10.03        14.83        11.57        10.55         1.12         1.35 
TCGA-EE-A20C TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29N TCGA-EE-A29S 
        4.34        37.97        11.15        38.63         9.50         9.99 
TCGA-EE-A29V TCGA-EE-A2A0 TCGA-EE-A2GD TCGA-EE-A2GI TCGA-EE-A2GL TCGA-EE-A2GM 
        2.43        11.31        17.98        30.08        35.54        28.31 
TCGA-EE-A2GO TCGA-EE-A2MD TCGA-EE-A2MJ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MU 
       30.84         9.53        63.42        29.65        27.16         5.56 
TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AH TCGA-EE-A3J5 TCGA-EE-A3JD 
        3.68        30.15        13.81        12.72        21.60        27.35 
TCGA-ER-A193 TCGA-ER-A198 TCGA-ER-A19M TCGA-FR-A3YN TCGA-FS-A1YY TCGA-FS-A1Z0 
       31.40        38.40        28.60        18.41        11.01        23.80 
TCGA-FS-A1ZA TCGA-FS-A1ZC TCGA-FS-A1ZQ TCGA-FS-A1ZZ TCGA-FW-A3R5 TCGA-GF-A6C8 
        7.30        20.38         8.65         5.23         0.99        12.85 
TCGA-GN-A266 
       10.13 

$`KCNB2 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       16.47         8.52       111.09        32.42       110.79        28.08 
TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA 
       81.24        10.29        85.32         8.38        21.14        88.50 
TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK 
       68.22        69.90        30.87         7.50        36.16         6.31 
TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 
       56.19        45.11       114.67        15.25        46.98        46.32 
TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO 
       82.29        61.38        13.32        24.00         6.31         9.34 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J 
      103.59        26.37        80.22        42.71        15.09        41.10 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS 
       17.72         8.84        52.01        47.87         1.55         6.97 
TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY 
        2.89         9.90        11.31        48.79        35.80        51.12 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 
       39.19        13.68         9.99        44.52        36.69        25.15 
TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 
        4.93        22.36         6.64        19.36         7.00        17.56 
TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EE-A17Z 
       13.15         0.20         0.00         0.00        13.22         6.31 
TCGA-EE-A180 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20F 
        8.12        12.20         5.13         4.31        36.07         5.13 
TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29G TCGA-EE-A29H 
        9.21         1.18         7.99         9.90         8.55         4.41 
TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29W 
        1.08        27.12        12.03         8.09         8.84         8.68 
TCGA-EE-A29X TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB 
        8.09        49.22        23.90         9.67         8.94        39.39 
TCGA-EE-A2GC TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GN 
       34.29        34.92        47.21        19.43        16.01        33.83 
TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 
        5.42         1.15        13.02        34.98        36.33         8.84 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2ME TCGA-EE-A2MG 
       98.27         2.70         6.18        47.51        29.46        44.25 
TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN 
        7.96        14.56       111.78       111.91        56.02        25.08 
TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC 
       26.99        21.60        23.05       124.31       122.73        25.84 
TCGA-EE-A3AG TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA 
       15.95         3.22        22.92        21.60        16.14        22.22 
TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 
        0.46        13.94        33.60        18.61        12.95         5.72 
TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F 
       76.41        25.18         3.78         3.52        11.90        11.11 
TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19N TCGA-ER-A19P 
      114.15        34.88         4.21        13.45        42.84        34.68 
TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
        9.57        36.07        17.72        78.44        11.80         1.87 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET 
        1.51        13.08        12.62        11.74         9.04         6.58 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX 
       22.49         1.71        85.74         4.90        64.47         3.45 
TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZB TCGA-FS-A1ZD TCGA-FS-A1ZE 
       14.24        15.52         7.33         3.39         8.22        19.53 
TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM 
       11.08         7.17        30.87        12.92        12.89        47.38 
TCGA-FS-A1ZP TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW 
       52.08         8.81        49.15        40.64         8.68        27.39 
TCGA-FS-A1ZY TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 
        0.82        53.85         7.36        28.73        14.20        10.78 
TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV 
        5.98         6.41         2.27         0.20         0.13         0.16 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        0.43         9.90         7.23        24.85        31.33        84.72 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS 
       16.24        15.42        12.16        14.70         5.79 

  KCNB2 MUTATED KCNB2 WILD-TYPE 
           0.99            0.00 
  KCNB2 MUTATED KCNB2 WILD-TYPE 
          92.42          124.31 
  KCNB2 MUTATED KCNB2 WILD-TYPE 
          13.94           15.09 
[1] "1.0 - 92.4 (13.9)"  "0.0 - 124.3 (15.1)"
[1] "hr=" "1.2"
D144V2, survival
                 sevent
clus2               0   1
  KCNB2 MUTATED    25  31
  KCNB2 WILD-TYPE 107 100
  KCNB2 MUTATED KCNB2 WILD-TYPE 
             56             207 
  KCNB2 MUTATED KCNB2 WILD-TYPE 
             31             100 
$`KCNB2 MUTATED`
TCGA-D3-A1Q6 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A2JD TCGA-D3-A2JL TCGA-D3-A2JO 
       71.80        31.59        90.90        11.87       171.58        66.08 
TCGA-D3-A3MV TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GU TCGA-D9-A1JW TCGA-D9-A3Z1 
       21.47        51.68        15.06       125.19         3.65        11.34 
TCGA-D9-A6EC TCGA-DA-A1I0 TCGA-DA-A3F8 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A181 
       66.25        20.38        15.68        29.82        27.22        33.73 
TCGA-EE-A182 TCGA-EE-A20C TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29N 
       14.70       151.27        47.84        13.97        39.62        18.61 
TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A2A0 TCGA-EE-A2GD TCGA-EE-A2GI TCGA-EE-A2GL 
       55.92        25.87        46.82       314.56        48.72        79.66 
TCGA-EE-A2GM TCGA-EE-A2GO TCGA-EE-A2MD TCGA-EE-A2MJ TCGA-EE-A2MR TCGA-EE-A2MS 
       75.48       101.95        47.28        96.23       103.56       136.47 
TCGA-EE-A2MU TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AH TCGA-EE-A3J5 
       53.26         3.68        54.51        13.81       138.81        36.95 
TCGA-EE-A3JD TCGA-ER-A193 TCGA-ER-A198 TCGA-ER-A19M TCGA-FR-A3YN TCGA-FS-A1YY 
       27.35        31.40        50.76        61.05        92.98       228.59 
TCGA-FS-A1Z0 TCGA-FS-A1ZA TCGA-FS-A1ZC TCGA-FS-A1ZQ TCGA-FS-A1ZZ TCGA-FW-A3R5 
      202.65        27.72       357.37       133.55        27.02        22.92 
TCGA-GF-A6C8 TCGA-GN-A266 
       14.04        10.13 

$`KCNB2 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       16.57        16.67       112.04       112.57       133.25        28.08 
TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA 
       95.74        43.43       103.10        65.49        23.77       115.53 
TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK 
      168.00        69.90        48.76       113.52        42.08        12.10 
TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 
       56.19        45.11       130.72        58.06        46.98        46.32 
TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO 
      166.52        86.93        60.23        24.53        13.87         9.34 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J 
      103.59        39.75       161.85        43.69        40.14       131.90 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS 
       18.38        10.03       135.75       137.92       166.19         7.43 
TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JX TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA 
      151.53        54.67         6.41         3.25         9.90        25.18 
TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 
       48.89        36.03       117.21       194.83       176.55        35.93 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC 
      107.34        61.18        53.92        65.92        23.44        68.09 
TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG 
       28.60        10.49       215.44        13.87        10.16        45.11 
TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A183 
       35.01         3.55        52.01         8.65        94.98        26.89 
TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I 
       68.15         4.96       109.64        78.87       168.26        13.55 
TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M 
       63.35        80.61        72.07        32.19         2.60        44.35 
TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A1 
       56.42        37.35        14.47       171.55        17.92       102.90 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GE 
       24.43        39.29        58.75        47.54        67.43       135.95 
TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR 
      208.04        89.33        54.74        90.97        13.91        14.30 
TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 
       55.59        44.88        94.82        21.67       129.27        28.83 
TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI 
       19.76        61.51       103.27       103.20        16.96       204.66 
TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ 
      144.76       203.05       167.90        47.54       248.65        43.23 
TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AG TCGA-EE-A3J3 
       41.59       124.31       122.73        25.84        23.47       172.18 
TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JE TCGA-EE-A3JH 
      127.20        64.08        34.32        53.19        33.40       101.79 
TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B 
      148.08        35.44        13.94         9.17        77.75        98.40 
TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H 
       48.89        12.59        13.02        26.37       268.93       152.35 
TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S 
        6.44       131.51        44.05       162.08        50.89        37.25 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF 
      148.18        79.99        43.82        23.34        20.15        16.37 
TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL 
       31.27        32.05       247.04        80.32        46.98        33.21 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1Z3 TCGA-FS-A1Z4 
      174.21         4.90       216.92        48.59        20.91        28.08 
TCGA-FS-A1Z7 TCGA-FS-A1ZB TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG 
        7.79        48.85        53.52        40.27        15.45         9.70 
TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZR 
       32.75        47.38        23.93       101.26        74.73        11.41 
TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A4F0 
      148.80        53.16        26.56        49.48        27.09        77.82 
TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC 
       66.67        28.73       174.84        12.43        26.73        49.45 
TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
       77.88         0.20        47.54         0.16         2.40         9.90 
TCGA-GF-A4EO TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 
        7.23       120.46       117.93        84.72        64.44        62.79 
TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS 
       32.48        39.58         6.67 

  KCNB2 MUTATED KCNB2 WILD-TYPE 
           3.65            0.16 
  KCNB2 MUTATED KCNB2 WILD-TYPE 
         357.37          268.93 
  KCNB2 MUTATED KCNB2 WILD-TYPE 
          47.56           48.76 
[1] "3.6 - 357.4 (47.6)" "0.2 - 268.9 (48.8)"
[1] "hr=" "1.1"
D144V3, continuous
                 vv
clus              DISTANT METASTASIS PRIMARY TUMOR
  KCNB2 MUTATED                   10             1
  KCNB2 WILD-TYPE                 25             3
                 vv
clus              REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  KCNB2 MUTATED                                          12                  34
  KCNB2 WILD-TYPE                                        46                 136
D144V4, multiclass
                                           clus
vv                                          KCNB2 MUTATED KCNB2 WILD-TYPE
  DISTANT METASTASIS                                   10              25
  PRIMARY TUMOR                                         1               3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE            12              46
  REGIONAL LYMPH NODE                                  34             136
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  KCNB2 MUTATED             5       1       1        5        5        5
  KCNB2 WILD-TYPE           5       5      21        5       19       12
                 vv
clus              STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  KCNB2 MUTATED           5         4         1         6          1          6
  KCNB2 WILD-TYPE         5        10         8        25         12         16
                 vv
clus              STAGE IIIC STAGE IV
  KCNB2 MUTATED            8        1
  KCNB2 WILD-TYPE         36       11
D144V5, multiclass
             clus
vv            KCNB2 MUTATED KCNB2 WILD-TYPE
  I OR II NOS             5               5
  STAGE 0                 1               5
  STAGE I                 1              21
  STAGE IA                5               5
  STAGE IB                5              19
  STAGE II                5              12
  STAGE IIA               5               5
  STAGE IIB               4              10
  STAGE IIC               1               8
  STAGE III               6              25
  STAGE IIIA              1              12
  STAGE IIIB              6              16
  STAGE IIIC              8              36
  STAGE IV                1              11
[1] 14  2
[1] 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
  KCNB2 MUTATED       9  9 18 11
  KCNB2 WILD-TYPE    42 49 35 44
D144V6, multiclass
       clus
vv      KCNB2 MUTATED KCNB2 WILD-TYPE
  T0+T1             9              42
  T2                9              49
  T3               18              35
  T4               11              44
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  KCNB2 MUTATED    32  11   7   4
  KCNB2 WILD-TYPE 106  37  25  29
D144V7, multiclass
    clus
vv   KCNB2 MUTATED KCNB2 WILD-TYPE
  N0            32             106
  N1            11              37
  N2             7              25
  N3             4              29
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               M0  M1 M1A M1B M1C
  KCNB2 MUTATED    55   0   1   0   0
  KCNB2 WILD-TYPE 185   4   1   2   5
D144V8, multiclass
     clus
vv    KCNB2 MUTATED KCNB2 WILD-TYPE
  M0             55             185
  M1              0               4
  M1A             1               1
  M1B             0               2
  M1C             0               5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D144V9, binary
                 cls
clus               0  1
  KCNB2 MUTATED   26 17
  KCNB2 WILD-TYPE 76 50
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCNB2 MUTATED     26   17
  KCNB2 WILD-TYPE   76   50
     clus
vv    KCNB2 MUTATED KCNB2 WILD-TYPE
  NO             26              76
  YES            17              50
[1] 2 2
[1] FALSE
D144V10, binary
                 cls
clus                0   1
  KCNB2 MUTATED     4  53
  KCNB2 WILD-TYPE  29 182
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCNB2 MUTATED      4   53
  KCNB2 WILD-TYPE   29  182
     clus
vv    KCNB2 MUTATED KCNB2 WILD-TYPE
  NO              4              29
  YES            53             182
[1] 2 2
[1] FALSE
D144V11, continuous
D144V12, binary
                 cls
clus                0   1
  KCNB2 MUTATED    20  37
  KCNB2 WILD-TYPE  83 128
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCNB2 MUTATED     20   37
  KCNB2 WILD-TYPE   83  128
        clus
vv       KCNB2 MUTATED KCNB2 WILD-TYPE
  FEMALE            20              83
  MALE              37             128
[1] 2 2
[1] FALSE
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  KCNB2 MUTATED       1                         0    56
  KCNB2 WILD-TYPE     2                         1   208
D144V13, multiclass
                           clus
vv                          KCNB2 MUTATED KCNB2 WILD-TYPE
  ASIAN                                 1               2
  BLACK OR AFRICAN AMERICAN             0               1
  WHITE                                56             208
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D144V14, binary
                 cls
clus                0   1
  KCNB2 MUTATED     1  54
  KCNB2 WILD-TYPE   2 207
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCNB2 MUTATED      1   54
  KCNB2 WILD-TYPE    2  207
                        clus
vv                       KCNB2 MUTATED KCNB2 WILD-TYPE
  HISPANIC OR LATINO                 1               2
  NOT HISPANIC OR LATINO            54             207
[1] 2 2
[1] FALSE

Clustering(145) Variable = ART3 MUTATION ANALYSIS
D145V1, survival
                sevent
clus2              0   1
  ART3 MUTATED     5   7
  ART3 WILD-TYPE 123 123
  ART3 MUTATED ART3 WILD-TYPE 
            12            246 
  ART3 MUTATED ART3 WILD-TYPE 
             7            123 
$`ART3 MUTATED`
TCGA-D3-A3C7 TCGA-D3-A3CB TCGA-EE-A2A6 TCGA-EE-A2MD TCGA-EE-A2MJ TCGA-EE-A3AG 
       46.98        82.29         8.94         9.53        63.42        15.95 
TCGA-ER-A193 TCGA-ER-A19P TCGA-FS-A1ZZ TCGA-FS-A4FC TCGA-FW-A3R5 TCGA-GN-A26A 
       31.40        34.68         5.23         6.41         0.99        12.16 

$`ART3 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.47         8.52       111.09        32.42        70.16       110.79 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       28.08        22.55        45.83        81.24        10.29        85.32 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
        8.38        21.14        88.50        68.22        69.90        11.41 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       30.87         7.50        36.16         6.31        92.42        56.19 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C8 TCGA-D3-A3CC 
       64.44        45.11       114.67        15.25        46.32        61.38 
TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU 
       13.32        24.00         6.31         9.34       103.59        26.37 
TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K 
        5.39        80.22        42.71        15.09        41.10        17.72 
TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR 
        8.84        20.48        13.94        52.01        47.87         1.55 
TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA 
        6.97        23.11         4.01         2.89         9.90        11.31 
TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 
       13.22        48.79        35.80        51.12        10.03        39.19 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA 
       13.68         9.99        44.52        36.69        25.15         4.93 
TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 
       22.36         6.64        19.36         7.00        17.56        14.83 
TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EE-A17X 
       13.15         0.20         0.00         0.00        13.22        11.57 
TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 
       10.55         6.31         8.12         1.12         1.35        12.20 
TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H 
        5.13         4.31        36.07         4.34         5.13         9.21 
TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E 
        1.18         7.99         9.90        37.97        11.15        38.63 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P 
        8.55         4.41         1.08        27.12         9.50        12.03 
TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X 
        8.09         8.84         9.99         2.43         8.68         8.09 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2GB TCGA-EE-A2GC 
       11.31        49.22        23.90         9.67        39.39        34.29 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK 
       17.98        34.92        47.21        30.08        19.43        16.01 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR 
       35.54        28.31        33.83        30.84         5.42         1.15 
TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 
       13.02        34.98        36.33         8.84        98.27         2.70 
TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI 
        6.18        47.51        29.46        44.25         7.96        14.56 
TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ 
      111.78       111.91        56.02        25.08        26.99        21.60 
TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB 
       29.65        27.16        23.05         5.56       124.31       122.73 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AH TCGA-EE-A3J3 
       25.84         3.68        30.15        13.81        12.72         3.22 
TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JD 
       22.92        21.60        21.60        16.14        22.22        27.35 
TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 
        0.46        13.94        33.60        18.61        12.95        38.40 
TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E 
        5.72        76.41        25.18         3.78         3.52        11.90 
TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M 
       11.11       114.15        34.88         4.21        13.45        28.60 
TCGA-ER-A19N TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
       42.84         9.57        36.07        17.72        78.44        11.80 
TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES 
        1.87         1.51        13.08        12.62        11.74         9.04 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
        6.58        22.49         1.71        18.41        85.74         4.90 
TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 
       64.47         3.45        11.01        23.80        14.24        15.52 
TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE 
        7.33         7.30         3.39        20.38         8.22        19.53 
TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM 
       11.08         7.17        30.87        12.92        12.89        47.38 
TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU 
       52.08         8.65         8.81        49.15        40.64         8.68 
TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 
       27.39         0.82        53.85         7.36        28.73        14.20 
TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV 
       10.78         5.98         2.27         0.20         0.13         0.16 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 
        0.43         9.90         7.23        12.85        24.85        31.33 
TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26D TCGA-QB-A6FS 
       84.72        10.13        16.24        15.42        14.70         5.79 

  ART3 MUTATED ART3 WILD-TYPE 
          0.99           0.00 
  ART3 MUTATED ART3 WILD-TYPE 
         82.29         124.31 
  ART3 MUTATED ART3 WILD-TYPE 
        14.055         14.765 
[1] "1.0 - 82.3 (14.1)"  "0.0 - 124.3 (14.8)"
[1] "hr=" "1.1"
D145V2, survival
                sevent
clus2              0   1
  ART3 MUTATED     5   7
  ART3 WILD-TYPE 127 124
  ART3 MUTATED ART3 WILD-TYPE 
            12            251 
  ART3 MUTATED ART3 WILD-TYPE 
             7            124 
$`ART3 MUTATED`
TCGA-D3-A3C7 TCGA-D3-A3CB TCGA-EE-A2A6 TCGA-EE-A2MD TCGA-EE-A2MJ TCGA-EE-A3AG 
       46.98       166.52        58.75        47.28        96.23        23.47 
TCGA-ER-A193 TCGA-ER-A19P TCGA-FS-A1ZZ TCGA-FS-A4FC TCGA-FW-A3R5 TCGA-GN-A26A 
       31.40       162.08        27.02        49.45        22.92        32.48 

$`ART3 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.57        16.67       112.04       112.57        71.80       133.25 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       28.08        31.59        90.90        95.74        43.43       103.10 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
       65.49        23.77       115.53       168.00        69.90        11.87 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       48.76       113.52        42.08        12.10       171.58        56.19 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C8 TCGA-D3-A3CC 
       66.08        45.11       130.72        58.06        46.32        86.93 
TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU 
       60.23        24.53        13.87         9.34       103.59        39.75 
TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K 
       21.47       161.85        43.69        40.14       131.90        18.38 
TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR 
       10.03        51.68        15.06       135.75       137.92       166.19 
TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX 
        7.43       125.19       151.53        54.67         3.65         6.41 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1HV 
       11.34         3.25         9.90        25.18        66.25        48.89 
TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 
       36.03       117.21        20.38       194.83       176.55        35.93 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC 
      107.34        61.18        53.92        65.92        23.44        68.09 
TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R 
       28.60        10.49       215.44        15.68        13.87        10.16 
TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y 
       45.11        35.01         3.55        52.01        29.82        27.22 
TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 
        8.65        94.98        33.73        14.70        26.89        68.15 
TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I 
        4.96       109.64       151.27        78.87       168.26        13.55 
TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G 
       63.35        80.61        47.84        13.97        39.62        72.07 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
       32.19         2.60        44.35        18.61        56.42        37.35 
TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 
       14.47        55.92        25.87       171.55        17.92        46.82 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD 
      102.90        24.43        39.29        47.54        67.43       314.56 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
      135.95       208.04        48.72        89.33        54.74        79.66 
TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS 
       75.48        90.97       101.95        13.91        14.30        55.59 
TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 
       44.88        94.82        21.67       129.27        28.83        19.76 
TCGA-EE-A2MC TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MK 
       61.51       103.27       103.20        16.96       204.66       144.76 
TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR 
      203.05       167.90        47.54       248.65        43.23       103.56 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC 
      136.47        41.59        53.26       124.31       122.73        25.84 
TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 
        3.68        54.51        13.81       138.81       172.18       127.20 
TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE 
       36.95        64.08        34.32        53.19        27.35        33.40 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 
      101.79       148.08        35.44        13.94        50.76         9.17 
TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F 
       77.75        98.40        48.89        12.59        13.02        26.37 
TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N 
      268.93       152.35         6.44       131.51        61.05        44.05 
TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
       50.89        37.25       148.18        79.99        43.82        23.34 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET 
       20.15        16.37        31.27        32.05       247.04        80.32 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW 
       46.98        33.21        92.98       174.21         4.90       216.92 
TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 
       48.59       228.59       202.65        20.91        28.08         7.79 
TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF 
       27.72        48.85       357.37        53.52        40.27        15.45 
TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP 
        9.70        32.75        47.38        23.93       101.26        74.73 
TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW 
      133.55        11.41       148.80        53.16        26.56        49.48 
TCGA-FS-A1ZY TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 
       27.09        77.82        66.67        28.73       174.84        12.43 
TCGA-FS-A4FB TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY 
       26.73        77.88         0.20        47.54         0.16         2.40 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        9.90         7.23        14.04       120.46       117.93        84.72 
TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26D TCGA-QB-A6FS 
       10.13        64.44        62.79        39.58         6.67 

  ART3 MUTATED ART3 WILD-TYPE 
         22.92           0.16 
  ART3 MUTATED ART3 WILD-TYPE 
        166.52         357.37 
  ART3 MUTATED ART3 WILD-TYPE 
         47.13          48.72 
[1] "22.9 - 166.5 (47.1)" "0.2 - 357.4 (48.7)" 
[1] "hr=" "1.3"
D145V3, continuous
                vv
clus             DISTANT METASTASIS PRIMARY TUMOR
  ART3 MUTATED                    1             0
  ART3 WILD-TYPE                 34             4
                vv
clus             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  ART3 MUTATED                                           3                   8
  ART3 WILD-TYPE                                        55                 162
D145V4, multiclass
                                           clus
vv                                          ART3 MUTATED ART3 WILD-TYPE
  DISTANT METASTASIS                                   1             34
  PRIMARY TUMOR                                        0              4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE            3             55
  REGIONAL LYMPH NODE                                  8            162
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  ART3 MUTATED             1       0       0        1        0        1
  ART3 WILD-TYPE           9       6      22        9       24       16
                vv
clus             STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  ART3 MUTATED           1         2         0         4          1          0
  ART3 WILD-TYPE         9        12         9        27         12         22
                vv
clus             STAGE IIIC STAGE IV
  ART3 MUTATED            0        0
  ART3 WILD-TYPE         44       12
D145V5, multiclass
             clus
vv            ART3 MUTATED ART3 WILD-TYPE
  I OR II NOS            1              9
  STAGE 0                0              6
  STAGE I                0             22
  STAGE IA               1              9
  STAGE IB               0             24
  STAGE II               1             16
  STAGE IIA              1              9
  STAGE IIB              2             12
  STAGE IIC              0              9
  STAGE III              4             27
  STAGE IIIA             1             12
  STAGE IIIB             0             22
  STAGE IIIC             0             44
  STAGE IV               0             12
[1] 14  2
[1] 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
  ART3 MUTATED       3  1  5  1
  ART3 WILD-TYPE    48 57 48 54
D145V6, multiclass
       clus
vv      ART3 MUTATED ART3 WILD-TYPE
  T0+T1            3             48
  T2               1             57
  T3               5             48
  T4               1             54
[1] 4 2
[1] TRUE
[1] "dimension 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
  ART3 MUTATED     8   2   2   0
  ART3 WILD-TYPE 130  46  30  33
D145V7, multiclass
    clus
vv   ART3 MUTATED ART3 WILD-TYPE
  N0            8            130
  N1            2             46
  N2            2             30
  N3            0             33
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              M0  M1 M1A M1B M1C
  ART3 MUTATED    12   0   0   0   0
  ART3 WILD-TYPE 228   4   2   2   5
D145V8, multiclass
     clus
vv    ART3 MUTATED ART3 WILD-TYPE
  M0            12            228
  M1             0              4
  M1A            0              2
  M1B            0              2
  M1C            0              5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D145V9, binary
                cls
clus              0  1
  ART3 MUTATED    5  2
  ART3 WILD-TYPE 97 65
[1] "tbl2"
                cls
clus             [,1] [,2]
  ART3 MUTATED      5    2
  ART3 WILD-TYPE   97   65
     clus
vv    ART3 MUTATED ART3 WILD-TYPE
  NO             5             97
  YES            2             65
[1] 2 2
[1] FALSE
D145V10, binary
                cls
clus               0   1
  ART3 MUTATED     2  10
  ART3 WILD-TYPE  31 225
[1] "tbl2"
                cls
clus             [,1] [,2]
  ART3 MUTATED      2   10
  ART3 WILD-TYPE   31  225
     clus
vv    ART3 MUTATED ART3 WILD-TYPE
  NO             2             31
  YES           10            225
[1] 2 2
[1] FALSE
D145V11, continuous
D145V12, binary
                cls
clus               0   1
  ART3 MUTATED     5   7
  ART3 WILD-TYPE  98 158
[1] "tbl2"
                cls
clus             [,1] [,2]
  ART3 MUTATED      5    7
  ART3 WILD-TYPE   98  158
        clus
vv       ART3 MUTATED ART3 WILD-TYPE
  FEMALE            5             98
  MALE              7            158
[1] 2 2
[1] FALSE
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ART3 MUTATED       0                         0    12
  ART3 WILD-TYPE     3                         1   252
D145V13, multiclass
                           clus
vv                          ART3 MUTATED ART3 WILD-TYPE
  ASIAN                                0              3
  BLACK OR AFRICAN AMERICAN            0              1
  WHITE                               12            252
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D145V14, binary
                cls
clus               0   1
  ART3 MUTATED     1  11
  ART3 WILD-TYPE   2 250
[1] "tbl2"
                cls
clus             [,1] [,2]
  ART3 MUTATED      1   11
  ART3 WILD-TYPE    2  250
                        clus
vv                       ART3 MUTATED ART3 WILD-TYPE
  HISPANIC OR LATINO                1              2
  NOT HISPANIC OR LATINO           11            250
[1] 2 2
[1] FALSE

Clustering(146) Variable = CLDN4 MUTATION ANALYSIS
D146V1, survival
                 sevent
clus2               0   1
  CLDN4 MUTATED     5   4
  CLDN4 WILD-TYPE 123 126
  CLDN4 MUTATED CLDN4 WILD-TYPE 
              9             249 
  CLDN4 MUTATED CLDN4 WILD-TYPE 
              4             126 
$`CLDN4 MUTATED`
TCGA-D3-A2JH TCGA-DA-A1I1 TCGA-EE-A181 TCGA-EE-A29D TCGA-EE-A2GM TCGA-EE-A2MC 
       36.16        39.19         1.12        11.15        28.31        47.51 
TCGA-EE-A2MS TCGA-FS-A1ZA TCGA-FW-A3R5 
       27.16         7.30         0.99 

$`CLDN4 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.47         8.52       111.09        32.42        70.16       110.79 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       28.08        22.55        45.83        81.24        10.29        85.32 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
        8.38        21.14        88.50        68.22        69.90        11.41 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO 
       30.87         7.50         6.31        92.42        56.19        64.44 
TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB 
       45.11       114.67        15.25        46.98        46.32        82.29 
TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR 
       61.38        13.32        24.00         6.31         9.34       103.59 
TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J 
       26.37         5.39        80.22        42.71        15.09        41.10 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO 
       17.72         8.84        20.48        13.94        52.01        47.87 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 
        1.55         6.97        23.11         4.01         2.89         9.90 
TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 
       11.31        13.22        48.79        35.80        51.12        10.03 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA 
       13.68         9.99        44.52        36.69        25.15         4.93 
TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 
       22.36         6.64        19.36         7.00        17.56        14.83 
TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EE-A17X 
       13.15         0.20         0.00         0.00        13.22        11.57 
TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 
       10.55         6.31         8.12         1.35        12.20         5.13 
TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I 
        4.31        36.07         4.34         5.13         9.21         1.18 
TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H 
        7.99         9.90        37.97        38.63         8.55         4.41 
TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R 
        1.08        27.12         9.50        12.03         8.09         8.84 
TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 
        9.99         2.43         8.68         8.09        11.31        49.22 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD 
       23.90         9.67         8.94        39.39        34.29        17.98 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
       34.92        47.21        30.08        19.43        16.01        35.54 
TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT 
       33.83        30.84         5.42         1.15        13.02        34.98 
TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MD 
       36.33         8.84        98.27         2.70         6.18         9.53 
TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK 
       29.46        44.25         7.96        14.56        63.42       111.78 
TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR 
      111.91        56.02        25.08        26.99        21.60        29.65 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD 
       23.05         5.56       124.31       122.73        25.84         3.68 
TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 
       30.15        13.81        15.95        12.72         3.22        22.92 
TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE 
       21.60        21.60        16.14        22.22        27.35         0.46 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 
       13.94        33.60        31.40        18.61        12.95        38.40 
TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E 
        5.72        76.41        25.18         3.78         3.52        11.90 
TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M 
       11.11       114.15        34.88         4.21        13.45        28.60 
TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 
       42.84        34.68         9.57        36.07        17.72        78.44 
TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH 
       11.80         1.87         1.51        13.08        12.62        11.74 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A 
        9.04         6.58        22.49         1.71        18.41        85.74 
TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
        4.90        64.47         3.45        11.01        23.80        14.24 
TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE 
       15.52         7.33         3.39        20.38         8.22        19.53 
TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM 
       11.08         7.17        30.87        12.92        12.89        47.38 
TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU 
       52.08         8.65         8.81        49.15        40.64         8.68 
TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 
       27.39         0.82         5.23        53.85         7.36        28.73 
TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 
       14.20        10.78         5.98         6.41         2.27         0.20 
TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 
        0.13         0.16         0.43         9.90         7.23        12.85 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 
       24.85        31.33        84.72        10.13        16.24        15.42 
TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS 
       12.16        14.70         5.79 

  CLDN4 MUTATED CLDN4 WILD-TYPE 
           0.99            0.00 
  CLDN4 MUTATED CLDN4 WILD-TYPE 
          47.51          124.31 
  CLDN4 MUTATED CLDN4 WILD-TYPE 
          27.16           14.70 
[1] "1.0 - 47.5 (27.2)"  "0.0 - 124.3 (14.7)"
[1] "hr=" "1.1"
D146V2, survival
                 sevent
clus2               0   1
  CLDN4 MUTATED     5   4
  CLDN4 WILD-TYPE 127 127
  CLDN4 MUTATED CLDN4 WILD-TYPE 
              9             254 
  CLDN4 MUTATED CLDN4 WILD-TYPE 
              4             127 
$`CLDN4 MUTATED`
TCGA-D3-A2JH TCGA-DA-A1I1 TCGA-EE-A181 TCGA-EE-A29D TCGA-EE-A2GM TCGA-EE-A2MC 
       42.08       194.83        33.73        13.97        75.48        61.51 
TCGA-EE-A2MS TCGA-FS-A1ZA TCGA-FW-A3R5 
      136.47        27.72        22.92 

$`CLDN4 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.57        16.67       112.04       112.57        71.80       133.25 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       28.08        31.59        90.90        95.74        43.43       103.10 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
       65.49        23.77       115.53       168.00        69.90        11.87 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO 
       48.76       113.52        12.10       171.58        56.19        66.08 
TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB 
       45.11       130.72        58.06        46.98        46.32       166.52 
TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR 
       86.93        60.23        24.53        13.87         9.34       103.59 
TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J 
       39.75        21.47       161.85        43.69        40.14       131.90 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO 
       18.38        10.03        51.68        15.06       135.75       137.92 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW 
      166.19         7.43       125.19       151.53        54.67         3.65 
TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC 
        6.41        11.34         3.25         9.90        25.18        66.25 
TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 
       48.89        36.03       117.21        20.38       176.55        35.93 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC 
      107.34        61.18        53.92        65.92        23.44        68.09 
TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R 
       28.60        10.49       215.44        15.68        13.87        10.16 
TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y 
       45.11        35.01         3.55        52.01        29.82        27.22 
TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 
        8.65        94.98        14.70        26.89        68.15         4.96 
TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A 
      109.64       151.27        78.87       168.26        13.55        63.35 
TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L 
       80.61        47.84        39.62        72.07        32.19         2.60 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S 
       44.35        18.61        56.42        37.35        14.47        55.92 
TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 
       25.87       171.55        17.92        46.82       102.90        24.43 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE 
       39.29        58.75        47.54        67.43       314.56       135.95 
TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GN 
      208.04        48.72        89.33        54.74        79.66        90.97 
TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU 
      101.95        13.91        14.30        55.59        44.88        94.82 
TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MD TCGA-EE-A2ME 
       21.67       129.27        28.83        19.76        47.28       103.27 
TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML 
      103.20        16.96       204.66        96.23       144.76       203.05 
TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MT 
      167.90        47.54       248.65        43.23       103.56        41.59 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE 
       53.26       124.31       122.73        25.84         3.68        54.51 
TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 
       13.81        23.47       138.81       172.18       127.20        36.95 
TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH 
       64.08        34.32        53.19        27.35        33.40       101.79 
TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 
      148.08        31.40        35.44        13.94        50.76         9.17 
TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F 
       77.75        98.40        48.89        12.59        13.02        26.37 
TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N 
      268.93       152.35         6.44       131.51        61.05        44.05 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
      162.08        50.89        37.25       148.18        79.99        43.82 
TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES 
       23.34        20.15        16.37        31.27        32.05       247.04 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
       80.32        46.98        33.21        92.98       174.21         4.90 
TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 
      216.92        48.59       228.59       202.65        20.91        28.08 
TCGA-FS-A1Z7 TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF 
        7.79        48.85       357.37        53.52        40.27        15.45 
TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP 
        9.70        32.75        47.38        23.93       101.26        74.73 
TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW 
      133.55        11.41       148.80        53.16        26.56        49.48 
TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 
       27.09        27.02        77.82        66.67        28.73       174.84 
TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU 
       12.43        26.73        49.45        77.88         0.20        47.54 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 
        0.16         2.40         9.90         7.23        14.04       120.46 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
      117.93        84.72        10.13        64.44        62.79        32.48 
TCGA-GN-A26D TCGA-QB-A6FS 
       39.58         6.67 

  CLDN4 MUTATED CLDN4 WILD-TYPE 
          13.97            0.16 
  CLDN4 MUTATED CLDN4 WILD-TYPE 
         194.83          357.37 
  CLDN4 MUTATED CLDN4 WILD-TYPE 
         42.080          48.655 
[1] "14.0 - 194.8 (42.1)" "0.2 - 357.4 (48.7)" 
[1] "hr=" "1.1"
D146V3, continuous
                 vv
clus              DISTANT METASTASIS PRIMARY TUMOR
  CLDN4 MUTATED                    1             0
  CLDN4 WILD-TYPE                 34             4
                 vv
clus              REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  CLDN4 MUTATED                                           3                   6
  CLDN4 WILD-TYPE                                        55                 164
D146V4, multiclass
                                           clus
vv                                          CLDN4 MUTATED CLDN4 WILD-TYPE
  DISTANT METASTASIS                                    1              34
  PRIMARY TUMOR                                         0               4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE             3              55
  REGIONAL LYMPH NODE                                   6             164
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  CLDN4 MUTATED             1       0       1        0        1        2
  CLDN4 WILD-TYPE           9       6      21       10       23       15
                 vv
clus              STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  CLDN4 MUTATED           0         0         1         1          0          1
  CLDN4 WILD-TYPE        10        14         8        30         13         21
                 vv
clus              STAGE IIIC STAGE IV
  CLDN4 MUTATED            2        0
  CLDN4 WILD-TYPE         42       12
D146V5, multiclass
             clus
vv            CLDN4 MUTATED CLDN4 WILD-TYPE
  I OR II NOS             1               9
  STAGE 0                 0               6
  STAGE I                 1              21
  STAGE IA                0              10
  STAGE IB                1              23
  STAGE II                2              15
  STAGE IIA               0              10
  STAGE IIB               0              14
  STAGE IIC               1               8
  STAGE III               1              30
  STAGE IIIA              0              13
  STAGE IIIB              1              21
  STAGE IIIC              2              42
  STAGE IV                0              12
[1] 14  2
[1] 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
  CLDN4 MUTATED       2  1  3  2
  CLDN4 WILD-TYPE    49 57 50 53
D146V6, multiclass
       clus
vv      CLDN4 MUTATED CLDN4 WILD-TYPE
  T0+T1             2              49
  T2                1              57
  T3                3              50
  T4                2              53
[1] 4 2
[1] TRUE
[1] "dimension 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
  CLDN4 MUTATED     6   1   2   1
  CLDN4 WILD-TYPE 132  47  30  32
D146V7, multiclass
    clus
vv   CLDN4 MUTATED CLDN4 WILD-TYPE
  N0             6             132
  N1             1              47
  N2             2              30
  N3             1              32
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               M0  M1 M1A M1B M1C
  CLDN4 MUTATED    10   0   0   0   0
  CLDN4 WILD-TYPE 230   4   2   2   5
D146V8, multiclass
     clus
vv    CLDN4 MUTATED CLDN4 WILD-TYPE
  M0             10             230
  M1              0               4
  M1A             0               2
  M1B             0               2
  M1C             0               5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D146V9, binary
                 cls
clus               0  1
  CLDN4 MUTATED    3  3
  CLDN4 WILD-TYPE 99 64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CLDN4 MUTATED      3    3
  CLDN4 WILD-TYPE   99   64
     clus
vv    CLDN4 MUTATED CLDN4 WILD-TYPE
  NO              3              99
  YES             3              64
[1] 2 2
[1] FALSE
D146V10, binary
                 cls
clus                0   1
  CLDN4 MUTATED     1   9
  CLDN4 WILD-TYPE  32 226
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CLDN4 MUTATED      1    9
  CLDN4 WILD-TYPE   32  226
     clus
vv    CLDN4 MUTATED CLDN4 WILD-TYPE
  NO              1              32
  YES             9             226
[1] 2 2
[1] FALSE
D146V11, continuous
D146V12, binary
                 cls
clus                0   1
  CLDN4 MUTATED     3   7
  CLDN4 WILD-TYPE 100 158
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CLDN4 MUTATED      3    7
  CLDN4 WILD-TYPE  100  158
        clus
vv       CLDN4 MUTATED CLDN4 WILD-TYPE
  FEMALE             3             100
  MALE               7             158
[1] 2 2
[1] FALSE
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CLDN4 MUTATED       0                         0    10
  CLDN4 WILD-TYPE     3                         1   254
D146V13, multiclass
                           clus
vv                          CLDN4 MUTATED CLDN4 WILD-TYPE
  ASIAN                                 0               3
  BLACK OR AFRICAN AMERICAN             0               1
  WHITE                                10             254
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D146V14, binary
                 cls
clus                0   1
  CLDN4 MUTATED     0  10
  CLDN4 WILD-TYPE   3 251
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CLDN4 MUTATED      0   10
  CLDN4 WILD-TYPE    3  251
                        clus
vv                       CLDN4 MUTATED CLDN4 WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO            10             251
[1] 2 2
[1] FALSE

Clustering(147) Variable = RAG2 MUTATION ANALYSIS
D147V1, survival
                sevent
clus2              0   1
  RAG2 MUTATED    10   8
  RAG2 WILD-TYPE 118 122
  RAG2 MUTATED RAG2 WILD-TYPE 
            18            240 
  RAG2 MUTATED RAG2 WILD-TYPE 
             8            122 
$`RAG2 MUTATED`
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A2JF TCGA-EE-A20C TCGA-EE-A29B TCGA-EE-A29C 
       70.16       110.79        30.87         4.34         9.90        37.97 
TCGA-EE-A29S TCGA-EE-A2GE TCGA-EE-A2GP TCGA-EE-A2MJ TCGA-EE-A2MR TCGA-EE-A3AG 
        9.99        34.92         5.42        63.42        29.65        15.95 
TCGA-EE-A3JD TCGA-FR-A69P TCGA-FS-A1Z3 TCGA-FS-A1ZC TCGA-GF-A3OT TCGA-QB-A6FS 
       27.35         4.90        14.24        20.38         9.90         5.79 

$`RAG2 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q8 TCGA-D3-A1Q9 
       16.47         8.52       111.09        32.42        28.08        22.55 
TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 
       45.83        81.24        10.29        85.32         8.38        21.14 
TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JH 
       88.50        68.22        69.90        11.41         7.50        36.16 
TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ 
        6.31        92.42        56.19        64.44        45.11       114.67 
TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE 
       15.25        46.98        46.32        82.29        61.38        13.32 
TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV 
       24.00         6.31         9.34       103.59        26.37         5.39 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N 
       80.22        42.71        15.09        41.10        17.72         8.84 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS 
       20.48        13.94        52.01        47.87         1.55         6.97 
TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC 
       23.11         4.01         2.89         9.90        11.31        13.22 
TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 
       48.79        35.80        51.12        10.03        39.19        13.68 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB 
        9.99        44.52        36.69        25.15         4.93        22.36 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q 
        6.64        19.36         7.00        17.56        14.83        13.15 
TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y 
        0.20         0.00         0.00        13.22        11.57        10.55 
TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 
        6.31         8.12         1.12         1.35        12.20         5.13 
TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A 
        4.31        36.07         5.13         9.21         1.18         7.99 
TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M 
       11.15        38.63         8.55         4.41         1.08        27.12 
TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29V TCGA-EE-A29W 
        9.50        12.03         8.09         8.84         2.43         8.68 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 
        8.09        11.31        49.22        23.90         9.67         8.94 
TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ 
       39.39        34.29        17.98        47.21        30.08        19.43 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GR 
       16.01        35.54        28.31        33.83        30.84         1.15 
TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 
       13.02        34.98        36.33         8.84        98.27         2.70 
TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH 
        6.18        47.51         9.53        29.46        44.25         7.96 
TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP 
       14.56       111.78       111.91        56.02        25.08        26.99 
TCGA-EE-A2MQ TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB 
       21.60        27.16        23.05         5.56       124.31       122.73 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AH TCGA-EE-A3J3 
       25.84         3.68        30.15        13.81        12.72         3.22 
TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JE 
       22.92        21.60        21.60        16.14        22.22         0.46 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 
       13.94        33.60        31.40        18.61        12.95        38.40 
TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E 
        5.72        76.41        25.18         3.78         3.52        11.90 
TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M 
       11.11       114.15        34.88         4.21        13.45        28.60 
TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 
       42.84        34.68         9.57        36.07        17.72        78.44 
TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH 
       11.80         1.87         1.51        13.08        12.62        11.74 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A 
        9.04         6.58        22.49         1.71        18.41        85.74 
TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1Z7 
       64.47         3.45        11.01        23.80        15.52         7.33 
TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG 
        7.30         3.39         8.22        19.53        11.08         7.17 
TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ 
       30.87        12.92        12.89        47.38        52.08         8.65 
TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY 
        8.81        49.15        40.64         8.68        27.39         0.82 
TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 
        5.23        53.85         7.36        28.73        14.20        10.78 
TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU 
        5.98         6.41         2.27         0.20         0.99         0.13 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 
        0.16         0.43         7.23        12.85        24.85        31.33 
TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D 
       84.72        10.13        16.24        15.42        12.16        14.70 

  RAG2 MUTATED RAG2 WILD-TYPE 
          4.34           0.00 
  RAG2 MUTATED RAG2 WILD-TYPE 
        110.79         124.31 
  RAG2 MUTATED RAG2 WILD-TYPE 
        18.165         14.630 
[1] "4.3 - 110.8 (18.2)" "0.0 - 124.3 (14.6)"
[1] "hr=" "1.2"
D147V2, survival
                sevent
clus2              0   1
  RAG2 MUTATED    10   8
  RAG2 WILD-TYPE 122 123
  RAG2 MUTATED RAG2 WILD-TYPE 
            18            245 
  RAG2 MUTATED RAG2 WILD-TYPE 
             8            123 
$`RAG2 MUTATED`
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A2JF TCGA-EE-A20C TCGA-EE-A29B TCGA-EE-A29C 
       71.80       133.25        48.76       151.27        80.61        47.84 
TCGA-EE-A29S TCGA-EE-A2GE TCGA-EE-A2GP TCGA-EE-A2MJ TCGA-EE-A2MR TCGA-EE-A3AG 
       55.92       135.95        13.91        96.23       103.56        23.47 
TCGA-EE-A3JD TCGA-FR-A69P TCGA-FS-A1Z3 TCGA-FS-A1ZC TCGA-GF-A3OT TCGA-QB-A6FS 
       27.35         4.90        20.91       357.37         9.90         6.67 

$`RAG2 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q8 TCGA-D3-A1Q9 
       16.57        16.67       112.04       112.57        28.08        31.59 
TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 
       90.90        95.74        43.43       103.10        65.49        23.77 
TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JH 
      115.53       168.00        69.90        11.87       113.52        42.08 
TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ 
       12.10       171.58        56.19        66.08        45.11       130.72 
TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE 
       58.06        46.98        46.32       166.52        86.93        60.23 
TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV 
       24.53        13.87         9.34       103.59        39.75        21.47 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N 
      161.85        43.69        40.14       131.90        18.38        10.03 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS 
       51.68        15.06       135.75       137.92       166.19         7.43 
TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 
      125.19       151.53        54.67         3.65         6.41        11.34 
TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1HW 
        3.25         9.90        25.18        66.25        48.89        36.03 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 
      117.21        20.38       194.83       176.55        35.93       107.34 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
       61.18        53.92        65.92        23.44        68.09        28.60 
TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG 
       10.49       215.44        15.68        13.87        10.16        45.11 
TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z 
       35.01         3.55        52.01        29.82        27.22         8.65 
TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 
       94.98        33.73        14.70        26.89        68.15         4.96 
TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29D 
      109.64        78.87       168.26        13.55        63.35        13.97 
TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N 
       39.62        72.07        32.19         2.60        44.35        18.61 
TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X 
       56.42        37.35        14.47        25.87       171.55        17.92 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB 
       46.82       102.90        24.43        39.29        58.75        47.54 
TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK 
       67.43       314.56       208.04        48.72        89.33        54.74 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GR TCGA-EE-A2GS 
       79.66        75.48        90.97       101.95        14.30        55.59 
TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 
       44.88        94.82        21.67       129.27        28.83        19.76 
TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI 
       61.51        47.28       103.27       103.20        16.96       204.66 
TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ 
      144.76       203.05       167.90        47.54       248.65        43.23 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC 
      136.47        41.59        53.26       124.31       122.73        25.84 
TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 
        3.68        54.51        13.81       138.81       172.18       127.20 
TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JE TCGA-EE-A3JH 
       36.95        64.08        34.32        53.19        33.40       101.79 
TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 
      148.08        31.40        35.44        13.94        50.76         9.17 
TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F 
       77.75        98.40        48.89        12.59        13.02        26.37 
TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N 
      268.93       152.35         6.44       131.51        61.05        44.05 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
      162.08        50.89        37.25       148.18        79.99        43.82 
TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES 
       23.34        20.15        16.37        31.27        32.05       247.04 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A1YW 
       80.32        46.98        33.21        92.98       174.21       216.92 
TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA 
       48.59       228.59       202.65        28.08         7.79        27.72 
TCGA-FS-A1ZB TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH 
       48.85        53.52        40.27        15.45         9.70        32.75 
TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR 
       47.38        23.93       101.26        74.73       133.55        11.41 
TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ 
      148.80        53.16        26.56        49.48        27.09        27.02 
TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB 
       77.82        66.67        28.73       174.84        12.43        26.73 
TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV 
       49.45        77.88         0.20        22.92        47.54         0.16 
TCGA-FW-A5DY TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        2.40         7.23        14.04       120.46       117.93        84.72 
TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D 
       10.13        64.44        62.79        32.48        39.58 

  RAG2 MUTATED RAG2 WILD-TYPE 
          4.90           0.16 
  RAG2 MUTATED RAG2 WILD-TYPE 
        357.37         314.56 
  RAG2 MUTATED RAG2 WILD-TYPE 
         52.34          47.54 
[1] "4.9 - 357.4 (52.3)" "0.2 - 314.6 (47.5)"
[1] "hr=" "1.4"
D147V3, continuous
                vv
clus             DISTANT METASTASIS PRIMARY TUMOR
  RAG2 MUTATED                    5             0
  RAG2 WILD-TYPE                 30             4
                vv
clus             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  RAG2 MUTATED                                           3                  10
  RAG2 WILD-TYPE                                        55                 160
D147V4, multiclass
                                           clus
vv                                          RAG2 MUTATED RAG2 WILD-TYPE
  DISTANT METASTASIS                                   5             30
  PRIMARY TUMOR                                        0              4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE            3             55
  REGIONAL LYMPH NODE                                 10            160
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  RAG2 MUTATED             1       1       2        1        2        0
  RAG2 WILD-TYPE           9       5      20        9       22       17
                vv
clus             STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  RAG2 MUTATED           1         1         0         4          0          1
  RAG2 WILD-TYPE         9        13         9        27         13         21
                vv
clus             STAGE IIIC STAGE IV
  RAG2 MUTATED            3        1
  RAG2 WILD-TYPE         41       11
D147V5, multiclass
             clus
vv            RAG2 MUTATED RAG2 WILD-TYPE
  I OR II NOS            1              9
  STAGE 0                1              5
  STAGE I                2             20
  STAGE IA               1              9
  STAGE IB               2             22
  STAGE II               0             17
  STAGE IIA              1              9
  STAGE IIB              1             13
  STAGE IIC              0              9
  STAGE III              4             27
  STAGE IIIA             0             13
  STAGE IIIB             1             21
  STAGE IIIC             3             41
  STAGE IV               1             11
[1] 14  2
[1] 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
  RAG2 MUTATED       4  3  3  3
  RAG2 WILD-TYPE    47 55 50 52
D147V6, multiclass
       clus
vv      RAG2 MUTATED RAG2 WILD-TYPE
  T0+T1            4             47
  T2               3             55
  T3               3             50
  T4               3             52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  RAG2 MUTATED    11   2   2   3
  RAG2 WILD-TYPE 127  46  30  30
D147V7, multiclass
    clus
vv   RAG2 MUTATED RAG2 WILD-TYPE
  N0           11            127
  N1            2             46
  N2            2             30
  N3            3             30
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              M0  M1 M1A M1B M1C
  RAG2 MUTATED    16   1   0   0   0
  RAG2 WILD-TYPE 224   3   2   2   5
D147V8, multiclass
     clus
vv    RAG2 MUTATED RAG2 WILD-TYPE
  M0            16            224
  M1             1              3
  M1A            0              2
  M1B            0              2
  M1C            0              5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D147V9, binary
                cls
clus              0  1
  RAG2 MUTATED    7  2
  RAG2 WILD-TYPE 95 65
[1] "tbl2"
                cls
clus             [,1] [,2]
  RAG2 MUTATED      7    2
  RAG2 WILD-TYPE   95   65
     clus
vv    RAG2 MUTATED RAG2 WILD-TYPE
  NO             7             95
  YES            2             65
[1] 2 2
[1] FALSE
D147V10, binary
                cls
clus               0   1
  RAG2 MUTATED     5  13
  RAG2 WILD-TYPE  28 222
[1] "tbl2"
                cls
clus             [,1] [,2]
  RAG2 MUTATED      5   13
  RAG2 WILD-TYPE   28  222
     clus
vv    RAG2 MUTATED RAG2 WILD-TYPE
  NO             5             28
  YES           13            222
[1] 2 2
[1] FALSE
D147V11, continuous
D147V12, binary
                cls
clus               0   1
  RAG2 MUTATED     4  14
  RAG2 WILD-TYPE  99 151
[1] "tbl2"
                cls
clus             [,1] [,2]
  RAG2 MUTATED      4   14
  RAG2 WILD-TYPE   99  151
        clus
vv       RAG2 MUTATED RAG2 WILD-TYPE
  FEMALE            4             99
  MALE             14            151
[1] 2 2
[1] FALSE
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RAG2 MUTATED       0                         0    18
  RAG2 WILD-TYPE     3                         1   246
D147V13, multiclass
                           clus
vv                          RAG2 MUTATED RAG2 WILD-TYPE
  ASIAN                                0              3
  BLACK OR AFRICAN AMERICAN            0              1
  WHITE                               18            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"
D147V14, binary
                cls
clus               0   1
  RAG2 MUTATED     0  18
  RAG2 WILD-TYPE   3 243
[1] "tbl2"
                cls
clus             [,1] [,2]
  RAG2 MUTATED      0   18
  RAG2 WILD-TYPE    3  243
                        clus
vv                       RAG2 MUTATED RAG2 WILD-TYPE
  HISPANIC OR LATINO                0              3
  NOT HISPANIC OR LATINO           18            243
[1] 2 2
[1] FALSE
